Contacts of the helix formed by residues 167 - 184 (chain B) in PDB entry 6G4O
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 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLY 4.0 5.3 + - - -
155B PHE* 4.1 15.7 + - - +
166B GLY* 1.3 72.5 + - - +
168B VAL* 1.3 55.1 + - - +
169B GLY 3.0 3.1 - - - -
170B LEU* 2.7 37.3 + - + +
171B LEU* 2.8 16.6 + - + +
293B VAL 5.7 0.2 + - - -
294B PRO* 3.2 10.1 - - - +
295B VAL* 2.7 48.1 + - - +
297B ASP* 3.4 26.0 + - - +
300B PHE* 3.5 19.3 - - + +
301B PHE* 4.3 1.4 - - - -
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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
----------------------------------------------------------
45B PHE* 3.5 24.0 - - - +
46B ARG 3.6 20.6 - - - +
47B ARG* 3.9 7.9 - - + +
149B ARG* 3.6 15.7 - - - +
153B PHE 3.8 16.4 - - - +
154B GLY 3.2 15.9 + - - +
156B LEU 5.9 1.3 - - - +
165B PRO* 3.7 16.4 - - + -
166B GLY* 3.7 15.0 - - - +
167B ASN* 1.3 76.3 - - - +
169B GLY* 1.3 55.7 + - - +
171B LEU* 3.6 10.4 - - + +
172B ASP* 2.8 36.4 + - - +
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Residues in contact with GLY 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 3.2 24.6 - - - +
149B ARG 3.8 17.3 - - - -
154B GLY* 2.8 19.1 + - - -
155B PHE* 3.8 11.4 - - - -
167B ASN 3.0 0.4 - - - -
168B VAL* 1.3 79.3 - - - +
170B LEU* 1.3 59.9 + - - +
172B ASP* 3.4 16.7 - - - +
173B GLN* 3.5 2.9 + - - +
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 4.6 3.1 - - + -
155B PHE* 3.7 12.3 - - + -
167B ASN* 2.7 21.4 + - - +
169B GLY* 1.3 72.1 - - - +
171B LEU* 1.3 57.2 + - - +
173B GLN* 3.0 41.6 + - - +
174B ARG* 3.1 9.2 + - - +
205B SER* 3.9 20.4 - - - +
208B MET* 3.9 15.7 - - + -
209B HIS* 3.9 8.3 - - - +
294B PRO* 3.8 27.6 - - + -
300B PHE* 3.5 43.5 - - + -
301B PHE* 4.1 2.5 - - + -
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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
----------------------------------------------------------
47B ARG* 3.4 43.7 - - + +
48B PRO* 3.7 13.6 - - + +
166B GLY 4.7 2.9 - - - +
167B ASN* 2.8 13.1 + - + +
168B VAL* 3.2 21.5 + - + +
170B LEU* 1.3 72.8 - - - +
172B ASP* 1.3 59.3 + - - +
174B ARG* 3.2 41.1 + - - +
175B MET* 2.9 29.3 + - - +
300B PHE* 3.9 9.9 - - + -
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Residues in contact with ASP 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 3.2 14.9 - - + -
48B PRO* 3.2 17.7 - - - +
95B LEU* 3.6 13.4 - - + +
147B SER 4.2 3.1 - - - +
148B TYR* 3.9 12.1 - - + -
149B ARG* 2.7 61.8 + - - +
168B VAL 2.8 23.2 + - - +
169B GLY* 3.4 9.6 - - - +
171B LEU* 1.3 76.2 - - - +
173B GLN* 1.3 57.6 + - - +
175B MET 3.2 1.4 + - - -
176B ALA 2.9 23.6 + - - -
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Residues in contact with GLN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 3.3 18.1 - - + +
120B PHE* 5.0 0.2 - - - -
146B LEU* 3.8 22.1 - - + +
147B SER 4.8 1.8 - - - -
148B TYR* 3.3 48.1 - - + -
169B GLY 3.5 14.6 - - - +
170B LEU* 3.0 21.3 + - - +
172B ASP* 1.3 76.3 - - - +
174B ARG* 1.3 57.3 + - - +
176B ALA* 3.5 2.6 + - - +
177B LEU* 3.0 33.9 + - + +
205B SER* 3.4 18.4 + - - -
209B HIS* 3.0 24.8 + - - +
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU 3.1 11.0 + - - +
171B LEU* 3.4 27.8 - - - +
172B ASP 3.1 0.4 - - - -
173B GLN* 1.3 78.6 - - - +
175B MET* 1.3 51.9 + - - +
177B LEU* 3.1 6.5 + - + +
178B GLN* 2.7 34.6 + - - +
209B HIS* 4.2 6.2 - - + -
212B SER* 3.7 5.7 + - - -
214B GLY* 2.4 54.9 + - - +
215B SER* 2.6 30.5 + - - +
218B LEU* 3.8 17.8 - - + +
300B PHE* 3.3 33.1 - - + +
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Residues in contact with MET 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 3.9 13.5 - - + +
36B ALA* 3.7 21.8 - - - -
48B PRO* 3.4 36.6 - - + +
50B PRO* 3.6 39.7 - - + -
171B LEU 2.9 14.7 + - - +
172B ASP 3.9 3.1 - - - +
174B ARG* 1.3 75.8 - - - +
176B ALA* 1.3 60.7 + - - +
178B GLN* 3.4 11.2 + - + +
179B TRP* 2.9 25.8 + - - +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 3.5 43.6 - - + -
97B LEU* 4.2 4.1 - - + +
146B LEU* 3.9 22.9 - - + -
172B ASP 2.9 10.9 + - - +
173B GLN 3.7 5.2 - - - +
175B MET* 1.3 77.7 - - - +
177B LEU* 1.3 56.8 + - - +
179B TRP* 3.1 4.7 + - - +
180B VAL* 3.0 31.9 + - + +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 3.9 29.4 - - + -
115B ILE* 5.9 2.2 - - + -
146B LEU* 4.6 5.4 - - + -
173B GLN* 3.0 21.0 + - + +
174B ARG* 3.5 13.2 - - + +
176B ALA* 1.3 72.8 - - - +
178B GLN* 1.3 60.9 + - - +
180B VAL* 3.3 6.4 + - + +
181B HIS* 2.8 29.1 + - - +
194B VAL* 4.9 1.8 - - + -
196B ILE* 3.5 32.5 - - + -
209B HIS* 4.4 24.7 - - + +
215B SER* 5.5 1.3 - - - +
218B LEU* 4.0 32.1 - - + +
219B PHE* 4.8 6.7 - - + -
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Residues in contact with GLN 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG* 2.7 22.1 + - + +
175B MET* 3.5 13.7 - - + +
177B LEU* 1.3 73.9 - - - +
179B TRP* 1.3 59.3 + - - +
181B HIS* 3.4 12.8 + - - +
182B ASP* 3.2 58.8 + - - +
218B LEU* 3.4 30.8 - - + +
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Residues in contact with TRP 179 (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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10B THR* 4.3 13.2 - - + -
12B SER* 4.0 22.3 + - - -
33B ILE* 3.8 26.0 - - + -
34B PRO 4.3 7.4 + - - -
35B PHE* 4.0 28.0 - - + +
51B LYS* 6.1 0.9 - - + -
54B TRP* 5.5 1.9 - + - -
97B LEU* 3.9 20.0 - - + -
99B ILE* 3.7 22.7 - - + -
175B MET 2.9 14.0 + - - +
176B ALA 3.1 10.7 + - - +
178B GLN* 1.3 78.3 - - - +
180B VAL* 1.3 71.0 + - + +
182B ASP* 3.2 2.8 + - - -
183B ASN* 2.7 63.9 + - + +
184B ILE* 5.1 1.6 - - + -
187B PHE* 3.9 20.9 - + - -
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.8 2.9 - - + -
111B VAL* 4.0 16.4 - - + -
113B VAL* 4.3 15.3 - - + -
144B VAL* 4.3 23.8 - - + -
176B ALA* 3.0 16.5 + - + +
177B LEU* 3.3 10.1 + - + +
179B TRP* 1.3 85.6 - - + +
181B HIS* 1.3 66.1 + - - +
184B ILE* 2.9 59.6 + - + +
194B VAL* 4.5 10.1 - - + -
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Residues in contact with HIS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU 2.8 14.0 + - - +
178B GLN* 3.4 19.7 - - - +
179B TRP 3.3 0.2 - - - -
180B VAL* 1.3 77.3 - - - +
182B ASP* 1.3 78.3 + - - +
183B ASN 3.8 0.2 + - - -
185B GLN* 4.0 3.8 - - - +
191B PRO* 3.5 43.5 + - + +
194B VAL* 5.9 2.4 - - - +
217B ASP 4.9 8.4 + - - -
218B LEU* 3.8 26.4 + - + +
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Residues in contact with ASP 182 (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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11B LYS* 3.4 36.0 + - + +
178B GLN* 3.2 27.1 - - - +
179B TRP* 3.2 3.1 + - - -
181B HIS* 1.3 101.3 - - - +
183B ASN* 1.3 72.9 + - - +
185B GLN* 3.9 7.1 - - - +
186B PHE* 3.5 9.5 - - - -
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Residues in contact with ASN 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 3.4 6.4 + - - -
11B LYS* 2.8 48.1 - - - +
12B SER* 4.3 1.6 + - - +
179B TRP* 2.7 64.3 + - + +
182B ASP* 1.3 85.2 - - - +
184B ILE* 1.3 66.8 + - - +
185B GLN 2.9 4.0 - - - +
186B PHE* 2.8 26.1 + - + +
187B PHE* 3.2 13.4 - - + -
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Residues in contact with ILE 184 (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 ILE* 4.1 19.5 - - + -
111B VAL* 3.7 23.1 - - + -
142B VAL* 3.7 20.9 - - + -
144B VAL* 3.9 21.1 - - + -
179B TRP* 5.1 0.6 - - + -
180B VAL* 2.9 38.6 + - + +
183B ASN* 1.3 76.4 - - - +
185B GLN* 1.3 58.5 + - - +
187B PHE* 3.0 19.2 + - + -
189B GLY* 2.8 41.4 + - - +
190B ASP 4.1 1.1 - - - -
191B PRO* 3.7 19.5 - - + -
194B VAL* 5.0 0.2 - - + -
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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