Contacts of the helix formed by residues 1095 - 1106 (chain A) in PDB entry 2B7A
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 PRO1095 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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950A HIS* 3.8 20.9 - - + +
1048A PHE* 3.9 8.5 - - + -
1093A GLY 3.5 6.7 - - - +
1094A CYS* 1.4 92.7 - - - +
1096A ASP* 1.3 64.5 + - - +
1097A GLU* 4.3 14.1 - - + +
1098A ILE* 3.0 29.9 + - + -
1099A TYR* 3.1 9.7 + - - +
1130A MET* 5.5 11.7 - - + -
1118B ASP* 3.4 32.5 - - - +
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Residues in contact with ASP1096 (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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1090A ARG* 4.8 10.7 - - - +
1094A CYS 3.6 3.1 + - - -
1095A PRO* 1.3 71.8 - - - +
1097A GLU* 1.3 57.2 + - - +
1099A TYR* 3.3 13.1 + - - +
1100A MET* 3.0 46.2 + - + +
1118B ASP* 3.5 10.1 + - - +
1121B LEU* 5.7 13.1 - - + +
1122B ARG* 4.4 20.0 - - + +
1125B GLN* 4.3 18.4 + - - +
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Residues in contact with GLU1097 (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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1095A PRO* 4.3 14.8 - - + +
1096A ASP* 1.3 77.8 - - - +
1098A ILE* 1.3 64.8 + - + +
1100A MET* 3.6 25.4 - - + +
1101A ILE* 3.5 24.6 + - - +
1122A ARG* 5.0 0.5 + - - -
1126A ILE* 3.5 45.3 - - + +
1129A GLN* 4.4 9.8 - - - +
1130A MET* 5.1 4.9 - - - +
1117B ARG* 4.4 21.4 + - - -
1118B ASP* 5.5 2.1 - - - +
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Residues in contact with ILE1098 (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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954A LEU* 3.7 24.5 - - + -
1044A LEU* 4.1 16.6 - - + -
1048A PHE* 3.7 33.4 - - + -
1094A CYS* 3.8 12.8 - - - -
1095A PRO* 3.0 32.9 + - + +
1097A GLU* 1.3 75.6 - - + +
1099A TYR* 1.3 65.7 + - - +
1101A ILE* 3.1 20.6 + - + +
1102A MET* 3.3 13.1 + - - +
1123A VAL* 5.9 0.4 - - + -
1126A ILE* 3.8 35.9 - - + -
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Residues in contact with TYR1099 (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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1087A ARG* 4.9 4.0 - - - +
1088A LEU 2.8 22.8 + - - -
1089A PRO* 3.8 1.9 - - - +
1090A ARG* 3.5 56.0 + - + -
1091A PRO* 4.3 0.4 - - + -
1094A CYS* 3.8 3.2 - - - -
1095A PRO 3.1 9.0 + - - +
1096A ASP* 3.6 14.6 - - - +
1098A ILE* 1.3 76.9 - - - +
1100A MET* 1.3 57.3 + - + +
1102A MET* 3.2 35.5 + - + +
1103A THR* 2.9 52.2 + - + +
1106A TRP* 4.1 2.4 - + - -
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Residues in contact with MET1100 (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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1096A ASP* 3.0 29.3 + - + +
1097A GLU* 3.6 29.8 - - + +
1098A ILE 3.2 0.2 - - - -
1099A TYR* 1.3 78.5 - - + +
1101A ILE* 1.3 56.8 + - - +
1103A THR* 2.9 21.6 + - - +
1104A GLU* 2.9 36.3 + - + +
1122A ARG* 4.7 5.2 - - - +
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Residues in contact with ILE1101 (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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1040A PHE* 4.6 3.6 - - + -
1044A LEU* 3.6 18.8 - - + -
1097A GLU 3.5 9.6 + - - +
1098A ILE* 3.1 16.0 + - + +
1100A MET* 1.3 76.5 - - - +
1102A MET* 1.3 61.9 + - - +
1104A GLU* 3.3 4.3 + - - +
1105A CYS* 3.0 26.5 + - - -
1119A LEU* 3.6 26.9 - - + +
1122A ARG* 3.6 35.9 - - + +
1123A VAL* 4.1 21.8 - - + -
1126A ILE* 3.8 28.5 - - + -
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Residues in contact with MET1102 (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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1041A GLY* 3.6 19.5 - - - +
1044A LEU* 3.8 21.8 - - + +
1045A TYR* 3.5 37.0 - - + -
1048A PHE* 5.6 0.2 - - - -
1091A PRO* 3.9 11.0 - - + -
1094A CYS* 4.7 6.1 - - - -
1098A ILE* 3.3 3.7 + - - +
1099A TYR* 3.2 39.7 + - + +
1101A ILE* 1.3 77.4 - - - +
1103A THR* 1.3 56.3 + - - +
1105A CYS* 3.1 8.8 + - - +
1106A TRP* 3.0 67.9 + - + -
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Residues in contact with THR1103 (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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1087A ARG* 5.2 7.3 + - + +
1099A TYR* 2.9 51.8 + - + +
1100A MET* 2.9 24.3 + - - +
1102A MET* 1.3 75.3 - - - +
1104A GLU* 1.3 61.5 + - - +
1106A TRP* 3.3 31.5 + - + +
1107A ASN* 3.8 1.7 + - - +
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Residues in contact with GLU1104 (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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1100A MET* 2.9 24.9 + - - +
1101A ILE 3.7 4.3 - - - +
1102A MET 3.3 0.2 - - - -
1103A THR* 1.3 76.1 - - - +
1105A CYS* 1.3 62.9 + - - +
1106A TRP 3.5 0.2 + - - -
1107A ASN* 3.6 20.4 + - - +
1112A GLN 4.5 2.3 - - - +
1113A ARG* 3.9 1.9 - - - -
1114A PRO* 3.4 24.5 - - + +
1122A ARG* 2.6 46.9 + - - +
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Residues in contact with CYS1105 (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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1037A VAL* 3.5 41.7 - - - +
1038A TRP* 3.6 10.4 - - - -
1040A PHE* 3.9 13.7 - - - -
1041A GLY* 3.8 12.8 - - - -
1101A ILE 3.0 23.5 + - - -
1102A MET 3.4 8.3 - - - +
1104A GLU* 1.3 77.1 - - - +
1106A TRP* 1.3 59.3 + - - +
1107A ASN 3.2 4.7 + - - -
1113A ARG* 3.4 21.3 + - - -
1114A PRO* 4.2 2.7 - - - -
1119A LEU* 3.8 22.9 - - - -
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Residues in contact with TRP1106 (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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1038A TRP* 3.3 46.0 + + + -
1041A GLY* 3.3 22.4 - - - -
1042A VAL* 3.3 26.1 - - + +
1045A TYR* 3.9 6.5 - - + -
1087A ARG* 2.7 55.7 + - + +
1088A LEU* 3.7 43.7 - - + -
1099A TYR* 4.1 6.7 - + - -
1102A MET* 3.0 53.7 + - + +
1103A THR* 3.3 16.5 + - + +
1104A GLU 3.2 0.6 - - - -
1105A CYS* 1.3 75.8 - - - +
1107A ASN* 1.3 55.5 + - - +
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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