Contacts of the helix formed by residues 173 - 185 (chain B) in PDB entry 2GPC
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 ASP 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B TYR* 3.0 29.0 + - + +
171B LYS 3.2 1.7 - - - -
172B ASN* 1.3 81.3 - - - +
174B ARG* 1.3 64.5 + - - +
175B ALA* 3.7 10.6 + - - +
176B ALA* 3.1 31.6 + - + +
177B TYR 3.3 13.2 + - - -
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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
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162A TRP* 6.0 2.4 - - - -
116B ALA 2.9 29.8 + - - -
117B VAL* 3.3 24.9 + - + +
119B HIS* 2.8 35.5 + - - +
121B GLY 3.7 16.0 + - - +
161B VAL* 3.8 22.2 + - - +
163B GLU* 5.2 4.0 + - - +
166B TYR* 3.0 51.7 + - + +
172B ASN 3.0 10.4 + - - +
173B ASP* 1.3 70.3 - - - +
175B ALA* 1.3 66.0 + - - +
177B TYR* 3.1 9.3 + - + +
178B VAL* 2.9 24.7 + - + +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 4.0 29.2 - - + +
173B ASP* 3.2 8.5 - - - +
174B ARG* 1.3 77.2 - - - +
176B ALA* 1.3 61.1 + - - +
178B VAL* 3.3 4.0 + - - +
179B GLN* 3.1 28.2 + - + +
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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
----------------------------------------------------------
170B TYR* 3.7 20.9 - - + -
173B ASP* 3.1 31.9 + - - +
174B ARG 3.3 0.2 - - - -
175B ALA* 1.3 76.1 - - - +
177B TYR* 1.3 62.1 + - - +
179B GLN* 3.3 10.1 + - - +
180B THR* 3.1 23.2 + - - -
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Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.1 23.8 - - + -
78B TYR* 2.8 34.2 + + - -
159B CYS* 3.6 18.6 - - - -
160B ASP 2.6 29.9 + - - -
161B VAL* 4.5 4.5 - - + -
165B ALA* 3.9 15.3 - - + +
166B TYR* 3.3 40.6 - + + -
170B TYR* 3.8 21.0 - + + -
173B ASP 3.3 5.8 + - - +
174B ARG* 3.1 16.0 + - + +
176B ALA* 1.3 80.2 - - - +
178B VAL* 1.3 60.4 + - + +
180B THR* 3.1 7.4 + - + -
181B PHE* 2.9 28.0 + + + +
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 5.3 4.0 - - + -
113B THR* 4.4 17.5 - - + -
116B ALA* 4.0 28.7 - - + -
117B VAL* 4.0 13.2 - - + +
159B CYS* 4.6 8.3 - - - -
161B VAL* 4.8 0.4 - - + -
174B ARG* 2.9 26.3 + - + +
175B ALA 3.8 4.3 - - - +
177B TYR* 1.3 83.8 - - + +
179B GLN* 1.3 66.4 + - - +
181B PHE* 3.1 11.3 + - + +
182B TRP* 3.1 42.4 + - + +
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Residues in contact with GLN 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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109B LYS* 4.8 13.5 - - - +
113B THR* 4.4 14.4 + - - +
175B ALA* 3.1 17.2 + - + +
176B ALA* 3.6 11.4 - - - +
177B TYR 3.3 0.2 - - - -
178B VAL* 1.3 76.3 - - - +
180B THR* 1.3 62.2 + - - +
182B TRP* 3.3 32.6 + - - +
183B ASN* 3.4 18.2 + - - +
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Residues in contact with THR 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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17B LYS 3.4 22.7 + - - +
18B GLY* 3.7 11.3 - - - +
19B LEU* 4.4 14.4 - - + -
170B TYR* 2.6 33.1 + - + +
176B ALA 3.1 8.8 + - - -
177B TYR* 3.1 11.3 + - + +
179B GLN* 1.3 74.3 - - - +
181B PHE* 1.3 67.0 + - - +
183B ASN* 3.0 22.8 + - - +
184B VAL* 3.4 14.1 + - + +
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Residues in contact with PHE 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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19B LEU* 6.3 0.9 - - - -
78B TYR* 4.4 3.4 - + - -
81B SER 4.5 2.0 - - - -
82B MET* 3.9 33.4 - - + -
112B PHE* 4.1 13.0 - + - -
157B LEU* 4.0 29.4 - - + -
158B THR 3.3 28.7 - - - -
159B CYS* 3.7 34.1 - - + -
177B TYR* 2.9 17.4 + + + +
178B VAL* 3.1 15.9 + - + +
180B THR* 1.3 74.8 - - - +
182B TRP* 1.3 72.4 + + - +
184B VAL* 2.9 20.5 + - - +
185B VAL* 3.1 34.0 + - + +
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Residues in contact with TRP 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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87B GLY* 3.2 19.6 - - - -
88B GLY 3.5 8.6 + - - +
105B PHE* 4.5 9.6 - + - -
108B PHE* 3.7 33.2 - + - -
109B LYS* 3.7 43.0 - - + +
112B PHE* 3.5 35.4 - + + -
113B THR* 2.9 26.7 + - - -
157B LEU* 5.1 1.8 - - + -
178B VAL* 3.1 32.6 + - + +
179B GLN* 3.5 26.5 - - - +
180B THR 3.2 0.6 - - - -
181B PHE* 1.3 81.2 - + - +
183B ASN* 1.3 60.1 + - - +
185B VAL* 3.7 24.2 + - + +
187B TRP* 4.3 12.1 - + - -
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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
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17B LYS* 3.6 32.6 + - + +
86B GLY 3.5 6.4 - - - +
87B GLY* 3.3 15.4 - - - -
88B GLY 4.7 2.6 + - - +
179B GLN* 3.7 14.9 + - - +
180B THR* 3.0 16.5 + - - +
182B TRP* 1.3 79.4 - - - +
184B VAL* 1.3 59.0 + - - +
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Residues in contact with VAL 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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14B LEU* 4.0 20.6 - - + -
17B LYS* 3.6 30.5 - - + +
19B LEU* 5.3 2.5 - - + -
82B MET* 3.2 34.3 - - + -
83B OCS 2.9 36.4 + - - +
87B GLY 3.7 1.8 - - - +
180B THR* 3.6 14.8 - - + +
181B PHE* 2.9 16.9 + - - +
183B ASN* 1.3 83.0 - - - +
185B VAL* 1.3 66.8 + - - +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B SER 3.5 5.8 - - - -
86B GLY* 3.3 4.5 - - - -
87B GLY* 2.8 26.3 + - - +
157B LEU* 3.6 23.6 - - + -
181B PHE* 3.1 38.1 + - + +
182B TRP* 3.7 29.3 + - + +
183B ASN 3.8 0.2 - - - -
184B VAL* 1.3 75.6 - - - +
186B ASN* 1.3 61.0 + - - +
187B TRP* 3.4 48.2 + - + +
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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
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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