Contacts of the helix formed by residues 119 - 147 (chain B) in PDB entry 3EUP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 119 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 4.0 18.4 - - + +
54B GLU* 3.9 35.4 - - + +
57B ALA* 5.3 0.2 - - + -
58B ILE* 4.2 13.3 - - + +
115B ALA* 3.0 19.2 + - + +
116B ASP 5.2 0.2 + - - -
118B THR* 1.3 87.3 - - - +
120B ASP* 1.3 67.8 + - - +
121B ALA* 3.9 13.7 - - + +
122B LEU* 3.3 40.6 + - + +
123B ARG 2.9 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LYS* 4.1 18.6 + - - -
116B ASP 5.6 2.0 - - - +
118B THR 4.2 0.6 - - - -
119B HIS* 1.3 74.5 - - - +
121B ALA* 1.3 63.9 + - - +
123B ARG* 3.2 14.0 + - - +
124B LYS* 2.7 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 4.2 15.7 - - + -
119B HIS* 3.3 16.0 - - + +
120B ASP* 1.3 79.1 - - - +
122B LEU* 1.3 61.8 + - - +
124B LYS* 3.4 13.4 + - - +
125B LYS* 3.3 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 5.7 4.3 - - + -
57B ALA* 4.4 23.8 - - + +
58B ILE* 4.4 11.2 - - + -
61B PHE* 3.9 24.5 - - + -
111B THR* 3.3 29.8 - - + +
114B GLU* 6.1 1.3 - - - +
115B ALA* 3.8 9.9 - - + -
119B HIS* 3.3 34.1 + - + +
120B ASP 3.2 0.4 - - - -
121B ALA* 1.3 77.5 - - - +
123B ARG* 1.3 67.8 + - - +
125B LYS* 3.1 13.8 + - + -
126B ALA* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG 3.5 13.0 - - - +
176A ALA* 2.8 41.8 + - - +
177A THR* 4.0 12.7 + - - +
178A LYS* 3.6 31.0 - - - +
112B THR* 5.5 1.3 - - + +
115B ALA* 3.6 12.4 - - - +
116B ASP* 3.6 30.5 - - + +
119B HIS 2.9 17.4 + - - +
120B ASP* 3.6 13.8 + - - +
122B LEU* 1.3 74.6 - - - +
124B LYS* 1.3 103.5 + - - +
126B ALA* 3.1 9.3 + - + +
127B GLY* 2.9 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LYS* 5.5 1.6 - - - +
120B ASP* 2.7 43.0 + - - +
121B ALA* 3.5 13.7 - - - +
122B LEU 3.2 0.2 - - - -
123B ARG* 1.3 105.8 + - - +
125B LYS* 1.3 58.0 + - + +
127B GLY* 3.4 0.9 + - - -
128B GLU* 3.0 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 3.6 25.1 - - + -
61B PHE* 4.0 19.1 - - + -
62B ASP* 2.9 36.4 + - - -
121B ALA 3.3 15.5 + - - +
122B LEU* 3.1 15.7 + - + +
124B LYS* 1.3 78.7 - - + +
126B ALA* 1.3 58.8 + - - +
128B GLU* 3.3 16.7 + - - +
129B ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ALA* 4.2 7.0 - - + -
61B PHE* 4.2 6.8 - - + -
108B LEU* 3.4 19.8 - - + +
111B THR* 4.6 6.3 - - + -
112B THR* 3.4 34.1 - - - +
122B LEU 3.0 12.7 + - - +
123B ARG* 3.3 11.9 - - - +
125B LYS* 1.3 76.3 - - - +
127B GLY* 1.3 56.5 + - - +
129B ALA 3.1 1.0 + - - -
130B ILE* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ALA* 3.2 27.0 + - - -
177A THR* 4.3 6.0 - - - +
123B ARG* 2.9 15.0 + - - -
124B LYS 3.7 3.8 - - - -
126B ALA* 1.3 75.6 - - - +
128B GLU* 1.3 60.2 + - - +
130B ILE* 3.3 3.3 + - - +
131B LEU* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LYS* 3.0 30.3 + - - +
125B LYS* 3.7 23.1 + - - +
127B GLY* 1.3 73.6 - - - +
129B ALA* 1.3 59.6 + - - +
131B LEU* 3.8 6.8 - - + +
132B SER* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 4.0 14.1 - - + -
65B TRP* 3.5 35.9 + - + +
108B LEU* 4.0 9.4 - - + -
125B LYS 2.9 17.2 + - - +
126B ALA 3.1 5.1 + - - +
128B GLU* 1.3 76.8 - - - +
130B ILE* 1.3 63.7 + - - +
132B SER* 3.4 4.1 + - - -
133B TRP* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 5.0 8.3 - - + -
173A ILE* 3.7 26.5 - - + +
176A ALA* 4.2 9.4 - - + -
177A THR* 4.1 19.3 - - + -
108B LEU* 3.6 28.5 - - + -
126B ALA 2.9 14.1 + - - +
127B GLY 3.7 6.5 - - - +
128B GLU 3.3 0.2 - - - -
129B ALA* 1.3 78.5 - - - +
131B LEU* 1.3 60.2 + - - +
133B TRP* 3.4 5.3 + - - +
134B LYS* 3.0 25.8 + - - +
161B PHE* 4.3 17.0 - - + -
164B ILE* 3.7 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A THR* 4.3 11.4 - - + -
182A TYR* 3.7 40.8 - - + +
127B GLY 3.0 22.4 + - - +
128B GLU* 4.0 7.0 - - + +
129B ALA 3.3 0.2 - - - -
130B ILE* 1.3 76.1 - - - +
132B SER* 1.3 58.3 + - - +
134B LYS* 3.4 7.4 + - + +
135B LYS* 2.9 28.8 + - - +
161B PHE* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TRP* 6.3 0.2 - - - -
69B LYS* 6.1 5.6 - - - -
128B GLU* 2.9 22.8 + - - +
129B ALA* 3.9 5.2 - - - -
131B LEU* 1.3 74.2 - - - +
133B TRP* 1.3 65.3 + - - +
135B LYS* 3.4 11.4 + - - +
136B ASN* 3.1 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TRP* 4.1 21.3 - + + -
72B LEU* 4.1 13.8 - - + +
89B TYR* 3.0 46.9 + + - -
108B LEU* 4.0 22.0 - - + -
129B ALA 3.0 16.4 + - - +
130B ILE* 3.5 4.3 - - - +
132B SER* 1.3 75.9 - - - +
134B LYS* 1.3 62.4 + - - +
136B ASN* 3.0 15.2 + - + +
137B LEU* 2.9 34.4 + - + +
163B MET* 5.6 0.4 - - + -
164B ILE* 3.7 39.7 - - + -
167B VAL* 4.2 18.6 - - + -
168B GLU* 3.4 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TYR* 6.1 0.8 - - - -
130B ILE 3.0 18.9 + - - +
131B LEU* 3.6 9.6 - - + +
132B SER 3.3 0.2 - - - -
133B TRP* 1.3 74.2 - - - +
135B LYS* 1.3 60.1 + - - +
137B LEU* 3.1 8.3 + - - +
138B VAL* 2.9 53.1 + - + +
157B THR* 3.3 32.3 + - - +
160B ALA* 3.9 11.4 - - + -
161B PHE* 3.6 44.8 - - + +
164B ILE* 3.6 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU 2.9 17.8 + - - +
132B SER* 3.6 13.0 - - - +
133B TRP 3.2 0.2 - - - -
134B LYS* 1.3 82.0 - - + +
136B ASN* 1.3 70.6 + - - +
138B VAL* 3.4 8.4 + - + +
139B THR* 3.1 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 5.8 7.1 - - - +
72B LEU* 6.2 1.8 - - - +
132B SER* 3.1 21.6 + - - +
133B TRP* 3.0 16.8 + - + +
135B LYS* 1.3 87.9 - - - +
137B LEU* 1.3 64.4 + - + +
139B THR* 3.3 9.1 + - - -
140B ILE* 3.1 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET 5.7 0.4 - - - +
86B LEU* 3.8 11.0 - - + -
89B TYR* 3.5 22.7 - - + +
133B TRP* 2.9 25.9 + - + +
134B LYS 3.1 6.3 + - - +
136B ASN* 1.3 78.0 - - + +
138B VAL* 1.3 56.6 + - - +
140B ILE* 3.1 10.4 + - + +
141B ILE* 2.8 40.1 + - + +
160B ALA* 3.7 24.5 - - + +
163B MET* 3.6 30.7 - - + -
164B ILE* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LYS* 2.9 47.2 + - + +
135B LYS* 3.6 11.0 - - - +
137B LEU* 1.3 73.2 - - - +
139B THR* 1.3 58.7 + - - +
141B ILE* 3.3 1.6 + - - +
142B LYS* 2.9 53.7 + - + +
156B VAL* 3.8 26.9 - - + +
157B THR* 4.7 3.4 - - - +
160B ALA* 4.1 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LYS* 3.1 22.0 + - - +
136B ASN* 3.5 11.4 - - - -
137B LEU 3.2 0.2 - - - -
138B VAL* 1.3 78.6 - - - +
140B ILE* 1.3 64.7 + - + +
142B LYS* 3.4 4.9 + - - +
143B LYS* 3.0 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 4.6 10.8 - - + -
82B TYR* 3.8 30.4 - - + +
85B MET* 3.9 39.7 - - + +
86B LEU* 3.5 28.9 - - + -
89B TYR* 6.0 0.2 - - - +
136B ASN* 3.1 25.4 + - + +
137B LEU* 3.1 10.5 + - + +
139B THR* 1.3 76.1 - - + +
141B ILE* 1.3 66.2 + - - +
143B LYS* 3.3 11.0 + - + +
144B GLY* 3.0 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.9 21.8 - - + -
137B LEU 2.8 24.8 + - - +
138B VAL 3.8 3.1 - - - +
140B ILE* 1.3 76.3 - - - +
142B LYS* 1.3 57.4 + - - +
144B GLY* 3.0 4.3 + - - -
145B ILE* 2.9 29.3 + - + +
150B PHE* 3.5 16.0 - - + -
154B THR* 4.3 15.3 - - + -
156B VAL* 3.8 46.2 - - + +
159B ILE* 3.9 22.9 - - + -
160B ALA* 4.2 9.0 - - + +
163B MET* 4.5 6.3 - - - -
197B ILE* 4.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 2.9 40.4 + - + +
139B THR* 4.0 4.9 - - - +
141B ILE* 1.3 76.9 - - - +
143B LYS* 1.3 58.4 + - - +
145B ILE* 3.6 11.7 + - + +
146B GLN* 3.3 29.8 + - + +
156B VAL* 4.3 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.6 39.0 - - + +
85B MET* 6.6 0.2 - - + -
139B THR* 3.0 38.6 + - + +
140B ILE* 3.3 8.5 + - + +
142B LYS* 1.3 74.6 - - - +
144B GLY* 1.3 59.5 + - - +
146B GLN* 3.4 6.7 + - - +
147B ALA* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.8 16.5 - - - -
140B ILE 3.0 10.5 + - - -
141B ILE 3.0 0.4 + - - -
143B LYS* 1.3 73.4 - - - +
145B ILE* 1.3 61.9 + - - +
147B ALA 3.5 0.3 + - - -
148B LYS 3.2 2.8 + - - -
149B GLU* 2.8 33.1 + - - +
150B PHE* 3.1 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE* 2.9 17.4 + - + +
142B LYS* 3.7 13.9 - - + +
143B LYS 3.3 0.2 - - - -
144B GLY* 1.3 75.7 - - - +
146B GLN* 1.3 69.9 + - - +
148B LYS* 3.0 21.5 + - - +
150B PHE* 3.4 18.7 - - + +
151B ARG 3.5 21.8 - - - +
152B PRO* 3.7 35.5 - - + +
154B THR* 4.0 7.9 - - - -
156B VAL* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 3.3 17.9 + - + +
143B LYS* 3.4 6.9 + - - +
144B GLY 3.3 0.2 - - - -
145B ILE* 1.3 87.8 - - - +
147B ALA* 1.3 59.0 + - - +
148B LYS* 3.1 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.9 22.2 - - + -
143B LYS 3.0 18.5 + - - +
144B GLY 3.8 4.9 - - - +
145B ILE 3.3 0.2 - - - -
146B GLN* 1.3 75.5 - - - +
148B LYS* 1.3 69.4 + - - +
149B GLU* 3.3 9.3 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il