Contacts of the helix formed by residues 1168 - 1177 (chain G) in PDB entry 2X4X
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 ASN1168 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1197C GLN* 4.1 14.4 + - - +
1200C SER* 4.7 17.1 + - - -
1201C LYS* 6.3 1.4 - - - +
1164G PRO 5.4 1.8 + - - +
1166G GLY 4.8 0.2 - - - +
1167G VAL* 1.3 80.9 - - + +
1169G GLN* 1.3 63.3 + - - +
1170G ASP* 3.1 21.0 + - - +
1171G LEU* 3.1 28.3 + - + +
1172G ASP* 3.0 26.5 + - - +
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Residues in contact with GLN1169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167G VAL 4.0 2.6 + - - -
1168G ASN* 1.3 73.7 + - - +
1170G ASP* 1.3 60.9 + - - +
1172G ASP* 3.3 7.1 + - - +
1173G LYS* 2.9 59.8 + - + +
1192G TYR* 4.9 11.9 + - - +
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Residues in contact with ASP1170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193C HIS* 3.1 49.9 + - - +
1196C LEU* 3.4 39.6 - - + +
1197C GLN* 3.5 10.0 + - + +
1200C SER* 5.0 4.6 + - - +
1168G ASN* 3.1 7.8 + - - +
1169G GLN* 1.3 77.4 - - - +
1171G LEU* 1.3 59.3 + - - +
1173G LYS* 3.3 2.7 + - - +
1174G GLU 2.8 24.4 + - - -
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Residues in contact with LEU1171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197C GLN* 3.3 28.3 - - - +
1090G TRP* 3.7 28.5 - - + +
1163G VAL* 3.7 26.7 - - + -
1164G PRO 3.9 5.6 - - - +
1168G ASN* 3.1 29.8 + - + +
1170G ASP* 1.3 73.8 - - - +
1172G ASP* 1.3 71.9 + - - +
1174G GLU* 3.1 3.8 + - - +
1175G LYS* 2.8 41.0 + - + +
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Residues in contact with ASP1172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090G TRP* 2.9 28.0 + - + +
1164G PRO 4.4 0.5 - - - +
1165G LEU* 3.8 1.7 - - - -
1166G GLY* 3.2 31.8 + - - -
1167G VAL 4.6 0.2 + - - -
1168G ASN 3.0 21.6 + - - +
1169G GLN* 3.6 10.4 - - - +
1171G LEU* 1.3 79.6 - - - +
1173G LYS* 1.3 59.2 + - + +
1175G LYS* 3.2 2.6 + - - +
1176G MET* 3.0 32.5 + - + +
1192G TYR* 2.8 41.4 + - + +
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Residues in contact with LYS1173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193C HIS* 3.7 37.3 - - + +
1169G GLN* 2.9 48.7 + - + +
1170G ASP* 3.8 4.0 - - - +
1172G ASP* 1.3 77.7 - - + +
1174G GLU* 1.3 61.7 + - - +
1176G MET* 3.3 27.9 + - + +
1177G LEU* 3.5 19.6 + - + +
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Residues in contact with GLU1174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190C ILE* 4.3 17.1 - - + +
1193C HIS* 4.1 12.4 - - + +
1194C ARG* 3.2 37.9 + - - +
1197C GLN* 2.9 26.5 + - - +
1170G ASP 2.8 20.4 + - - +
1171G LEU* 3.1 6.3 + - - +
1173G LYS* 1.3 71.7 - - - +
1175G LYS* 1.3 74.3 - - + +
1177G LEU* 3.1 20.8 + - - +
1178G GLU* 3.7 5.2 + - - +
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Residues in contact with LYS1175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090G TRP* 3.5 46.9 - - + +
1097G PRO* 5.8 0.2 - - - +
1098G SER* 4.0 26.3 + - - +
1163G VAL* 4.4 22.9 - - - +
1171G LEU* 2.8 38.0 + - + +
1172G ASP 3.5 2.2 - - - +
1174G GLU* 1.3 87.3 - - + +
1176G MET* 1.3 63.8 + - - +
1177G LEU 3.0 1.2 + - - -
1178G GLU* 3.1 28.9 + - - +
1188G VAL* 4.8 2.9 - - - +
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Residues in contact with MET1176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090G TRP* 3.8 17.7 - - + -
1172G ASP* 3.0 21.5 + - + +
1173G LYS* 3.8 28.5 - - + +
1174G GLU 3.2 0.8 - - - -
1175G LYS* 1.3 76.6 - - - +
1177G LEU* 1.3 63.1 + - + +
1178G GLU 3.4 1.4 + - - -
1179G GLY 4.6 0.5 + - - -
1185G ARG* 3.9 23.9 - - - +
1188G VAL* 4.1 19.5 - - + +
1189G GLN* 4.0 28.2 + - + +
1192G TYR* 3.4 41.1 - - + -
1193G HIS* 5.2 4.0 - - + -
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Residues in contact with LEU1177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186C LYS* 2.9 44.5 + - + +
1189C GLN* 3.6 41.1 - - + +
1190C ILE* 3.6 37.4 - - + +
1193C HIS* 4.4 7.4 - - + +
1173G LYS 3.5 15.5 - - - +
1174G GLU* 3.1 5.8 + - - +
1175G LYS 3.0 1.6 - - - -
1176G MET* 1.3 81.1 - - + +
1178G GLU* 1.3 56.6 + - - +
1179G GLY 3.4 2.4 + - - -
1185G ARG* 4.0 11.0 - - - +
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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