Contacts of the helix formed by residues 167 - 184 (chain A) in PDB entry 1GQR
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLY 4.1 4.6 + - - -
155A PHE* 4.1 15.4 + - - +
166A GLY* 1.3 71.0 - - - +
168A VAL* 1.3 57.4 + - - +
169A GLY 3.2 3.4 - - - -
170A LEU* 2.9 32.2 + - + +
171A LEU* 3.1 15.4 + - + +
294A PRO* 3.1 14.0 - - - +
295A VAL* 2.8 48.9 + - - +
297A ASP* 3.3 27.0 + - - +
300A PHE* 3.6 19.1 - - + +
301A PHE* 4.1 1.8 - - - -
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.2 27.8 - - - +
46A ARG 3.6 22.0 - - - +
47A ARG* 3.7 9.6 - - + +
149A ARG* 3.7 9.6 + - - +
153A PHE 3.6 15.0 - - - +
154A GLY* 3.1 22.8 + - - +
155A PHE* 5.1 0.4 - - - -
156A LEU 5.7 1.8 - - - +
165A PRO* 4.0 11.2 - - + -
166A GLY* 3.0 13.2 + - - +
167A ASN* 1.3 77.4 - - - +
169A GLY* 1.3 56.5 + - - +
171A LEU* 3.2 10.5 + - - +
172A ASP* 3.0 33.8 + - - +
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Residues in contact with GLY 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR* 3.2 24.5 - - - +
149A ARG 3.5 25.1 - - - -
154A GLY* 2.8 15.5 + - - -
155A PHE* 3.7 9.0 - - - -
168A VAL* 1.3 77.7 - - - +
170A LEU* 1.3 61.2 + - - +
172A ASP* 3.3 9.0 + - - -
173A GLN* 3.3 9.2 + - - +
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PHE* 4.8 0.9 - - + -
155A PHE* 3.8 11.1 - - + -
167A ASN* 2.9 20.9 + - - +
169A GLY* 1.3 75.8 - - - +
171A LEU* 1.3 59.4 + - - +
173A GLN* 3.2 27.5 + - - +
174A ARG* 3.0 22.3 + - - +
205A SER* 3.9 16.8 - - - +
208A MET* 4.1 12.6 - - + -
209A HIS* 3.4 15.4 - - - +
294A PRO* 3.7 28.9 - - + -
300A PHE* 3.7 33.9 - - + -
301A PHE* 3.9 9.9 - - + -
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 3.5 51.1 - - + +
48A PRO* 3.5 19.2 - - + +
166A GLY 5.2 2.0 - - - +
167A ASN* 3.1 12.7 + - + +
168A VAL* 3.2 9.8 + - + +
170A LEU* 1.3 75.2 - - - +
172A ASP* 1.3 58.3 + - - +
174A ARG* 3.3 36.7 + - - +
175A MET* 2.8 30.5 + - - +
300A PHE* 3.7 19.1 - - + -
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Residues in contact with ASP 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 3.2 18.7 - - + -
48A PRO* 3.2 16.3 - - - +
95A LEU* 3.5 15.7 - - + +
147A SER 4.1 1.1 - - - +
148A TYR* 3.7 13.2 - - + -
149A ARG* 2.9 64.8 + - - +
168A VAL 3.0 16.7 + - - +
169A GLY* 3.4 7.5 - - - +
170A LEU 3.2 0.2 - - - -
171A LEU* 1.3 73.9 - - - +
173A GLN* 1.3 67.0 + - - +
175A MET* 3.2 1.1 + - - -
176A ALA 3.0 18.5 + - - -
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Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 3.7 11.1 - - + +
120A PHE* 4.7 0.8 - - - -
146A LEU* 3.9 20.4 - - + +
148A TYR* 3.4 44.6 - - + +
169A GLY 3.4 10.1 + - - +
170A LEU* 3.3 19.0 - - - +
171A LEU 3.2 0.2 - - - -
172A ASP* 1.3 77.9 - - - +
174A ARG* 1.3 57.6 + - - +
176A ALA* 3.1 5.4 + - - +
177A LEU* 2.9 33.2 + - + +
205A SER* 3.0 34.3 + - - -
209A HIS* 2.7 32.2 + - + +
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Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU 3.0 12.8 + - - +
171A LEU* 3.4 30.3 - - - +
173A GLN* 1.3 75.9 - - - +
175A MET* 1.3 51.4 + - - +
177A LEU* 3.1 12.0 + - - +
178A GLN* 2.8 31.3 + - + +
209A HIS* 4.0 3.5 - - + -
212A SER* 2.7 29.1 + - - -
214A GLY* 3.1 29.6 + - - +
215A SER* 2.8 26.1 + - - +
218A LEU* 3.4 19.3 - - + +
300A PHE* 3.4 19.4 - - - +
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Residues in contact with MET 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.5 27.4 - - + +
36A ALA* 3.7 7.9 - - - -
48A PRO* 3.1 32.1 - - + +
49A GLU 3.5 22.4 - - - +
50A PRO* 3.6 24.0 - - + -
171A LEU 2.8 18.6 + - - +
172A ASP* 3.6 6.1 - - - +
174A ARG* 1.3 71.2 - - - +
176A ALA* 1.3 59.9 + - - +
178A GLN* 3.1 10.8 + - + +
179A TRP* 2.9 28.1 + - + +
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.7 29.1 - - + -
97A LEU* 4.2 4.7 - - + +
113A VAL* 6.0 0.2 - - + -
146A LEU* 3.6 31.4 - - + -
172A ASP 3.0 12.6 + - - +
173A GLN 3.3 9.0 - - - +
175A MET* 1.3 75.2 - - - +
177A LEU* 1.3 58.6 + - - +
179A TRP* 3.2 3.5 + - - +
180A VAL* 3.0 33.1 + - + +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 3.9 26.2 - - + -
115A ILE* 5.3 1.8 - - + -
146A LEU* 4.1 6.3 - - + -
173A GLN 2.9 17.7 + - - +
174A ARG* 3.3 14.6 - - - +
176A ALA* 1.3 77.4 - - - +
178A GLN* 1.3 55.3 + - - +
180A VAL* 3.3 6.7 + - + +
181A HIS* 2.9 27.9 + - - +
194A VAL* 5.3 1.6 - - + -
196A ILE* 3.5 34.8 - - + -
209A HIS* 4.4 25.6 - - + +
215A SER* 5.2 1.8 - - - +
218A LEU* 4.0 33.1 - - + +
219A PHE* 4.6 6.7 - - + -
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Residues in contact with GLN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ARG* 2.8 14.1 + - + +
175A MET* 3.1 16.4 + - + +
177A LEU* 1.3 74.9 - - - +
179A TRP* 1.3 60.2 + - - +
181A HIS* 3.1 18.8 + - - +
182A ASP* 2.9 66.4 + - - +
218A LEU* 3.3 23.9 - - + +
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Residues in contact with TRP 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR* 3.9 21.1 - - + -
12A SER* 3.3 26.8 + - - -
15A VAL* 5.4 0.2 - - + -
33A ILE* 3.8 26.7 - - + -
34A PRO 4.2 6.0 + - - -
35A PHE* 4.1 28.7 - - + +
51A LYS* 5.9 1.6 - - + -
54A TRP* 5.2 0.6 - + - -
97A LEU* 3.9 18.2 - - + -
99A ILE* 4.0 21.5 - - + -
175A MET* 2.9 13.4 + - + +
176A ALA 3.2 7.6 + - - +
178A GLN* 1.3 76.9 - - - +
180A VAL* 1.3 65.7 + - + +
182A ASP* 4.7 2.0 - - - -
183A ASN* 2.9 57.5 + - + +
184A ILE* 5.0 1.3 - - + -
187A PHE* 3.7 27.8 - + - -
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.5 7.4 - - + -
111A VAL* 4.2 7.6 - - + -
113A VAL* 4.3 13.2 - - + -
144A VAL* 3.9 30.5 - - + -
176A ALA* 3.0 20.1 + - + +
177A LEU* 3.6 10.3 - - + +
179A TRP* 1.3 79.3 - - + +
181A HIS* 1.3 66.2 + - - +
184A ILE* 2.9 53.2 + - + +
194A VAL* 4.1 24.5 - - + -
218A LEU 6.1 0.2 - - - +
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Residues in contact with HIS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU 2.9 13.9 + - - +
178A GLN* 3.2 21.9 + - - +
180A VAL* 1.3 80.8 - - - +
182A ASP* 1.3 78.6 + - - +
184A ILE 4.8 0.3 + - - -
185A GLN* 4.6 4.3 + - - +
191A PRO* 3.5 41.7 - - + +
194A VAL* 5.8 1.6 - - - -
217A ASP 4.5 16.8 + - - -
218A LEU* 4.5 18.4 - - + +
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Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS* 3.0 48.3 + - + +
178A GLN* 2.9 37.1 + - - +
179A TRP* 4.7 0.9 - - - -
181A HIS* 1.3 98.9 + - - +
183A ASN* 1.3 68.6 + - - +
185A GLN* 3.8 9.7 - - - +
186A PHE* 3.8 1.4 - - - -
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Residues in contact with ASN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR* 3.3 5.5 - - + -
11A LYS* 2.8 42.7 + - - +
12A SER* 4.8 1.2 + - - -
179A TRP* 2.9 74.8 + - + +
182A ASP* 1.3 87.7 - - - +
184A ILE* 1.3 62.5 + - - +
185A GLN 3.0 6.3 - - - -
186A PHE* 2.9 30.1 + - + +
187A PHE* 3.4 6.2 - - - -
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ILE* 4.1 17.7 - - + -
111A VAL* 3.7 27.1 - - + -
142A VAL* 3.7 23.3 - - + -
144A VAL* 3.7 20.6 - - + -
179A TRP* 4.1 1.7 + - + -
180A VAL* 2.9 36.2 + - + +
181A HIS 4.8 0.2 + - - -
182A ASP 4.0 0.2 - - - -
183A ASN* 1.3 75.9 - - - +
185A GLN* 1.3 62.2 + - - +
186A PHE 3.1 0.2 - - - -
187A PHE* 3.1 15.6 + - + -
189A GLY* 2.8 39.0 + - - +
191A PRO* 3.8 20.0 - - + -
194A 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