Contacts of the helix formed by residues 1087 - 1097 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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825B MET* 3.1 38.5 + - - -
826B GLU* 3.4 15.8 - - - +
827B ALA* 4.1 7.4 - - + +
1076B MET* 3.4 8.5 - - - -
1079B GLN* 3.9 15.1 + - - +
1086B VAL* 1.3 77.1 - - - +
1088B VAL* 1.3 66.2 + - - +
1089B LEU* 4.5 1.2 + - - +
1090B GLY* 3.4 17.8 + - - -
1091B PHE* 3.0 27.7 + - + +
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Residues in contact with VAL1088 (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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833B PHE* 4.0 16.2 - - + -
1072B VAL* 4.3 8.7 - - + +
1076B MET* 4.2 9.6 - - + -
1086B VAL* 3.9 12.9 - - + +
1087B ASN* 1.3 73.2 - - - +
1089B LEU* 1.3 59.0 + - - +
1091B PHE* 3.8 2.2 - - - +
1092B LEU* 2.9 35.0 + - + +
1109B TYR* 4.0 12.6 - - + -
1112B ILE* 4.1 14.4 - - + -
1113B HIS* 3.6 30.3 - - + +
1116B LEU* 3.8 28.7 - - + -
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Residues in contact with LEU1089 (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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825B MET* 5.1 16.6 - - + +
851B ASP* 3.9 27.4 - - - +
854B GLU* 4.0 21.5 - - + +
855B VAL* 3.7 25.6 - - + -
1087B ASN* 3.4 1.3 + - - +
1088B VAL* 1.3 78.8 - - - +
1090B GLY* 1.3 58.6 - - - +
1092B LEU* 3.7 3.0 - - - +
1093B LYS* 3.1 51.1 + - + +
1109B TYR* 3.7 21.1 - - - +
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Residues in contact with GLY1090 (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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825B MET* 4.1 18.2 - - - +
1087B ASN* 3.4 25.5 + - - -
1088B VAL 3.3 0.6 - - - -
1089B LEU* 1.3 77.5 - - - +
1091B PHE* 1.3 63.5 + - - +
1093B LYS* 3.6 7.0 + - - +
1094B HIS* 3.2 21.1 + - - +
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Residues in contact with PHE1091 (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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913B ASP* 3.7 15.5 - - + -
914B GLY 4.1 13.7 - - - -
915B TYR* 5.1 1.6 - - - -
1071B ILE* 4.0 4.9 - - + -
1072B VAL* 3.9 31.2 - - + -
1075B SER* 3.6 24.2 - - - -
1076B MET* 3.9 22.7 - - + -
1079B GLN* 5.7 1.1 - - - +
1087B ASN* 3.0 22.6 + - + +
1088B VAL 4.0 1.3 - - - +
1090B GLY* 1.3 73.4 - - - +
1092B LEU* 1.3 66.5 + - - +
1094B HIS* 3.2 16.5 + + - +
1095B ILE* 3.0 57.7 + - + +
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Residues in contact with LEU1092 (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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852B PHE* 5.7 1.3 - - + -
855B VAL* 4.1 20.9 - - + -
1072B VAL* 4.2 6.7 - - + -
1088B VAL* 2.9 19.6 + - + +
1089B LEU* 3.7 5.2 - - - +
1091B PHE* 1.3 77.7 - - - +
1093B LYS* 1.3 65.9 + - - +
1095B ILE* 3.2 19.4 + - + +
1096B ARG* 3.0 25.2 + - + +
1102B LEU 3.7 12.3 - - - +
1103B VAL* 3.6 36.6 - - + -
1109B TYR* 3.6 36.6 - - + -
1112B ILE* 5.2 0.9 - - + -
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Residues in contact with LYS1093 (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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825B MET* 5.1 10.8 - - + +
854B GLU* 2.6 48.8 + - - -
855B VAL* 4.4 10.1 - - + +
858B CYS* 3.4 34.6 - - + -
1089B LEU* 3.1 39.9 + - + +
1090B GLY* 3.8 8.1 - - - +
1092B LEU* 1.3 74.8 - - - +
1094B HIS* 1.3 64.6 - - - +
1096B ARG* 3.4 18.5 + - - +
1097B THR* 3.7 10.9 + - - +
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Residues in contact with HIS1094 (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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913B ASP* 2.8 35.3 + - + +
1090B GLY 3.2 12.2 + - - +
1091B PHE* 3.3 19.3 - + - +
1092B LEU 3.1 0.2 - - - -
1093B LYS* 1.3 79.5 - - - +
1095B ILE* 1.3 75.5 + - + +
1097B THR* 2.6 36.2 + - - +
1098B GLN* 4.2 9.3 + - + +
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Residues in contact with ILE1095 (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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912B VAL* 3.6 22.2 - - + -
913B ASP 4.2 1.3 - - - +
1068B GLY* 4.7 2.9 - - - +
1071B ILE* 4.3 10.8 - - + -
1072B VAL* 3.9 18.6 - - + -
1091B PHE* 3.0 53.4 + - + +
1092B LEU* 3.3 21.3 - - + +
1094B HIS* 1.3 79.1 - - + +
1096B ARG* 1.3 57.7 + - - +
1097B THR 3.1 0.2 - - - -
1098B GLN* 2.9 28.8 + - - +
1099B ARG 3.1 10.4 + - - -
1102B LEU* 3.2 27.9 - - + +
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Residues in contact with ARG1096 (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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852B PHE* 4.1 7.5 - - - -
855B VAL* 3.5 35.1 + - + +
856B GLN* 3.0 29.7 + - - +
858B CYS 6.4 0.2 - - - -
859B THR* 3.6 32.7 + - - +
864B ILE* 5.1 0.3 - - - +
886B TYR* 3.6 19.1 + - - -
1092B LEU* 3.0 19.9 + - + +
1093B LYS* 3.4 14.6 - - - +
1094B HIS 3.1 0.6 - - - -
1095B ILE* 1.3 78.6 - - - +
1097B THR* 1.3 59.2 + - - +
1098B GLN 3.2 0.6 + - - -
1099B ARG 3.6 8.2 - - - +
1100B ASN* 4.5 0.4 - - - +
1101B TYR* 3.5 34.5 + - - +
1102B LEU* 2.8 18.5 + - + +
1103B VAL 2.6 26.9 + - - -
1104B GLN* 4.4 2.8 + - - +
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Residues in contact with THR1097 (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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858B CYS 5.6 2.0 - - - +
859B THR* 6.5 0.2 - - - -
862B MET* 4.3 26.9 - - + -
864B ILE* 3.9 13.1 - - - +
886B TYR* 3.3 7.7 - - - -
888B HIS* 2.8 30.8 + - - -
1093B LYS 3.9 9.0 - - - +
1094B HIS* 2.6 28.0 + - - +
1096B ARG* 1.3 78.3 - - + +
1098B GLN* 1.3 64.7 + - - +
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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