Contacts of the helix formed by residues 1167 - 1176 (chain I) in PDB entry 6XAV
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 GLU1167 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1165I SER* 2.9 24.2 + - - +
1166I ASP* 1.3 81.4 - - + +
1168I GLU* 1.3 68.4 + - + +
1169I VAL 3.2 1.1 - - - -
1170I MET* 3.3 8.4 + - - +
1171I ARG* 3.2 20.9 + - - +
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Residues in contact with GLU1168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I TYR* 5.6 5.4 - - - -
8I LYS* 4.0 38.1 + - - +
1163I THR 4.2 3.8 - - - +
1164I PHE* 3.4 46.6 + - + +
1165I SER* 4.8 3.6 - - - +
1167I GLU* 1.3 75.2 - - + +
1169I VAL* 1.3 55.5 + - - +
1171I ARG* 3.3 33.1 + - - +
1172I LEU* 2.6 36.6 + - - +
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Residues in contact with VAL1169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138I VAL* 5.2 7.9 - - + +
1141I LEU* 4.6 24.7 - - + -
1142I ARG* 3.8 28.0 - - + +
1145I ILE* 4.9 10.7 - - + +
1161I LEU* 4.5 12.8 - - + +
1164I PHE* 3.6 29.6 - - + -
1166I ASP* 4.7 7.0 - - - -
1167I GLU 3.2 0.8 - - - +
1168I GLU* 1.3 78.3 - - - +
1170I MET* 1.3 58.5 + - - +
1172I LEU* 3.1 8.4 + - + +
1173I ALA* 2.6 36.2 + - + +
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Residues in contact with MET1170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132I LEU* 5.3 10.9 - - + +
1136I GLN 5.4 4.7 - - - +
1138I VAL* 3.7 24.0 - - + -
1141I LEU* 4.0 22.4 - - + -
1166I ASP 3.6 19.1 - - - +
1167I GLU* 3.3 9.2 + - - +
1169I VAL* 1.3 77.1 - - - +
1171I ARG* 1.3 57.2 + - - +
1173I ALA* 3.9 3.3 - - + +
1174I GLU* 3.1 27.9 + - - +
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Residues in contact with ARG1171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I TYR 4.8 2.2 + - - -
8I LYS* 4.5 5.3 + - - +
9I LYS* 3.3 46.3 - - - +
775I GLU* 5.3 5.2 + - - -
1167I GLU* 3.2 12.1 + - - +
1168I GLU* 3.3 40.6 + - - +
1169I VAL 3.2 0.6 - - - -
1170I MET* 1.3 76.1 - - - +
1172I LEU* 1.3 63.7 + - - +
1174I GLU* 3.4 5.9 + - - +
1175I ASN* 3.2 34.2 + - - +
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Residues in contact with LEU1172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LYS 4.2 5.8 + - - +
9I LYS 3.6 16.2 - - - +
10I ARG* 3.7 2.9 - - - -
11I ILE* 3.5 43.5 - - + +
1145I ILE* 4.8 7.9 - - + -
1149I TYR* 4.1 10.8 - - + +
1161I LEU* 4.2 24.7 - - + -
1164I PHE* 4.5 7.2 - - + -
1168I GLU 2.6 21.8 + - - +
1169I VAL* 3.5 8.3 - - + +
1171I ARG* 1.3 74.3 - - - +
1173I ALA* 1.3 62.7 + - - +
1175I ASN* 3.2 3.5 + - - +
1176I LEU* 3.0 45.5 + - + +
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Residues in contact with ALA1173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128I ILE* 3.9 8.0 - - + +
1132I LEU* 3.3 33.5 - - + +
1141I LEU* 4.5 9.6 - - + -
1145I ILE* 4.1 23.3 - - + +
1169I VAL* 2.6 22.5 + - + +
1170I MET* 4.2 4.9 - - + +
1172I LEU* 1.3 73.7 - - - +
1174I GLU* 1.3 60.2 + - - +
1176I LEU* 3.6 8.1 + - - -
1177I ARG 3.4 13.5 + - - -
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Residues in contact with GLU1174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132I LEU* 3.9 12.5 - - + +
1170I MET 3.1 19.3 + - - +
1171I ARG* 3.7 9.2 - - - +
1172I LEU 3.1 0.4 - - - -
1173I ALA* 1.3 78.7 - - - +
1175I ASN* 1.3 67.1 + - - +
1177I ARG* 3.4 32.8 + - - +
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Residues in contact with ASN1175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I LYS* 2.3 54.2 + - - +
10I ARG* 4.1 20.2 - - + +
697I LYS* 4.2 17.8 - - - -
791I LEU* 4.4 11.8 - - + +
1171I ARG* 3.2 16.2 + - - +
1172I LEU 3.2 3.6 + - - +
1174I GLU* 1.3 82.4 - - - +
1176I LEU* 1.3 60.4 + - - +
1177I ARG 3.1 7.7 + - - -
1178I LYS* 4.2 6.1 + - - +
1179I GLY 4.4 1.4 - - - +
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Residues in contact with LEU1176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I ARG* 4.2 14.6 - - + -
11I ILE 4.4 5.2 - - - +
1125I GLY* 3.8 11.6 - - - +
1128I ILE* 4.3 22.0 - - + +
1145I ILE* 4.7 4.5 - - + -
1149I TYR* 3.7 21.1 - - + +
1172I LEU* 3.0 31.0 + - + +
1173I ALA* 3.6 8.7 + - - +
1174I GLU 3.4 0.2 - - - -
1175I ASN* 1.3 73.1 - - - +
1177I ARG* 1.3 63.7 + - - +
1178I LYS 3.2 3.1 - - - -
1179I GLY* 3.3 15.2 + - - +
1180I MET* 3.8 27.8 - - + -
1181I PRO* 3.6 30.5 - - + -
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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