Contacts of the helix formed by residues 1087 - 1096 (chain A) in PDB entry 3QCF
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 ASN1087 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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825A MET* 2.9 29.4 - - - +
826A GLU* 2.7 47.4 + - - +
827A ALA* 4.2 7.2 - - + -
828A ILE* 4.6 7.6 - - - +
1076A MET* 3.6 10.4 - - - +
1079A GLN* 3.8 9.0 + - - +
1086A VAL* 1.3 77.3 - - - +
1088A VAL* 1.3 63.4 + - - +
1089A LEU* 4.0 4.7 + - - +
1090A GLY* 3.3 17.2 + - - -
1091A PHE* 3.2 20.1 + - - +
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Residues in contact with VAL1088 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A PHE* 4.0 19.9 - - + -
1072A VAL* 4.1 15.9 - - + +
1076A MET* 4.1 13.7 - - + -
1086A VAL* 4.1 2.1 - - + +
1087A ASN* 1.3 73.0 + - - +
1089A LEU* 1.3 58.3 + - - +
1091A PHE* 3.8 1.7 - - - +
1092A LEU* 2.9 30.6 + - + +
1109A TYR* 3.7 26.7 - - + +
1112A ILE* 4.3 8.7 - - + -
1113A HIS* 3.8 18.2 - - + +
1116A LEU* 3.7 31.0 - - + -
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Residues in contact with LEU1089 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851A ASP* 3.8 31.4 - - - +
854A GLU* 4.0 21.1 - - - +
855A VAL* 3.5 27.4 - - + -
1087A ASN* 3.4 4.2 + - - +
1088A VAL* 1.3 78.6 - - - +
1090A GLY* 1.3 58.9 + - - +
1092A LEU* 3.5 2.9 + - - +
1093A LYS* 2.9 50.4 + - + +
1109A TYR* 3.8 18.6 + - - +
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Residues in contact with GLY1090 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A MET* 3.7 14.0 - - - +
826A GLU* 4.0 5.4 - - - -
1087A ASN* 3.3 23.4 + - - -
1088A VAL 3.3 0.2 - - - -
1089A LEU* 1.3 78.9 - - - +
1091A PHE* 1.3 63.2 + - - +
1093A LYS* 3.9 6.9 - - - +
1094A HIS* 3.1 22.7 + - - +
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Residues in contact with PHE1091 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A MET* 4.0 6.3 - - + -
913A ASP* 3.3 22.7 - - + -
914A GLY 3.8 19.3 - - - -
915A TYR* 4.5 2.7 - + - -
1071A ILE* 4.1 6.5 - - + -
1072A VAL* 4.0 29.6 - - + -
1075A SER* 3.1 32.8 - - - -
1076A MET* 3.9 21.1 - - + -
1079A GLN* 5.9 0.7 - - - -
1087A ASN* 3.2 22.5 + - - +
1088A VAL 3.8 2.2 - - - +
1090A GLY* 1.3 76.4 - - - +
1092A LEU* 1.3 63.9 + - - +
1094A HIS* 3.1 13.9 + + - +
1095A ILE* 3.0 41.4 + - + +
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Residues in contact with LEU1092 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852A PHE* 5.5 0.7 - - + -
855A VAL* 3.9 24.9 - - + -
1072A VAL* 4.4 6.7 - - + -
1088A VAL* 2.9 21.8 + - + +
1089A LEU* 3.8 3.6 - - - +
1091A PHE* 1.3 78.5 - - - +
1093A LYS* 1.3 62.4 + - - +
1095A ILE* 3.3 20.0 + - + -
1096A ARG* 3.0 25.2 + - + +
1102A LEU 3.6 22.0 - - - +
1103A VAL* 4.0 26.0 - - + -
1109A TYR* 3.6 35.2 - - + -
1112A ILE* 5.4 0.4 - - + -
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Residues in contact with LYS1093 (chain A).
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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854A GLU* 2.7 40.6 + - + +
855A VAL* 4.1 10.3 - - + -
858A CYS* 3.7 38.6 - - + +
1089A LEU* 2.9 39.1 + - + +
1090A GLY* 3.9 6.7 - - - +
1092A LEU* 1.3 75.7 - - - +
1094A HIS* 1.3 65.4 + - - +
1096A ARG* 3.5 12.4 - - - +
1097A THR* 3.8 9.7 + - - +
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Residues in contact with HIS1094 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A MET* 4.9 12.2 - - + +
913A ASP* 2.9 32.4 + - + -
1090A GLY 3.1 14.3 + - - +
1091A PHE* 3.1 17.4 + + - +
1093A LYS* 1.3 76.6 - - - +
1095A ILE* 1.3 67.2 + - + +
1097A THR* 2.6 44.0 + - - +
1098A GLN* 3.4 11.0 + - - -
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Residues in contact with ILE1095 (chain A).
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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912A VAL* 3.8 15.7 - - + -
913A ASP 4.0 2.7 - - - +
1068A GLY 4.9 2.0 - - - +
1071A ILE* 4.4 11.0 - - + -
1072A VAL* 4.1 17.9 - - + -
1091A PHE* 3.0 44.9 + - + +
1092A LEU* 3.4 28.5 - - + +
1094A HIS* 1.3 73.0 - - + +
1096A ARG* 1.3 57.5 + - - +
1097A THR 2.9 5.2 - - - -
1098A GLN* 2.6 36.5 + - - +
1099A ARG 3.1 9.9 + - - -
1102A LEU* 3.4 30.1 - - + +
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Residues in contact with ARG1096 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852A PHE* 4.1 3.0 - - - -
855A VAL* 3.6 43.3 + - + +
856A GLN* 3.1 32.7 + - - +
858A CYS* 4.0 11.7 - - - -
859A THR* 3.7 12.8 + - + +
886A TYR* 3.7 11.3 + - - -
1092A LEU* 3.0 25.3 + - + +
1093A LYS 3.5 9.0 - - - +
1094A HIS 3.1 0.2 - - - -
1095A ILE* 1.3 75.9 - - - +
1097A THR* 1.3 59.4 + - - +
1098A GLN 3.2 0.2 - - - -
1099A ARG 3.4 13.4 - - - +
1100A ASN* 4.8 0.6 - - - +
1101A TYR* 3.6 36.1 + - - +
1102A LEU* 2.8 22.3 + - + +
1103A VAL 3.0 25.5 + - - -
1104A GLN* 4.4 1.4 - - - +
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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