Contacts of the helix formed by residues 1056 - 1066 (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 SER1056 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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938A ARG* 4.9 14.4 - - - -
1020A TRP* 5.8 0.2 - - - -
1049A THR* 5.7 1.8 - - - -
1051A ILE* 6.4 2.2 - - - -
1052A GLU 3.4 5.4 + - - -
1053A LYS* 3.6 11.0 + - - -
1054A SER 3.5 1.0 - - - -
1055A LYS* 1.3 77.5 - - - +
1057A PRO* 1.3 69.6 - - - +
1058A PRO* 3.4 11.4 - - - +
1059A ALA* 3.2 21.3 + - - +
1060A GLU* 2.8 26.3 + - - +
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Residues in contact with PRO1057 (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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1019A PHE* 4.0 20.2 - - + +
1020A TRP* 3.8 18.4 - - + -
1042A VAL* 3.6 24.9 - - + -
1045A TYR* 4.0 20.0 - - + -
1046A GLU* 4.3 9.2 - - + -
1049A THR* 6.0 0.2 - - - +
1055A LYS 3.6 0.2 - - - -
1056A SER* 1.3 83.6 - - - +
1058A PRO* 1.4 71.6 - - + +
1060A GLU* 3.9 0.2 - - - +
1061A PHE* 3.0 32.7 + - + -
1088A LEU* 3.9 17.9 - - + -
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Residues in contact with PRO1058 (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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938A ARG* 6.1 0.7 - - - +
1019A PHE* 3.6 29.6 - - + -
1020A TRP* 3.7 23.1 - - + -
1056A SER* 3.4 13.7 - - - +
1057A PRO* 1.4 96.1 - - + +
1059A ALA* 1.3 55.2 + - - +
1061A PHE* 4.1 0.5 - - - +
1062A MET* 3.0 39.0 + - + +
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Residues in contact with ALA1059 (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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1053A LYS 4.1 7.4 - - - +
1054A SER* 3.6 19.5 - - - +
1056A SER* 3.1 20.0 + - - +
1058A PRO* 1.3 78.9 - - - +
1060A GLU* 1.3 60.9 + - - +
1062A MET* 4.0 4.8 - - - +
1063A ARG* 3.2 37.7 + - - +
1067A ASN* 5.3 0.5 - - - +
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Residues in contact with GLU1060 (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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1045A TYR* 3.2 24.3 + - - +
1055A LYS* 3.5 32.5 + - - +
1056A SER 2.8 12.9 + - - +
1059A ALA* 1.3 70.6 - - - +
1061A PHE* 1.3 64.7 + - - +
1063A ARG* 3.0 34.8 + - - +
1064A MET* 3.1 33.2 + - + +
1088A LEU* 3.7 17.9 - - + -
1089A PRO* 3.4 26.4 - - + +
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Residues in contact with PHE1061 (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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1019A PHE* 3.6 53.6 - + + -
1038A TRP* 5.8 3.1 - + - -
1042A VAL* 5.9 1.3 - - + -
1057A PRO* 3.0 24.9 + - + +
1060A GLU* 1.3 75.2 - - - +
1062A MET* 1.3 53.2 + - - +
1064A MET* 3.2 17.9 + - + +
1065A ILE* 2.8 42.2 + - + +
1078A LEU* 3.9 10.8 - - + -
1081A LEU* 3.7 21.5 - - + -
1082A LEU* 4.0 29.2 - - + -
1087A ARG* 4.6 3.8 - - + -
1088A LEU* 3.6 37.2 - - + -
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Residues in contact with MET1062 (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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1019A PHE* 3.9 26.2 - - + -
1058A PRO* 3.0 26.4 + - + +
1059A ALA* 4.0 5.8 - - - +
1061A PHE* 1.3 76.7 - - - +
1063A ARG* 1.3 53.9 + - - +
1065A ILE* 4.0 6.7 - - - +
1066A GLY 2.8 40.0 + - - +
1067A ASN* 3.1 24.0 + - - +
1069A LYS* 3.8 27.4 - - + -
1074A ILE* 4.1 26.0 - - + -
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Residues in contact with ARG1063 (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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1054A SER* 2.7 40.5 + - - +
1055A LYS* 5.0 3.4 - - - +
1059A ALA* 3.2 25.3 + - - +
1060A GLU* 3.0 39.0 + - - +
1061A PHE 3.2 0.2 - - - -
1062A MET* 1.3 75.6 - - - +
1064A MET* 1.3 64.9 + - + +
1066A GLY* 3.3 11.1 + - - -
1067A ASN* 3.5 22.4 + - - +
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Residues in contact with MET1064 (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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1060A GLU* 3.1 35.1 + - + +
1061A PHE* 3.6 29.2 - - + +
1063A ARG* 1.3 76.1 - - + +
1065A ILE* 1.3 63.6 + - - +
1081A LEU* 3.8 31.6 - - + +
1086A GLY* 5.1 0.9 - - - -
1087A ARG 3.7 33.7 - - - +
1088A LEU* 4.3 7.4 - - + +
1089A PRO* 4.6 4.3 - - + -
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Residues in contact with ILE1065 (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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1019A PHE* 4.5 7.4 - - + -
1061A PHE* 2.8 29.7 + - + +
1062A MET* 4.0 11.2 - - - +
1064A MET* 1.3 73.4 - - - +
1066A GLY* 1.3 66.0 + - - +
1068A ASP* 5.7 0.3 - - - -
1069A LYS* 4.3 14.4 - - + -
1074A ILE* 4.1 8.3 - - + +
1077A HIS* 3.7 39.2 + - + +
1078A LEU* 3.9 36.3 - - + +
1081A LEU* 4.3 11.0 - - + -
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Residues in contact with GLY1066 (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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1062A MET* 2.8 11.6 + - - +
1063A ARG 3.3 8.7 + - - -
1064A MET 3.3 2.8 - - - -
1065A ILE* 1.3 79.8 - - - +
1067A ASN* 1.3 58.6 + - - -
1068A ASP* 3.0 23.4 + - - -
1069A LYS* 3.0 23.0 + - - +
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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