Contacts of the helix formed by residues 172 - 183 (chain B) in PDB entry 3GBA
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 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B LEU 5.8 3.6 - - - +
59B GLY 5.8 2.0 - - - +
137B VAL* 3.7 14.4 - - - -
170B VAL* 3.4 7.1 - - - +
171B LYS* 1.3 104.9 - - + +
173B SER* 1.3 65.9 + - - +
174B ASP* 3.4 10.9 + - - +
175B GLU* 2.9 36.0 + - - +
176B GLY 3.2 14.9 + - - -
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Residues in contact with SER 173 (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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13B GLU* 2.7 40.7 + - - -
137B VAL* 3.7 9.8 - - - +
172B ASN* 1.3 74.4 - - - +
174B ASP* 1.3 61.2 + - - +
176B GLY* 3.0 3.6 + - - -
177B ILE* 2.8 45.1 + - - +
187B LEU* 4.5 3.0 - - - +
189B MET* 5.9 1.3 - - - -
193B SER* 6.4 0.2 - - - -
258B DYH 3.3 23.7 - - - -
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Residues in contact with ASP 174 (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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14B GLU* 4.3 29.2 + - - +
172B ASN* 3.3 10.4 + - - +
173B SER* 1.3 79.6 - - - +
175B GLU* 1.3 63.7 + - - +
177B ILE* 3.4 13.7 + - - +
178B GLN* 3.0 32.5 + - + +
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Residues in contact with GLU 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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170B VAL* 3.4 17.4 - - + +
171B LYS* 3.0 39.4 + - - +
172B ASN* 2.9 23.3 + - - +
174B ASP* 1.3 76.3 - - - +
176B GLY* 1.3 62.0 + - - +
178B GLN* 3.5 6.3 + - - +
179B ARG* 3.1 24.5 + - - +
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Residues in contact with GLY 176 (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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170B VAL* 3.8 23.8 - - - +
172B ASN 3.2 5.1 + - - -
173B SER 3.0 6.5 + - - -
175B GLU* 1.3 79.4 - - - +
177B ILE* 1.3 61.7 + - - +
179B ARG* 3.2 5.9 + - - +
180B VAL* 3.0 26.2 + - - +
185B TYR* 4.0 1.8 - - - -
187B LEU* 3.9 19.1 - - - -
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Residues in contact with ILE 177 (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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14B GLU* 6.1 0.7 - - - +
113B LEU* 4.4 11.2 - - + -
173B SER* 2.8 38.0 + - - +
174B ASP* 3.8 12.8 - - - +
176B GLY* 1.3 72.7 - - - +
178B GLN* 1.3 67.5 + - - +
180B VAL* 3.2 8.7 + - - +
181B LEU* 3.0 39.8 + - + +
187B LEU* 4.6 6.1 - - + -
189B MET* 5.2 3.4 - - + -
197B VAL* 3.6 43.1 - - + -
201B ASN* 4.9 0.9 - - - +
204B LEU* 5.0 2.7 - - + -
261B CL 4.5 12.6 - - + -
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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
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174B ASP* 3.0 23.1 + - + +
175B GLU* 3.8 7.0 - - - +
177B ILE* 1.3 81.0 - - - +
179B ARG* 1.3 52.7 + - - +
181B LEU* 3.3 22.7 + - - +
182B THR* 2.7 53.4 + - + +
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Residues in contact with ARG 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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133B GLU* 3.7 16.2 + - - -
166B GLN* 3.3 53.6 + - - +
167B SER 2.7 23.2 + - - -
168B ALA* 3.8 6.1 - - - +
170B VAL* 3.8 21.1 - - - +
175B GLU* 3.1 14.8 + - - +
176B GLY* 3.2 9.4 + - - +
178B GLN* 1.3 77.7 - - - +
180B VAL* 1.3 57.3 + - - +
182B THR* 4.0 5.4 - - - -
183B THR* 2.7 53.4 + - + +
185B TYR* 3.5 37.0 - - + +
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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
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113B LEU* 4.0 13.9 - - + +
114B TYR* 4.1 17.3 - - + -
115B ARG* 4.4 8.0 + - - +
176B GLY 3.0 14.1 + - - +
177B ILE 3.6 6.3 - - - +
179B ARG* 1.3 76.1 - - - +
181B LEU* 1.3 61.6 + - - +
183B THR 3.3 11.8 - - - +
185B TYR* 3.5 34.3 - - + +
187B LEU* 3.8 23.1 - - + +
204B LEU* 3.8 31.7 - - + +
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Residues in contact with LEU 181 (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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177B ILE* 3.0 27.2 + - + +
178B GLN* 3.7 28.3 - - - +
179B ARG 3.3 0.2 - - - -
180B VAL* 1.3 79.5 - - - +
182B THR* 1.3 64.4 + - + +
183B THR 4.8 0.2 - - - -
201B ASN* 3.8 23.6 - - - +
203B ASN* 3.8 26.1 + - - +
204B LEU* 3.7 26.5 - - + -
210D LEU* 6.4 1.1 - - + -
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Residues in contact with THR 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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178B GLN* 2.7 34.4 + - + +
179B ARG* 4.0 1.6 - - - -
181B LEU* 1.3 86.6 - - + +
183B THR* 1.3 74.6 + - - +
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Residues in contact with THR 183 (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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115B ARG* 4.3 4.8 + - - -
179B ARG* 2.7 45.0 + - + +
180B VAL 3.3 11.3 - - - +
181B LEU 3.8 0.4 - - - -
182B THR* 1.3 93.5 - - - +
184B ASP* 1.3 60.0 + - - +
185B TYR* 3.0 13.5 + - - +
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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
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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