Contacts of the helix formed by residues 168 - 178 (chain B) in PDB entry 2G73
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 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B TYR* 3.5 46.8 + - + +
164B MET 3.4 5.6 + - - +
165B GLN 3.1 14.7 + - - +
167B THR* 1.3 76.3 - - - +
169B ARG* 1.3 59.9 + - - +
170B GLU* 2.9 18.7 + - - +
171B ALA* 2.7 29.4 + - + +
172B ARG* 2.8 30.0 + - - +
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Residues in contact with ARG 169 (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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167B THR 3.4 5.7 + - - +
168B ASN* 1.3 73.9 + - - +
170B GLU* 1.3 78.8 + - - +
172B ARG* 3.4 6.5 + - - +
173B LYS* 2.9 63.5 + - + +
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Residues in contact with GLU 170 (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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98B ILE 4.4 4.0 - - - +
168B ASN* 2.9 15.5 + - - +
169B ARG* 1.3 88.3 + - - +
171B ALA* 1.3 66.6 + - - +
173B LYS* 3.1 36.0 + - - +
174B ARG* 3.2 40.4 + - - +
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Residues in contact with ALA 171 (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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98B ILE* 3.5 32.0 + - + +
99B TYR* 4.1 11.4 - - + -
120B VAL* 6.0 0.2 - - + -
165B GLN* 3.4 24.9 - - + +
168B ASN* 2.7 21.4 + - + +
170B GLU* 1.3 72.8 - - - +
172B ARG* 1.3 58.8 + - - +
174B ARG* 2.8 21.0 + - - +
175B LEU* 3.0 17.6 + - + +
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Residues in contact with ARG 172 (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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148B LEU* 3.5 56.6 + - + +
151B ILE* 5.2 2.6 - - - +
152B ASP* 6.4 0.2 - - - +
166B ALA* 2.6 35.6 + - - +
167B THR* 3.7 20.6 - - - +
168B ASN 2.8 21.5 + - - +
169B ARG* 3.8 7.0 - - - +
171B ALA* 1.3 74.4 - - - +
173B LYS* 1.3 64.0 + - + +
175B LEU* 3.2 11.5 + - + +
176B SER* 2.9 29.4 + - - +
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Residues in contact with LYS 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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169B ARG* 2.9 70.8 - - + +
170B GLU* 3.1 24.2 + - - +
172B ARG* 1.3 77.3 - - + +
174B ARG* 1.3 74.2 + - - +
176B SER* 3.4 8.9 + - - -
177B ALA* 3.1 21.1 + - - +
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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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96B GLU* 3.4 17.0 - - - +
97B SER 5.0 3.2 + - - -
98B ILE* 3.3 48.3 + - + +
170B GLU* 3.2 46.4 + - - +
171B ALA 2.8 7.8 + - - +
173B LYS* 1.3 90.1 + - - +
175B LEU* 1.3 69.7 - - - +
177B ALA* 3.0 17.0 + - - +
178B PHE* 3.2 19.8 + - + -
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B TRP* 3.5 69.1 - - + +
40B PHE* 3.6 19.9 - - + -
98B ILE* 3.7 16.2 - - + -
122B ALA* 4.8 2.0 - - + -
144B LEU* 3.6 21.3 - - + -
148B LEU* 5.1 2.9 - - + -
165B GLN 5.3 1.1 - - - +
166B ALA* 4.5 12.8 - - + -
171B ALA* 3.0 18.4 + - + +
172B ARG* 3.5 14.4 - - + +
174B ARG* 1.3 76.8 - - - +
176B SER* 1.3 57.0 + - - +
178B PHE* 2.8 26.5 + - - +
179B THR* 3.6 3.8 + - - +
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Residues in contact with SER 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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144B LEU* 3.5 17.0 - - - +
148B LEU* 5.1 2.3 - - - +
172B ARG* 2.9 22.9 + - - +
173B LYS* 3.6 9.7 - - - -
175B LEU* 1.3 76.5 - - - +
177B ALA* 1.3 61.2 + - - +
179B THR* 2.5 29.9 + - - -
180B GLN 4.2 0.2 + - - -
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Residues in contact with ALA 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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124B ARG* 4.1 2.9 + - - -
173B LYS 3.1 13.0 + - - +
174B ARG* 3.0 16.3 + - - +
176B SER* 1.3 76.2 - - - +
178B PHE* 1.3 66.9 + - + +
179B THR 3.2 1.0 + - - -
180B GLN* 3.5 19.4 + - - +
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Residues in contact with PHE 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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40B PHE* 3.4 34.2 - + + +
44B GLY* 3.5 5.7 - - - -
93B THR* 5.1 1.3 - - - -
94B PRO 5.7 1.6 - - - -
96B GLU* 3.3 35.0 - - + -
122B ALA* 3.8 27.1 - - + -
123B ALA* 3.8 23.6 - - - -
124B ARG* 3.2 54.7 + - + +
174B ARG 3.2 20.5 + - - -
175B LEU 2.8 12.2 + - - +
177B ALA* 1.3 82.6 - - + +
179B THR* 1.3 56.4 + - - +
180B GLN 3.2 2.5 - - - -
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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