Contacts of the helix formed by residues 161 - 170 (chain E) in PDB entry 4GDK
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 ARG 161 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E TRP* 4.0 2.9 - - - -
156E GLY 2.9 8.4 + - - +
159E ASN* 3.4 30.6 - - + +
160E ASP* 1.3 75.4 - - - +
162E PHE* 1.3 66.7 + - - +
163E ASP 3.3 2.0 - - - -
164E GLN* 3.2 48.7 + - + +
165E PHE* 2.9 22.2 + - - +
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Residues in contact with PHE 162 (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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5E LYS* 4.1 14.8 - - + -
8E LEU* 3.5 42.8 - - + -
9E ARG* 3.6 36.8 - - + +
12E TRP* 3.5 44.3 - + + +
13E PHE* 4.0 14.0 - + + -
160E ASP 3.8 1.6 + - - -
161E ARG* 1.3 72.1 - - - +
163E ASP* 1.3 74.8 + - - +
165E PHE* 3.3 0.5 + - - +
166E TRP* 2.8 67.5 + + + +
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Residues in contact with ASP 163 (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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5E LYS* 4.5 10.6 + - - -
9E ARG* 4.2 9.6 + - - -
161E ARG 3.3 0.6 - - - -
162E PHE* 1.3 95.1 - - - +
164E GLN* 1.3 66.3 + - - +
166E TRP* 3.9 2.0 - - - -
167E ALA* 3.0 27.4 + - - +
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Residues in contact with GLN 164 (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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152E GLN* 3.0 52.9 + - + +
155E MET* 3.5 37.8 - - - +
156E GLY* 3.4 16.2 + - - -
159E ASN* 4.3 1.6 + - - +
161E ARG* 3.2 58.7 + - + +
163E ASP* 1.3 79.2 - - - +
165E PHE* 1.3 63.6 + - - +
167E ALA* 3.7 3.2 + - - +
168E ILE* 4.2 1.0 - - - +
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Residues in contact with PHE 165 (chain E).
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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12E TRP* 3.4 34.3 - + + -
125E PHE* 4.1 15.9 - + - -
129E MET* 4.7 0.7 - - + -
152E GLN 4.6 3.1 - - - -
153E LEU* 3.1 46.7 - - + +
156E GLY* 4.0 7.2 - - - -
157E LEU* 4.2 2.2 - - + -
161E ARG 2.9 15.9 + - - +
162E PHE 3.6 2.9 - - - +
164E GLN* 1.3 79.3 - - - +
166E TRP* 1.3 75.0 + + - +
168E ILE* 3.2 4.5 + - - +
169E ASN* 3.1 52.7 + - + +
261E PRO* 3.4 34.8 - - + -
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Residues in contact with TRP 166 (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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8E LEU* 3.6 38.0 + - + +
12E TRP* 4.4 7.0 - + - +
162E PHE* 2.8 65.8 + + + +
163E ASP* 4.5 2.0 - - - +
165E PHE* 1.3 84.8 - + - +
167E ALA* 1.3 60.2 + - - +
168E ILE 3.0 5.7 + - - -
169E ASN* 3.4 32.8 - - - +
170E ARG* 3.2 46.8 + - + +
173E MET* 4.0 21.5 - - + -
256E GLU 3.8 20.4 - - - -
257E HIS 5.6 0.4 - - - -
259E SER 6.0 1.3 - - - -
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Residues in contact with ALA 167 (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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152E GLN* 4.1 11.7 - - - +
163E ASP 3.0 18.9 + - - +
164E GLN* 3.9 7.9 - - - +
165E PHE 3.2 0.6 - - - -
166E TRP* 1.3 77.4 - - - +
168E ILE* 1.3 65.6 + - + +
170E ARG* 3.7 25.2 - - - +
171E LYS* 4.3 7.8 - - - -
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Residues in contact with ILE 168 (chain E).
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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145E MET* 3.9 18.8 - - + +
149E ASP* 3.9 38.4 - - + +
152E GLN* 3.7 45.5 - - + +
153E LEU* 3.7 26.7 - - + -
164E GLN 4.2 1.6 - - - +
165E PHE 3.2 1.4 + - - +
166E TRP 3.0 0.2 - - - -
167E ALA* 1.3 87.6 - - + +
169E ASN* 1.3 64.7 + - - +
170E ARG 3.1 2.5 - - - -
171E LYS* 3.1 32.0 + - + +
172E LEU 4.2 0.2 + - - -
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Residues in contact with ASN 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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129E MET* 3.6 2.9 - - - +
153E LEU* 3.6 6.9 - - + +
165E PHE* 3.1 47.0 + - + +
166E TRP* 3.4 34.6 + - + -
168E ILE* 1.3 74.3 - - - +
170E ARG* 1.3 64.9 + - - +
171E LYS 3.1 0.4 - - - -
172E LEU* 3.1 28.1 + - - +
173E MET* 3.6 18.4 - - - +
260E TYR 5.7 0.6 + - - -
261E PRO* 5.4 1.2 - - - +
263E ASN* 2.9 24.9 + - - +
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Residues in contact with ARG 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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166E TRP* 3.2 37.7 + - + +
167E ALA* 3.7 22.6 + - - +
169E ASN* 1.3 77.2 - - - +
171E LYS* 1.3 72.6 + - + +
173E MET* 3.2 15.2 + - - +
174E GLU* 3.5 20.9 + - - +
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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