Contacts of the helix formed by residues 123 - 141 (chain B) in PDB entry 1PN9
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 ASN 123 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B TYR* 3.3 14.6 + - + +
121B PRO 3.4 5.7 + - - +
122B ALA* 1.3 70.7 - - - +
124B PRO* 1.3 68.1 - - - +
125B GLU* 2.8 44.1 + - - +
126B ASN* 3.0 41.0 + - + +
127B GLU 3.0 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B TYR* 5.0 0.7 - - + -
122B ALA 3.2 12.2 - - - +
123B ASN* 1.3 84.9 - - - +
125B GLU* 1.3 65.0 + - + +
127B GLU* 3.2 15.8 + - + +
128B LYS* 3.1 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASN* 2.8 16.3 + - - +
124B PRO* 1.3 83.3 - - + +
126B ASN* 1.3 79.2 + - - +
128B LYS* 3.2 15.9 + - + +
129B LYS* 2.7 58.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 4.6 2.3 - - - +
110B ASP* 4.4 20.7 + - + +
111B TYR* 3.9 21.6 - - + +
123B ASN* 3.0 38.2 + - + +
125B GLU* 1.3 92.0 + - - +
127B GLU* 1.3 61.4 + - - +
129B LYS* 3.4 19.1 + - - +
130B MET* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B TYR* 3.3 43.7 + - + -
123B ASN 3.0 6.4 + - - +
124B PRO* 3.5 17.7 - - + +
125B GLU 3.2 0.4 - - - -
126B ASN* 1.3 75.8 - - - +
128B LYS* 1.3 59.5 + - + +
130B MET* 3.2 8.3 + - + +
131B LYS* 2.9 59.4 + - + +
171B PHE* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO* 3.1 24.7 + - - +
125B GLU* 3.4 13.4 - - + +
126B ASN 3.2 0.2 - - - -
127B GLU* 1.3 76.3 - - + +
129B LYS* 1.3 67.2 + - + +
131B LYS* 3.1 15.4 + - + +
132B ASP* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 3.1 40.7 + - + +
125B GLU* 2.7 46.1 + - - +
126B ASN* 3.7 21.9 + - - +
127B GLU 3.3 0.2 - - - -
128B LYS* 1.3 77.7 - - + +
130B MET* 1.3 63.9 + - - +
132B ASP* 3.2 9.3 + - - +
133B ALA 3.1 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 3.3 16.3 - - - +
108B PHE* 3.1 27.8 - - - +
111B TYR* 3.0 42.0 - - + -
112B HIS* 3.3 22.2 - - + -
126B ASN 3.0 13.0 + - - +
127B GLU* 3.4 12.3 - - - +
129B LYS* 1.3 78.0 - - - +
131B LYS* 1.3 61.2 + - - +
133B ALA* 3.1 17.8 + - - +
134B VAL* 3.3 9.7 + - - +
166B TYR* 3.3 37.5 - - + +
171B PHE* 4.5 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLU* 2.9 49.4 + - + +
128B LYS* 3.5 16.1 - - + +
130B MET* 1.3 77.7 - - - +
132B ASP* 1.3 65.1 + - - +
134B VAL* 3.2 4.0 + - - +
135B GLY* 3.0 15.9 + - - -
171B PHE* 3.7 29.6 - - + -
176B TYR* 3.2 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 4.2 8.9 + - - +
128B LYS* 3.0 26.3 + - - +
129B LYS* 3.2 12.5 + - - +
131B LYS* 1.3 74.4 - - - +
133B ALA* 1.3 60.4 + - - +
135B GLY* 2.9 5.0 + - - +
136B PHE* 2.7 44.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PHE* 3.5 7.3 - - - -
103B THR* 3.9 32.8 - - + +
104B LEU* 4.0 15.5 - - + -
107B ARG* 4.1 4.0 - - + +
129B LYS 3.1 12.2 + - - +
130B MET 3.1 11.2 + - - +
132B ASP* 1.3 77.4 - - - +
134B VAL* 1.3 62.4 + - - +
136B PHE* 3.0 25.0 + - - +
137B LEU* 3.1 10.2 + - - +
166B TYR* 4.2 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 4.0 11.0 - - + +
130B MET 3.3 2.2 + - - +
131B LYS 3.2 8.4 + - - +
133B ALA* 1.3 76.3 - - - +
135B GLY* 1.3 57.4 + - - +
137B LEU* 3.2 5.9 + - + +
138B ASN* 2.8 26.7 + - - +
163B ILE* 4.9 2.0 - - + -
166B TYR* 3.5 26.5 - - + -
171B PHE* 3.5 30.5 - - + -
173B PHE* 4.3 12.1 - - + -
176B TYR* 3.4 31.0 - - + -
179B VAL* 3.7 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS 3.0 8.1 + - - -
132B ASP* 2.9 10.3 + - - -
134B VAL* 1.3 76.2 - - - +
136B PHE* 1.3 64.9 + - - +
138B ASN* 3.2 3.6 + - - +
139B THR* 3.0 26.0 + - - -
176B TYR* 3.7 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 3.3 29.8 - - + -
49A GLN* 3.7 31.9 - - + -
50A HIS* 3.9 22.2 - + - -
99B PHE* 3.8 18.4 - + + -
103B THR* 4.4 3.1 - - + -
107B ARG* 4.4 21.1 - - - -
132B ASP* 2.7 29.5 + - + -
133B ALA* 3.0 14.1 + - - +
135B GLY* 1.3 74.1 - - - +
137B LEU* 1.3 58.7 + - - +
139B THR* 3.2 7.3 + - - +
140B PHE* 2.9 42.5 + + + -
----------------------------------------------------------
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
----------------------------------------------------------
99B PHE* 4.0 11.1 - - + -
104B LEU* 4.3 10.8 - - + -
133B ALA 3.1 11.9 + - - +
134B VAL* 3.2 10.1 + - - +
136B PHE* 1.3 74.4 - - - +
138B ASN* 1.3 66.0 + - - +
140B PHE* 3.3 17.3 + - + -
141B LEU* 3.1 43.6 + - + +
147B ALA* 5.0 3.1 - - + -
159B LEU* 4.1 22.4 - - + -
163B ILE* 4.1 20.6 - - + -
179B VAL* 4.2 9.4 - - + -
182B TRP* 4.0 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL 2.8 13.5 + - - +
135B GLY* 3.4 9.6 - - - +
137B LEU* 1.3 77.5 - - - +
139B THR* 1.3 64.3 + - - +
141B LEU 3.4 1.2 + - - -
142B GLU* 3.4 5.5 + - - +
175B PRO 5.1 0.4 - - - +
176B TYR* 3.0 51.9 + - + +
177B PRO* 3.4 5.1 - - - +
178B ASN* 2.8 52.6 + - - +
179B VAL* 3.3 10.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
48A PRO* 3.9 31.0 - - + +
135B GLY 3.0 14.1 + - - -
136B PHE* 3.5 12.0 - - - -
137B LEU 3.2 0.2 - - - -
138B ASN* 1.3 74.6 + - - +
140B PHE* 1.3 66.6 + - - +
141B LEU 3.0 1.6 - - - -
142B GLU* 2.9 28.8 + - + +
178B ASN* 5.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 4.0 18.6 - - + -
49A GLN* 3.7 23.6 - - + -
63A TRP* 3.6 26.0 - + - -
95B GLN* 4.4 6.5 - - - -
96B ARG* 3.2 44.4 + - + +
99B PHE* 3.6 38.1 - + + -
136B PHE* 2.9 30.8 + - + -
137B LEU* 3.3 20.2 + - + +
139B THR* 1.3 77.0 - - - +
141B LEU* 1.3 62.0 + - + +
142B GLU 3.4 0.9 + - - +
144B GLN* 3.4 16.1 - - - +
147B ALA 4.6 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.1 31.8 + - + +
138B ASN 3.9 0.4 - - - -
139B THR 3.0 1.0 - - - -
140B PHE* 1.3 76.1 - - - +
142B GLU* 1.3 54.0 + - - +
143B GLY 2.9 1.6 + - - -
144B GLN* 2.6 39.7 + - + +
145B GLU 5.0 0.2 - - - +
146B TYR* 3.7 9.0 - - - +
147B ALA* 3.6 35.9 - - + +
178B ASN* 3.6 27.1 - - + +
179B VAL* 3.8 13.7 - - + +
182B TRP* 3.5 38.8 - - + -
185B ARG* 6.2 0.2 - - - +
----------------------------------------------------------
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