Contacts of the helix formed by residues 168 - 173 (chain E) in PDB entry 2GRA
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 168 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E ARG* 4.0 15.7 + - - +
164E GLU 4.7 4.9 - - - +
165E ASP* 5.1 5.7 - - - +
166E LEU 3.1 1.5 + - - -
167E ILE* 1.3 75.7 - - - +
169E ALA* 1.3 62.2 + - - +
171E THR* 3.1 21.0 - - - -
172E GLY 3.5 3.3 + - - -
262E CYS* 4.0 11.6 - - - -
265E THR* 3.4 24.3 - - + +
266E ARG* 3.2 42.0 - - - +
269E GLN* 3.6 20.1 - - - +
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Residues in contact with ALA 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E LEU* 2.8 16.1 + - + +
168E ASP* 1.3 76.1 - - - +
170E VAL* 1.3 55.3 + - + +
171E THR 2.4 19.5 + - - -
172E GLY* 2.6 15.1 + - - -
173E LEU* 3.1 10.5 + - - +
258E VAL* 5.4 3.8 - - + +
262E CYS* 3.9 17.2 - - - -
266E ARG* 6.1 0.7 - - - +
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Residues in contact with VAL 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E MET* 3.6 12.2 - - + +
132E ALA 5.9 0.7 - - - +
134E VAL* 3.4 39.3 - - + -
162E VAL* 5.4 2.9 - - + -
166E LEU* 3.0 24.8 + - + +
167E ILE* 3.2 13.8 + - + +
169E ALA* 1.3 73.9 - - + +
171E THR* 1.3 57.8 + - - +
173E LEU* 4.1 9.4 - - + -
174E SER* 3.0 28.8 + - - +
175E GLY 3.3 3.7 + - - -
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Residues in contact with THR 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ALA* 5.5 8.7 - - + -
119E ARG* 5.8 0.3 + - - -
121E MET* 3.5 26.6 - - - -
167E ILE* 2.5 26.5 + - - +
168E ASP* 3.1 12.4 + - - -
169E ALA 2.4 17.0 + - - -
170E VAL* 1.3 68.1 - - - +
172E GLY* 1.3 58.0 + - - -
173E LEU 2.9 4.7 - - - -
175E GLY* 2.9 9.8 - - - -
176E SER* 2.7 34.8 + - - +
261E SER* 3.7 2.7 - - - +
265E THR* 3.7 23.3 - - + +
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Residues in contact with GLY 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ASP 3.5 3.4 + - - -
169E ALA 2.6 13.0 + - - -
171E THR* 1.3 75.7 - - - +
173E LEU* 1.3 54.3 + - - -
176E SER* 3.9 0.2 - - - -
180E TYR* 2.8 28.5 + - - -
258E VAL* 3.2 25.3 - - - -
261E SER* 2.8 25.5 + - - -
262E CYS* 3.8 5.4 - - - +
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Residues in contact with LEU 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E ALA 3.1 9.6 + - - +
170E VAL* 4.7 6.5 - - + -
171E THR 2.9 1.6 - - - -
172E GLY* 1.3 79.8 - - - +
174E SER* 1.3 58.7 + - - +
175E GLY 3.0 3.4 - - - -
177E GLY* 2.6 39.3 + - - -
180E TYR* 3.8 3.3 - - + -
258E VAL* 3.7 24.4 - - + +
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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