Contacts of the helix formed by residues 1083 - 1095 (chain A) in PDB entry 2XKK
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 ASP1083 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1071A VAL* 3.7 14.0 - - + +
1075A LEU* 3.6 22.4 - - + -
1081A HIS 3.5 1.0 + - - -
1082A GLY* 1.3 74.1 - - - -
1084A SER* 1.3 71.2 + - - +
1086A CYS* 3.3 6.3 - - - +
1087A TYR* 2.8 31.4 + - - +
1122A MET* 4.1 17.4 - - + +
1122C MET* 4.6 15.6 - - + +
1123C ARG* 3.7 21.9 + - - +
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Residues in contact with SER1084 (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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1082A GLY* 4.4 0.6 - - - -
1083A ASP* 1.3 84.8 - - - +
1085A ALA* 1.3 66.5 + - - +
1087A TYR* 3.0 9.4 + - - +
1088A GLU* 2.8 40.9 + - - +
1122A MET* 6.3 0.2 - - - -
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Residues in contact with ALA1085 (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 VAL* 5.8 0.4 - - - -
1082A GLY* 4.4 16.5 - - - +
1083A ASP 4.4 0.2 - - - +
1084A SER* 1.3 77.8 + - - +
1086A CYS* 1.3 64.7 + - - +
1088A GLU* 3.2 10.6 + - - +
1089A ALA* 2.9 23.7 + - - +
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Residues in contact with CYS1086 (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 VAL* 4.3 17.5 - - + -
1049A ILE* 3.5 22.0 - - - +
1071A VAL* 4.1 14.6 - - + -
1074A VAL* 3.6 35.2 - - - -
1075A LEU* 4.3 4.0 - - + -
1079A HIS* 5.1 1.3 + - + -
1082A GLY 3.4 16.5 + - - +
1083A ASP* 3.3 12.0 + - - +
1084A SER 3.1 0.8 - - - -
1085A ALA* 1.3 77.6 - - - +
1087A TYR* 1.3 60.1 + - - +
1089A ALA* 2.9 7.0 + - - +
1090A MET 2.8 23.6 + - - -
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Residues in contact with TYR1087 (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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1067A SER* 4.1 3.4 - - - -
1071A VAL* 3.9 15.7 - - + -
1083A ASP 2.8 20.9 + - - +
1084A SER* 3.5 7.0 - - - +
1086A CYS* 1.3 73.4 - - - +
1088A GLU* 1.3 59.5 + - + +
1090A MET* 3.3 14.8 + - - +
1091A VAL* 2.9 39.2 + - + +
1109A ASN 5.1 0.3 + - - -
1110A TRP* 4.1 11.0 - + - -
1119A PHE* 4.0 16.1 - + - -
1120A ALA 2.7 25.3 + - - -
1121A ALA* 3.8 1.6 - - - -
1122A MET* 3.2 45.9 - - + -
1125A THR* 2.7 30.2 + - - +
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Residues in contact with GLU1088 (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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1084A SER* 2.8 30.8 + - - +
1085A ALA* 3.7 10.1 - - - +
1087A TYR* 1.3 77.2 - - + +
1089A ALA* 1.3 59.6 + - - +
1090A MET 3.1 1.8 - - - -
1091A VAL* 3.0 19.9 + - - +
1092A LEU* 3.2 12.3 + - - +
1119A PHE* 3.4 34.9 - - + -
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Residues in contact with ALA1089 (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 VAL* 3.8 29.8 - - + -
1046A GLN* 5.2 4.0 + - + +
1049A ILE* 4.5 1.3 - - + -
1085A ALA 2.9 13.6 + - - +
1086A CYS* 3.4 8.1 - - - +
1088A GLU* 1.3 75.9 - - - +
1090A MET* 1.3 60.0 + - - +
1092A LEU* 3.8 8.7 + - - +
1093A MET* 3.4 30.3 + - + +
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Residues in contact with MET1090 (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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1049A ILE* 3.5 23.8 - - + +
1053A MET* 4.8 5.2 - - - -
1067A SER* 3.6 33.2 - - - +
1070A THR* 4.2 22.7 - - + +
1071A VAL* 3.8 25.6 - - - -
1086A CYS 2.8 7.5 + - - +
1087A TYR* 3.5 12.3 - - - +
1088A GLU 3.1 0.2 - - - -
1089A ALA* 1.3 76.2 - - - +
1091A VAL* 1.3 65.8 + - - +
1093A MET* 3.9 5.1 + - - -
1094A ALA* 3.5 16.8 + - - +
1104A ILE* 4.0 15.8 - - + +
1110A TRP* 3.6 18.2 - - + -
1127A ALA* 4.2 13.2 - - + +
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Residues in contact with VAL1091 (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 TYR* 2.9 30.4 + - + +
1088A GLU* 3.0 10.2 + - - +
1090A MET* 1.3 76.3 - - - +
1092A LEU* 1.3 66.3 + - - +
1094A ALA* 2.8 14.7 + - - +
1095A GLN* 3.0 45.0 + - + +
1110A TRP* 3.7 28.0 - - + +
1119A PHE* 3.6 39.3 - - + -
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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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1043A LYS* 5.9 5.2 - - - +
1046A GLN* 5.2 8.3 - - - +
1088A GLU 3.2 10.5 + - - +
1089A ALA* 3.9 12.3 - - - +
1091A VAL* 1.3 76.2 - - - +
1093A MET* 1.3 58.7 + - + +
1095A GLN* 2.9 32.5 + - - +
1098A SER* 3.7 27.0 - - - +
1099A TYR* 3.2 31.0 - - + -
1264A GLN* 6.0 2.0 - - - +
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Residues in contact with MET1093 (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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1042A LEU* 5.7 0.2 - - - -
1046A GLN* 3.4 37.7 - - + +
1049A ILE* 3.6 43.3 - - + -
1050A VAL* 4.1 12.6 - - + -
1089A ALA 3.4 20.5 + - - +
1090A MET* 4.0 6.5 - - - +
1091A VAL 3.3 0.4 - - - -
1092A LEU* 1.3 78.9 - - + +
1094A ALA* 1.3 58.8 + - - +
1095A GLN 3.6 0.2 + - - -
1099A TYR* 3.7 29.2 - - + +
1102A PRO* 3.5 7.6 - - - +
1103A LEU* 3.2 37.1 + - + -
1104A ILE* 3.4 15.1 + - + -
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Residues in contact with ALA1094 (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 MET 3.5 7.5 + - - +
1091A VAL 2.8 16.5 + - - +
1093A MET* 1.3 74.5 - - - +
1095A GLN* 1.3 56.6 + - - -
1096A PRO* 3.0 14.4 - - - +
1102A PRO* 4.7 2.2 - - - +
1104A ILE* 3.4 42.5 - - + +
1105A GLU* 5.2 0.3 - - - -
1106A GLY 4.2 9.4 + - - +
1110A TRP* 3.8 24.6 - - + +
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Residues in contact with GLN1095 (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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1091A VAL* 3.1 32.2 - - + +
1092A LEU* 2.9 16.8 + - - +
1093A MET 3.4 0.6 - - - -
1094A ALA* 1.3 77.4 - - - +
1096A PRO* 1.3 59.3 - - + +
1097A PHE* 3.2 30.7 - - + -
1098A SER* 3.1 15.8 + - - -
1099A TYR* 2.6 38.6 + - - +
1102A PRO* 4.5 0.4 - - - -
1110A TRP* 2.4 36.8 + - + +
1116A PRO* 3.1 29.8 + - - +
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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