Contacts of the helix formed by residues 161 - 177 (chain B) in PDB entry 4OGB
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 161 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B TYR* 3.4 17.2 - - - -
154B HIS 3.6 15.9 - - - +
155B ALA* 5.3 2.4 + - - -
157B VAL 2.9 26.2 + - - +
158B ALA 3.0 21.6 + - - -
159B TYR 2.8 11.6 + - - +
160B HIS* 1.3 73.2 - - - +
162B ASN* 1.3 71.1 + - - +
163B ILE* 2.9 24.1 + - - +
164B HIS* 3.1 12.0 + - - +
165B ALA 3.1 18.2 + - - -
332B TRP* 5.0 1.3 - - - -
335B ARG* 3.6 12.1 - - - +
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Residues in contact with ASN 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASN* 3.2 38.7 + - - +
117B PRO* 3.4 10.7 - - - +
118B LEU* 4.0 4.4 - - + +
150B GLU* 2.9 43.7 + - + +
153B TYR* 3.6 22.1 - - + +
155B ALA* 5.4 5.7 - - - +
161B ASN* 1.3 78.3 - - - +
163B ILE* 1.3 69.9 + - - +
165B ALA* 3.7 4.8 - - - +
166B ALA* 3.0 24.9 + - - +
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 4.1 21.8 - - + +
107B PHE* 3.8 17.3 - - + -
110B ALA* 4.3 13.9 - - + -
115B ASN* 4.3 7.6 - - - +
117B PRO* 4.1 16.6 - - + -
161B ASN* 2.9 9.8 + - - +
162B ASN* 1.3 85.3 - - - +
164B HIS* 1.3 57.4 + - - +
166B ALA* 3.3 3.6 + - - +
167B ASP* 2.9 27.4 + - - +
332B TRP* 3.6 18.8 - - + -
335B ARG* 3.9 34.1 - - - +
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Residues in contact with HIS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TYR* 3.2 59.3 + + + +
160B HIS* 4.4 4.7 - + - -
161B ASN* 3.1 10.2 + - - +
163B ILE* 1.3 73.7 - - - +
165B ALA* 1.3 60.3 + - - +
167B ASP* 3.1 5.8 + - - +
168B VAL* 2.9 50.5 + - + +
200B HIS* 3.3 7.5 + + - -
201B ASP* 3.0 21.1 - - + -
318B ASP* 3.2 13.7 - - - -
321B ASN* 5.0 1.2 + - - -
332B TRP* 3.7 16.7 - - + -
501B 2SR 6.1 0.2 - - - -
502B ZN 2.0 32.1 - - - -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 4.0 8.3 - - + -
153B TYR* 3.4 40.4 - - + +
161B ASN 3.1 8.0 + - - +
162B ASN* 3.7 8.3 - - - +
163B ILE 3.3 0.2 - - - -
164B HIS* 1.3 77.2 - - - +
166B ALA* 1.3 58.1 + - - +
168B VAL* 3.3 2.4 + - - +
169B VAL* 2.9 32.6 + - - +
197B SER 3.9 2.2 - - - +
198B ALA 3.9 9.4 - - - +
200B HIS* 4.5 11.9 - - - -
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL* 4.3 3.6 - - + -
117B PRO* 3.7 15.9 - - + +
118B LEU* 3.6 36.0 - - - +
121B ILE* 4.1 11.8 - - + +
162B ASN 3.0 17.7 + - - +
163B ILE 3.6 4.3 - - - +
165B ALA* 1.3 76.5 - - - +
167B ASP* 1.3 57.9 + - - +
169B VAL* 3.5 3.8 + - - +
170B GLN* 3.0 31.0 + - - +
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Residues in contact with ASP 167 (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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106B VAL* 4.1 3.9 - - + +
163B ILE 2.9 15.2 + - - +
164B HIS* 3.1 13.4 + - - +
166B ALA* 1.3 75.4 - - - +
168B VAL* 1.3 57.5 + - - +
171B SER* 2.7 37.9 + - - -
317B ALA 5.5 0.2 - - - -
320B SER* 4.4 6.5 + - - -
321B ASN* 4.9 7.1 + - - -
324B LYS* 3.3 10.1 + - - -
332B TRP* 3.4 38.6 + - + -
509B EDO 2.7 47.3 + - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B HIS* 2.9 50.5 + - + +
165B ALA 3.8 3.8 - - - +
167B ASP* 1.3 79.1 - - + +
169B VAL* 1.3 59.7 + - - +
171B SER* 4.3 4.3 - - - -
172B THR* 2.9 35.4 + - - +
197B SER* 4.1 14.1 - - - +
200B HIS* 3.8 21.5 - - + +
314B VAL* 4.6 7.0 - - + +
317B ALA* 3.7 29.8 - - + +
318B ASP* 4.0 8.5 - - + +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.9 6.1 - - + -
121B ILE* 4.1 7.9 - - + -
122B MET* 3.5 24.5 - - + -
125B ILE* 3.7 19.5 - - + -
165B ALA 2.9 21.5 + - - +
166B ALA* 3.5 7.0 - - - +
168B VAL* 1.3 78.7 - - - +
170B GLN* 1.3 59.3 + - - +
172B THR* 3.3 4.3 + - - +
173B HIS* 2.9 24.9 + - - +
194B ILE* 4.1 9.6 - - + +
197B SER* 3.8 8.7 - - - -
198B ALA* 3.4 39.5 - - + +
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Residues in contact with GLN 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASP 3.8 3.2 + - - -
99B VAL* 2.6 42.6 + - + +
101B LYS 2.9 24.4 + - - -
104B LEU* 3.7 21.0 - - + +
121B ILE* 4.0 8.7 - - + -
125B ILE* 4.0 4.5 - - + -
166B ALA 3.0 15.4 + - - +
167B ASP 4.1 1.3 - - - +
169B VAL* 1.3 76.7 - - - +
171B SER* 1.3 60.9 + - - +
173B HIS* 3.1 7.7 + - - +
174B VAL* 3.0 33.3 + - - +
509B EDO 2.8 35.8 + - - +
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TRP* 3.7 17.5 - - - -
167B ASP* 2.7 23.6 + - - -
168B VAL* 3.8 4.3 - - - -
170B GLN* 1.3 76.9 - - - +
172B THR* 1.3 59.2 + - - +
173B HIS 3.3 0.2 + - - -
174B VAL* 3.3 5.5 + - - +
175B LEU* 2.9 31.2 + - - +
317B ALA* 3.9 15.7 - - - -
320B SER* 3.6 9.2 + - - -
324B LYS* 3.1 27.2 + - - -
509B EDO 4.0 2.3 - - - -
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Residues in contact with THR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 2.9 19.8 + - - +
169B VAL 3.5 5.8 - - - +
171B SER* 1.3 75.0 - - - +
173B HIS* 1.3 56.0 + - - +
175B LEU* 3.6 6.8 - - - +
176B LEU* 2.8 46.4 + - + +
193B ALA* 3.9 15.3 - - + +
194B ILE* 4.6 3.1 - - + +
197B SER* 2.9 25.8 + - - +
313B MET* 4.4 6.1 - - - -
314B VAL* 3.9 15.9 - - + +
317B ALA* 3.3 17.3 - - - +
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Residues in contact with HIS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.3 26.9 - - - +
100B ASN* 2.6 26.7 + - - +
125B ILE* 3.5 34.8 - - + +
128B GLU* 3.4 18.7 + - - -
129B ARG* 2.9 60.1 + - - +
169B VAL 2.9 14.1 + - - +
170B GLN 3.2 7.9 - - - +
171B SER 3.1 0.4 - - - -
172B THR* 1.3 78.9 - - - +
174B VAL* 1.3 63.5 + - - +
176B LEU* 4.7 4.3 - - - -
177B SER* 3.4 11.7 + - - -
194B ILE* 5.0 3.4 - - + -
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL 4.0 2.2 - - - +
100B ASN* 3.4 36.6 - - - +
101B LYS 3.9 6.1 - - - +
102B TRP* 3.7 30.5 - - + +
170B GLN* 3.0 31.3 + - - +
171B SER 3.6 7.2 - - - +
173B HIS* 1.3 76.2 - - - +
175B LEU* 1.3 65.4 + - + +
177B SER* 3.1 16.6 + - - -
178B THR* 3.5 8.7 + - - -
395B ILE* 5.7 2.7 - - + -
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Residues in contact with LEU 175 (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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102B TRP* 4.2 11.4 - - + -
171B SER 2.9 17.8 + - - +
172B THR 3.3 7.8 + - - +
174B VAL* 1.3 77.2 - - + +
176B LEU* 1.3 61.9 + - - +
178B THR* 3.2 30.1 + - - +
181B LEU* 4.6 3.6 - - - +
313B MET* 3.5 44.0 - - + +
316B CYS* 4.1 7.0 - - + -
317B ALA* 4.2 10.1 - - + +
381B TRP* 4.0 28.7 - - + -
384B TRP* 3.8 24.1 - - + +
392B ALA* 6.3 0.7 - - + -
395B ILE* 4.8 7.4 - - + -
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 3.4 17.0 + - - +
172B THR* 2.8 27.5 + - + +
174B VAL 3.3 0.2 - - - -
175B LEU* 1.3 73.1 - - - +
177B SER* 1.3 58.3 + - - +
178B THR 3.2 5.2 + - - +
181B LEU* 4.8 12.1 - - - +
182B GLU* 5.8 1.0 - - - -
185B PHE* 4.4 17.8 - - + -
190B ILE* 3.9 35.8 - - + +
193B ALA* 4.3 8.1 - - + -
194B ILE* 3.7 36.6 - - + -
310B LEU* 4.7 3.6 - - + -
313B MET* 3.6 28.7 - - + -
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ASN* 5.7 3.3 + - - -
129B ARG* 2.7 27.0 + - - -
173B HIS* 3.4 11.6 + - - -
174B VAL* 3.1 13.8 + - - -
176B LEU* 1.3 74.8 - - - +
178B THR* 1.3 64.7 + - - +
179B PRO* 3.4 6.4 - - - +
182B GLU* 5.0 6.2 - - - +
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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
------------------------------------------------------------
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