Contacts of the helix formed by residues 158 - 172 (chain B) in PDB entry 4HI7
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 THR 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B SER 3.6 14.1 - - - +
85B LEU* 3.4 19.3 - - - +
87B PRO* 4.5 3.8 - - + -
96B VAL* 3.9 25.1 - - + +
153B ALA* 3.9 12.9 - - + +
156B GLN* 3.5 13.0 - - + +
157B LEU* 1.3 79.9 - - - +
159B ILE* 1.3 60.9 + - - +
160B ALA* 3.2 21.6 + - - +
161B ASP* 2.9 35.1 + - - +
162B PHE* 3.5 8.2 + - - -
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B THR* 4.0 18.6 - - + +
72B MET* 3.8 15.5 - - + +
73B ALA* 3.6 28.7 - - - +
76B VAL* 3.7 24.9 - - + -
85B LEU* 3.0 21.0 + - + +
86B TYR* 3.7 19.7 - - + -
96B VAL* 3.9 8.5 - - + -
100B MET* 3.7 26.7 - - + -
158B THR* 1.3 74.0 - - - +
160B ALA* 1.3 60.9 + - - +
161B ASP 3.2 0.2 - - - -
162B PHE* 3.3 12.6 + - + +
163B SER* 2.9 28.1 + - - -
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.8 16.6 - - + +
99B ARG* 3.7 22.7 - - + -
100B MET* 3.8 12.6 - - + +
152B VAL* 3.6 16.3 - - + +
153B ALA* 4.2 2.7 - - + -
158B THR* 3.0 12.9 + - - +
159B ILE* 1.3 82.3 - - - +
161B ASP* 1.3 58.0 + - - +
163B SER* 3.4 1.8 + - - -
164B LEU* 3.0 32.4 + - - +
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Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B TYR* 3.4 23.0 - - - +
152B VAL* 2.9 25.3 + - - +
153B ALA 4.9 0.2 + - - -
157B LEU* 3.6 15.9 - - + -
158B THR* 2.9 36.6 + - - +
160B ALA* 1.3 78.1 - - - +
162B PHE* 1.3 57.5 + - - +
164B LEU 3.4 0.2 + - - -
165B ILE* 2.8 34.3 + - - +
188B TRP* 2.8 33.3 + - - +
192B LEU* 4.4 3.8 - - + -
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Residues in contact with PHE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA* 3.7 18.5 - - - +
20B LEU* 3.8 18.3 - - + +
21B THR* 3.3 30.3 - - - +
24B ALA* 3.8 20.4 - - + -
72B MET* 4.3 1.3 - - - -
85B LEU* 4.1 15.5 - - + -
157B LEU* 3.8 31.2 - - + -
158B THR 3.5 2.2 + - - -
159B ILE* 3.3 17.9 + - + +
161B ASP* 1.3 80.4 - - - +
163B SER* 1.3 63.6 + - - +
165B ILE* 3.4 8.5 - - + +
166B SER* 3.1 24.8 + - - -
192B LEU* 5.9 0.9 - - + -
195B LEU* 4.2 7.0 - - + -
197B TYR* 3.4 35.9 - + - -
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA* 3.9 12.4 - - - +
68B SER* 5.0 0.9 + - - -
69B HIS* 3.1 32.0 + - - -
72B MET* 3.8 12.1 - - - +
100B MET* 4.2 8.3 - - - -
103B GLU* 3.2 17.6 + - - +
159B ILE 2.9 16.9 + - - -
160B ALA* 3.7 4.3 - - - -
162B PHE* 1.3 76.2 - - - +
164B LEU* 1.3 62.6 + - - +
166B SER* 2.7 20.8 + - - -
167B SER* 3.4 8.1 + - - -
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ARG* 4.1 15.7 - - + +
102B PHE* 4.0 9.9 - - + -
103B GLU* 3.6 28.3 - - + -
107B VAL* 3.9 21.3 - - + -
142B VAL* 4.4 2.9 - - + -
145B PHE* 4.3 15.7 - - + -
152B VAL* 4.0 27.1 - - + -
160B ALA 3.0 19.4 + - - +
163B SER* 1.3 73.3 - - - +
165B ILE* 1.3 60.2 + - - +
166B SER 3.3 0.2 + - - -
167B SER* 3.4 2.6 + - - +
168B ILE* 2.8 44.3 + - + +
188B TRP* 3.7 17.9 - - + -
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.7 22.7 - - + -
161B ASP 2.8 24.0 + - - +
162B PHE* 3.4 9.6 - - + +
164B LEU* 1.3 73.3 - - - +
166B SER* 1.3 57.5 + - - +
168B ILE* 4.4 0.9 - - + +
169B SER* 2.7 48.2 + - - +
188B TRP* 3.5 13.3 - - + -
189B ILE* 3.8 33.9 - - + -
192B LEU* 3.6 24.9 - - + -
198B TYR* 3.4 30.5 - - + +
201B ASN* 4.3 3.1 - - - +
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 3.1 34.3 + - - +
14B PRO* 4.3 1.2 - - - +
16B ARG* 3.1 9.5 + - - -
17B ALA* 3.6 16.9 - - - +
20B LEU* 5.3 0.4 - - - -
103B GLU* 4.4 3.5 + - - -
162B PHE 3.1 15.3 + - - -
163B SER 2.7 18.2 + - - -
165B ILE* 1.3 76.7 - - - +
167B SER* 1.3 56.6 + - - +
169B SER* 3.3 4.0 + - - -
170B SER* 2.7 22.2 + - - -
201B ASN* 3.7 16.8 - - - -
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 4.2 4.5 - - - -
103B GLU* 2.7 30.6 + - - +
107B VAL* 3.4 23.0 - - - +
108B PHE* 5.0 2.9 - - - -
112B LEU* 3.7 19.7 - - - +
163B SER 3.4 2.4 + - - -
164B LEU 3.4 8.8 + - - -
166B SER* 1.3 79.4 + - - +
168B ILE* 1.3 58.8 + - - +
169B SER 3.3 0.2 - - - -
170B SER* 3.0 4.4 + - - -
171B LEU* 2.9 31.4 + - - +
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B VAL* 4.8 9.9 - - + -
138B ALA* 6.4 1.3 - - + -
139B TYR* 4.3 23.6 - - + -
142B VAL* 4.0 27.4 - - + -
164B LEU* 2.8 31.4 + - + +
165B ILE* 4.4 1.1 - - + +
167B SER* 1.3 75.2 - - - +
169B SER* 1.3 62.6 + - - +
170B SER 3.1 1.0 + - - -
171B LEU* 3.2 7.8 + - + +
172B VAL* 3.2 23.3 + - + +
177B VAL* 4.6 5.2 - - + -
185B LEU* 4.2 11.7 - - + -
188B TRP* 3.9 24.7 - - + -
189B ILE* 4.1 27.1 - - + -
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Residues in contact with SER 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 3.5 5.0 + - - -
165B ILE* 2.7 29.2 + - - +
166B SER 3.3 8.1 + - - -
168B ILE* 1.3 77.4 - - - +
170B SER* 1.3 56.5 + - - +
172B VAL* 3.3 23.2 - - - +
189B ILE* 6.2 2.5 - - - -
198B TYR* 4.1 9.0 - - - -
201B ASN* 3.0 25.7 + - - -
205B ALA* 3.7 16.3 - - - +
209B VAL* 4.2 6.8 - - - +
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Residues in contact with SER 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 3.4 4.6 - - - +
16B ARG* 2.8 22.9 + - - +
112B LEU* 3.6 17.5 - - - -
166B SER 2.7 20.8 + - - -
167B SER 3.0 8.6 + - - -
169B SER* 1.3 77.1 + - - +
171B LEU* 1.3 66.3 + - - +
172B VAL 3.1 1.8 - - - -
173B ALA* 3.0 25.0 + - - +
174B PHE* 4.3 0.5 - - - -
205B ALA* 5.4 0.4 - - - -
208B PHE* 3.4 28.2 - - - -
209B VAL* 5.2 0.4 - - - -
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL* 3.8 29.2 - - + +
111B ALA* 4.1 9.2 - - + +
112B LEU* 3.9 31.6 - - + +
135B ILE* 3.7 35.6 - - + +
138B ALA* 4.9 5.2 - - + -
139B TYR* 3.5 28.3 + - + +
167B SER 2.9 15.7 + - - +
168B ILE* 3.2 8.0 + - + +
170B SER* 1.3 78.0 - - - +
172B VAL* 1.3 56.0 + - - +
173B ALA 3.0 0.4 - - - -
174B PHE* 2.9 30.9 + - + +
175B VAL* 3.0 10.2 + - - +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 3.9 1.8 - - - +
168B ILE* 3.2 14.8 + - + +
169B SER* 3.3 28.5 - - - +
171B LEU* 1.3 75.8 - - - +
173B ALA* 1.3 62.5 + - - +
174B PHE 3.1 0.7 + - - -
175B VAL 3.4 8.2 + - - +
176B PRO* 3.5 25.5 - - + +
177B VAL* 3.7 36.1 - - + +
189B ILE* 5.3 4.0 - - + -
209B VAL* 4.7 7.4 - - + -
213B LYS* 5.2 2.4 - - - -
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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
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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) + - + + + + + -
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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