Contacts of the helix formed by residues 137 - 163 (chain B) in PDB entry 2ITB
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 ASP 137 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLN* 4.7 5.5 + - - +
83B ARG* 2.8 44.3 + - - -
136B LEU* 1.3 74.8 - - - +
138B GLU* 1.3 67.7 + - - +
139B GLU* 3.4 5.2 + - - +
140B LEU* 3.0 18.0 + - - +
141B GLY* 2.9 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU 3.7 1.5 + - - -
137B ASP* 1.3 72.5 - - - +
139B GLU* 1.3 67.2 + - - +
141B GLY* 3.8 1.0 - - - -
142B ARG* 2.9 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 3.9 6.9 - - + +
82B ARG* 3.1 35.9 + - - +
83B ARG* 3.1 28.5 + - - +
137B ASP* 3.4 2.9 + - - +
138B GLU* 1.3 82.0 - - - +
140B LEU* 1.3 63.6 + - - +
142B ARG* 3.8 4.9 - - - +
143B PHE* 3.0 22.8 + - + +
512B EDO 4.7 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLN* 3.8 23.8 - - + +
30B LEU* 6.0 2.7 - - + -
31B LEU* 4.2 14.6 - - + -
79B LEU* 3.7 26.9 - - + -
83B ARG* 3.7 17.7 - - - +
136B LEU* 4.0 22.2 - - + -
137B ASP* 3.0 23.0 + - - +
139B GLU* 1.3 77.1 - - - +
141B GLY* 1.3 57.0 + - - +
143B PHE* 3.2 11.8 + - + +
144B TYR* 2.9 53.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 3.5 29.0 - - - +
136B LEU* 4.0 18.1 - - - +
137B ASP 2.9 15.9 + - - -
138B GLU* 3.8 0.9 - - - -
140B LEU* 1.3 77.1 - - - +
142B ARG* 1.3 55.8 + - - +
144B TYR* 3.4 1.0 + - - -
145B HIS* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLU* 2.9 56.3 + - - +
139B GLU* 3.8 4.5 - - - +
141B GLY* 1.3 72.4 - - - +
143B PHE* 1.3 65.9 + - - +
145B HIS* 3.7 9.8 - - + +
146B GLY* 3.1 19.4 + - - -
511B EDO 4.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 5.9 0.4 - - + -
72B HIS 4.7 0.2 - - - -
75B GLN* 3.7 50.0 - - + -
76B VAL* 4.0 24.5 - - + -
79B LEU* 5.0 13.9 - - + -
139B GLU* 3.0 15.4 + - + +
140B LEU* 3.4 17.7 - - + +
142B ARG* 1.3 76.8 - - - +
144B TYR* 1.3 93.7 + + - +
146B GLY 3.1 9.9 + - - -
147B LEU* 3.2 27.6 + - + +
511B EDO 3.2 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.6 14.4 - - + +
31B LEU* 3.8 14.7 - - + +
34B HIS* 2.9 42.2 + + - +
129B PHE* 3.6 27.9 - + + +
132B LEU* 4.2 20.4 - - + -
133B VAL* 4.0 12.1 - - + -
136B LEU* 3.5 25.4 - - + -
140B LEU* 2.9 30.1 + - + +
141B GLY 3.8 4.9 - - - +
142B ARG 3.3 0.2 - - - -
143B PHE* 1.3 94.5 - + - +
145B HIS* 1.3 64.6 + - - +
147B LEU* 3.2 20.4 + - + +
148B LEU* 3.4 12.6 + - - +
195B PHE* 4.5 3.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 3.7 17.9 - - + +
141B GLY 2.9 17.9 + - - +
142B ARG* 3.7 9.6 - - + +
143B PHE 3.3 0.2 - - - -
144B TYR* 1.3 74.9 - - - +
146B GLY* 1.3 62.4 + - - +
148B LEU* 3.1 47.1 + - + +
149B LYS* 4.1 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG 3.1 13.8 + - - -
143B PHE 3.1 0.6 + - - -
145B HIS* 1.3 80.2 - - - +
147B LEU* 1.3 57.5 - - - +
148B LEU 3.6 0.2 + - - -
149B LYS* 4.0 10.2 + - - +
150B SER* 3.7 11.8 + - - -
511B EDO 3.4 25.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B HIS* 3.5 32.1 - - + +
38B GLU* 4.5 1.6 - - - +
72B HIS* 3.4 48.2 - - + +
75B GLN* 4.3 2.9 - - - +
129B PHE* 3.7 25.1 - - + -
143B PHE* 3.2 29.2 + - + +
144B TYR* 3.2 12.7 + - + +
146B GLY* 1.3 76.5 - - - +
148B LEU* 1.3 63.5 + - - +
150B SER* 3.2 6.9 + - - -
151B GLU* 3.0 26.5 + - + +
511B EDO 3.7 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B CYS* 2.9 49.9 - - - +
129B PHE* 3.3 23.3 - - + -
130B ALA* 3.5 23.3 - - + +
133B VAL* 5.3 0.7 - - + -
144B TYR 3.4 6.1 + - - +
145B HIS* 3.1 41.5 + - + +
147B LEU* 1.3 76.2 - - - +
149B LYS* 1.3 63.9 + - - +
151B GLU* 3.2 4.5 + - - -
152B ALA* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B HIS 4.1 1.5 + - - +
146B GLY* 4.0 9.4 + - - +
147B LEU 3.4 0.4 - - - -
148B LEU* 1.3 78.3 - - - +
150B SER* 1.3 62.8 + - - +
152B ALA* 3.4 8.4 + - - +
153B ARG* 3.2 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLU* 4.4 10.7 + - - -
72B HIS* 3.9 30.5 + - - -
146B GLY 3.7 12.1 + - - -
147B LEU* 3.2 9.2 + - - -
149B LYS* 1.3 77.2 - - - +
151B GLU* 1.3 66.5 + - - +
153B ARG* 3.0 13.2 + - - +
154B HIS* 3.0 27.8 + - - -
511B EDO 4.5 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B HIS* 4.3 3.9 - - - -
122B GLU* 3.3 30.5 - - - +
125B SER* 3.6 13.8 - - - -
126B CYS* 3.7 19.3 - - + +
129B PHE* 3.6 25.6 - - + -
147B LEU* 3.0 20.7 + - - +
148B LEU 3.2 1.7 + - - +
150B SER* 1.3 76.7 - - - +
152B ALA* 1.3 58.2 + - - +
154B HIS* 3.2 5.5 + - - +
155B TYR* 2.9 30.0 + - - +
501B FE 3.2 8.9 - - - -
502B FE 2.6 20.1 - - - -
503B UNL 2.7 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.9 25.6 - - + -
126B CYS* 4.4 3.3 - - - -
148B LEU 3.0 15.9 + - - +
149B LYS* 3.6 9.9 - - - +
151B GLU* 1.3 78.8 - - - +
153B ARG* 1.3 56.9 + - + +
155B TYR* 3.5 4.0 + - + -
156B GLN* 3.1 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLU* 4.8 15.0 + - - -
149B LYS 3.2 15.0 + - - +
150B SER* 3.0 12.6 + - - +
152B ALA* 1.3 75.3 - - + +
154B HIS* 1.3 63.2 + - + +
156B GLN* 3.4 15.3 + - - +
157B GLY* 3.0 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B MSE 6.2 0.2 - - - -
65B LEU* 3.8 26.8 - - + +
68B GLU* 3.2 45.1 + - + +
69B GLU* 3.4 18.1 + - - -
72B HIS* 4.1 6.5 - + - -
122B GLU* 3.3 21.1 - - + +
150B SER 3.0 16.4 + - - -
151B GLU* 3.2 9.7 + - - +
153B ARG* 1.3 79.2 - - + +
155B TYR* 1.3 67.6 + - - +
157B GLY* 3.2 2.0 + - - -
158B TYR* 2.9 31.7 + - - -
502B FE 2.4 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.8 2.9 - - + -
5B PRO* 2.3 54.4 + - - +
7B ILE* 3.8 20.9 - - + -
10B PHE* 3.4 39.4 - + + +
119B ALA* 3.6 27.6 - - + +
122B GLU* 3.7 11.7 - - + +
123B ALA* 3.9 9.2 - - + +
151B GLU 2.9 17.2 + - - +
152B ALA* 3.6 11.4 - - + +
154B HIS* 1.3 77.7 - - - +
156B GLN* 1.3 82.8 + - + +
158B TYR* 3.5 2.9 + - - +
159B LEU* 3.2 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.4 15.7 - - + +
152B ALA* 3.1 31.2 + - - +
153B ARG* 3.7 14.1 - - - +
155B TYR* 1.3 94.2 - - + +
157B GLY* 1.3 57.3 + - - +
159B LEU* 3.5 4.0 + - - +
160B LYS* 2.9 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B MSE 3.5 22.3 - - - +
153B ARG 3.0 14.5 + - - -
154B HIS* 3.2 3.3 + - - -
156B GLN* 1.3 75.1 - - - +
158B TYR* 1.3 65.6 + - - +
160B LYS* 3.8 6.4 - - - +
161B LEU* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA 5.4 0.5 + - - -
44B THR* 5.1 2.4 - - - +
45B ALA* 5.4 1.7 - - - +
48B LEU* 4.7 8.6 - - + +
61B MSE 4.1 2.8 - - + -
62B MSE 3.5 32.7 - - + -
65B LEU* 3.9 19.6 - - + +
114B THR 5.1 0.9 - - - -
115B LEU* 3.5 44.1 - - + +
118B GLY* 3.6 20.2 - - - -
119B ALA* 3.6 9.6 - - - +
122B GLU* 3.8 8.7 - - + -
154B HIS 2.9 23.7 + - - +
155B TYR 3.7 3.8 - - - +
157B GLY* 1.3 75.8 - - - +
159B LEU* 1.3 57.6 + - - +
161B LEU* 3.3 5.6 + - - +
162B ALA* 2.9 27.5 + - - +
510B EDO 3.2 43.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.5 10.8 - - + -
5B PRO* 4.1 13.5 - - + -
10B PHE* 3.8 34.5 - - + -
115B LEU 5.4 0.2 - - - -
116B VAL* 4.7 5.2 - - + -
119B ALA* 4.3 7.2 - - + -
155B TYR* 3.2 35.4 + - + +
156B GLN* 3.9 3.6 - - - +
158B TYR* 1.3 76.6 - - - +
160B LYS* 1.3 65.2 + - - +
162B ALA* 3.1 15.0 + - + +
163B HIS* 3.0 31.1 + - + -
171B ILE* 4.4 13.0 - - + -
175B VAL* 4.3 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 5.8 5.8 - - + -
156B GLN* 2.9 29.6 + - + +
157B GLY* 3.8 6.1 - - - +
159B LEU* 1.3 75.0 - - - +
161B LEU* 1.3 63.5 + - - +
163B HIS* 3.2 23.2 + - - +
164B ASN* 3.9 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASP* 4.2 8.7 - - + +
58B LEU* 4.0 38.8 - - + +
61B MSE 3.7 24.9 - - + -
62B MSE 3.9 22.2 - - + -
115B LEU* 3.9 16.6 - - + -
157B GLY 2.9 15.3 + - - +
158B TYR* 3.5 4.9 - - - +
160B LYS* 1.3 79.5 - - - +
162B ALA* 1.3 61.7 + - - +
164B ASN* 3.1 34.8 + - - +
165B TYR* 3.3 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 4.5 3.9 - - - +
115B LEU* 3.8 23.7 - - + +
116B VAL* 4.3 16.4 - - + +
158B TYR 2.9 14.2 + - - +
159B LEU* 3.1 14.3 + - + +
161B LEU* 1.3 76.3 - - - +
163B HIS* 1.3 56.8 + - - +
164B ASN 3.1 0.2 - - - -
165B TYR* 3.1 19.4 + - - +
166B GLY 3.6 1.4 + - - -
171B ILE* 3.2 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 6.3 1.6 - - - -
159B LEU* 3.0 34.5 + - + -
160B LYS* 3.2 12.0 + - - +
161B LEU 3.1 1.8 - - - -
162B ALA* 1.3 74.6 - - - +
164B ASN* 1.3 62.8 + - - +
165B TYR 3.2 1.0 + - - -
166B GLY 3.7 9.6 - - - +
168B GLU* 4.2 29.5 + - + +
171B ILE* 3.7 37.1 - - + +
172B ALA 5.6 0.2 + - - -
507B EDO 3.5 15.9 + - - -
----------------------------------------------------------
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