Contacts of the helix formed by residues 172 - 178 (chain C) in PDB entry 2GTP
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 172 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B VAL* 3.8 13.4 - - + +
180B LYS 3.2 22.9 - - - +
181B THR* 3.2 9.1 + - - +
182B THR* 3.0 29.9 + - + +
168C LEU* 3.0 15.5 + - + +
171C LYS* 1.3 78.2 - - - +
173C SER* 1.3 66.0 + - - +
174C TYR 3.5 0.7 - - - -
175C PRO* 3.6 8.0 - - - +
176C ARG* 2.8 53.7 + - - +
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Residues in contact with SER 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B THR* 3.6 25.3 - - - +
86C PHE* 4.2 4.0 - - - -
89C PHE* 3.5 7.7 - - - -
90C LEU* 3.7 30.4 - - - +
93C GLU* 4.5 3.1 - - - -
95C SER* 4.1 1.9 + - - -
98C ASN* 5.1 0.3 + - - -
168C LEU 3.9 0.2 + - - -
169C MET* 3.2 19.7 + - - +
172C ASP* 1.3 74.7 - - - +
174C TYR* 1.3 59.7 + - - +
176C ARG* 3.3 19.0 + - - +
177C PHE* 2.9 23.0 + - - +
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Residues in contact with TYR 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C TRP 2.7 28.2 + - - -
70C SER 3.2 20.3 + - - -
71C GLN 5.5 0.7 - - - -
72C SER* 3.3 18.8 + - - -
73C LEU* 3.9 26.2 - - + -
76C LEU* 3.8 26.9 - - + -
86C PHE* 4.2 3.8 - + + -
169C MET 2.9 17.6 + - - +
170C GLU* 3.6 19.3 - - + +
173C SER* 1.3 72.1 - - - +
175C PRO* 1.4 73.2 - - + +
176C ARG 3.0 2.8 + - - -
177C PHE* 3.1 14.0 + + - +
178C LEU* 3.2 39.7 + - + +
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Residues in contact with PRO 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C GLU 3.1 19.3 - - - +
171C LYS* 3.4 19.5 - - - +
172C ASP 3.6 12.1 - - - +
174C TYR* 1.4 96.1 - - + +
176C ARG* 1.3 59.4 + - - +
178C LEU* 3.7 19.4 + - + +
179C LYS* 3.8 14.7 + - - +
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Residues in contact with ARG 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B THR* 4.6 3.4 - - - +
182B THR 4.2 3.8 + - - -
185B VAL* 3.8 30.2 - - - +
89C PHE* 3.9 8.9 - - + -
93C GLU* 2.9 38.4 + - - +
172C ASP* 2.8 54.9 + - - +
173C SER* 3.3 16.2 + - - +
174C TYR 3.0 0.4 - - - -
175C PRO* 1.3 77.9 - - - +
177C PHE* 1.3 66.8 + - - +
178C LEU 3.1 1.8 - - - -
179C LYS* 2.8 20.4 + - + +
180C SER* 3.3 11.1 + - - -
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Residues in contact with PHE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C TRP* 4.8 1.3 - + + -
76C LEU* 3.4 40.6 - - + -
85C VAL* 3.7 41.7 - - + -
86C PHE* 3.7 17.5 - + + -
89C PHE* 3.5 37.4 - + + -
173C SER 2.9 14.4 + - - +
174C TYR* 3.4 8.5 - + - +
176C ARG* 1.3 76.0 - - - +
178C LEU* 1.3 67.0 + - + +
180C SER* 2.6 28.7 + - - -
182C ILE* 4.2 5.8 - - + -
183C TYR* 3.2 42.7 - + + +
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Residues in contact with LEU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C TRP 4.0 3.8 - - - +
70C SER* 3.8 35.2 - - - +
174C TYR* 3.2 53.1 + - + +
175C PRO* 3.7 12.6 - - + +
176C ARG 3.1 0.8 - - - -
177C PHE* 1.3 84.7 - - + +
179C LYS* 1.3 61.2 + - + +
180C SER 3.5 0.4 - - - -
183C TYR* 3.4 33.4 - - + -
184C LEU* 3.8 9.5 - - - +
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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