Contacts of the helix formed by residues 1075 - 1088 (chain A) in PDB entry 5W0N
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 ASP1075 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1073A GLY 3.7 3.8 + - - +
1074A LEU* 1.3 71.1 - - - +
1076A CYS* 1.3 55.0 + - - +
1077A VAL* 3.2 26.3 - - - +
1078A ARG* 3.3 29.8 + - + +
1079A THR* 2.5 38.1 + - - +
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Residues in contact with CYS1076 (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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1071A ALA* 3.8 26.0 - - - -
1074A LEU* 3.2 20.6 + - - -
1075A ASP* 1.3 70.0 + - - +
1077A VAL* 1.3 64.0 + - + +
1079A THR* 3.3 0.6 + - - -
1080A ILE* 2.9 35.0 + - - +
1105A PRO* 5.3 10.1 - - + -
1122A LEU* 3.3 31.1 - - + +
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Residues in contact with VAL1077 (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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1075A ASP* 3.2 14.4 - - - +
1076A CYS* 1.3 78.5 - - + +
1078A ARG* 1.3 71.0 + - + +
1080A ILE* 3.2 16.2 + - - +
1081A GLU* 3.3 21.1 + - - +
1100A THR* 4.4 26.6 - - + +
1105A PRO* 5.4 8.5 - - + -
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Residues in contact with ARG1078 (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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1075A ASP* 3.3 29.7 + - + +
1077A VAL* 1.3 84.3 - - + +
1079A THR* 1.3 58.1 + - - +
1081A GLU* 3.3 14.6 + - + +
1082A GLU* 3.0 53.0 + - + +
1085A ARG* 6.2 0.9 - - - +
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Residues in contact with THR1079 (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 PHE* 5.9 4.0 - - + -
1063A MET* 5.0 10.8 - - + -
1065A ILE* 5.7 2.7 - - + -
1074A LEU* 3.4 25.5 - - + +
1075A ASP* 2.5 27.5 + - - +
1076A CYS 3.6 4.7 - - - -
1078A ARG* 1.3 73.7 - - - +
1080A ILE* 1.3 58.7 + - - +
1082A GLU* 3.2 13.3 + - + +
1083A LEU* 2.8 30.5 + - + +
1122A LEU* 3.6 29.6 - - + -
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Residues in contact with ILE1080 (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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1076A CYS 2.9 19.7 + - - +
1077A VAL* 3.2 8.7 + - - +
1079A THR* 1.3 75.0 - - - +
1081A GLU* 1.3 58.5 + - - +
1083A LEU* 3.3 8.0 + - + +
1084A ALA* 2.9 26.9 + - - +
1098A PRO* 3.8 17.3 - - + -
1100A THR* 3.7 23.6 - - + -
1105A PRO* 4.0 33.0 - - + +
1106A ILE* 3.9 20.9 - - - +
1107A VAL* 4.3 10.8 - - + +
1120A ILE 4.4 5.6 - - - +
1121A SER* 5.1 0.2 - - - -
1122A LEU* 3.8 23.6 - - + +
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Residues in contact with GLU1081 (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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1077A VAL* 3.3 17.0 + - - +
1078A ARG* 3.7 15.4 - - + +
1079A THR 3.2 0.6 - - - -
1080A ILE* 1.3 75.1 - - + +
1082A GLU* 1.3 66.4 + - - +
1084A ALA* 3.4 7.7 + - - +
1085A ARG* 3.2 48.3 + - - +
1088A ARG* 4.8 0.5 + - - -
1098A PRO* 5.3 8.3 - - + -
1100A THR* 4.4 19.9 + - + +
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Residues in contact with GLU1082 (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 PHE* 3.8 28.5 - - + -
1078A ARG* 3.0 48.3 + - + +
1079A THR* 3.6 11.7 + - - +
1081A GLU* 1.3 77.0 - - - +
1083A LEU* 1.3 61.5 + - - +
1085A ARG* 3.3 21.8 + - - +
1086A VAL* 3.2 24.3 + - - +
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Residues in contact with LEU1083 (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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1033A ILE* 3.7 42.4 - - + -
1037A PHE* 4.5 7.6 - - + -
1063A MET* 3.9 20.0 - - + -
1079A THR* 2.8 22.4 + - + +
1080A ILE* 3.6 11.2 - - + +
1082A GLU* 1.3 73.4 - - - +
1084A ALA* 1.3 61.8 + - - +
1086A VAL* 3.1 9.6 + - + +
1087A LEU* 3.0 31.9 + - + +
1107A VAL* 3.5 23.3 - - + -
1120A ILE* 3.8 23.1 - - + -
1122A LEU* 5.2 3.6 - - + -
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Residues in contact with ALA1084 (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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1080A ILE 2.9 16.9 + - - +
1081A GLU* 3.7 6.5 - - - +
1082A GLU 3.3 0.2 - - - -
1083A LEU* 1.3 76.8 - - - +
1085A ARG* 1.3 61.7 + - - +
1087A LEU* 3.2 3.8 + - - +
1088A ARG* 3.1 39.6 + - - +
1096A ILE* 3.8 17.9 - - + +
1098A PRO* 4.0 24.2 - - + -
1107A VAL* 4.1 10.1 - - + +
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Residues in contact with ARG1085 (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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1078A ARG* 6.2 1.0 - - - +
1081A GLU* 3.2 42.3 + - - +
1082A GLU* 3.6 20.6 - - - +
1083A LEU 3.3 0.2 - - - -
1084A ALA* 1.3 76.8 - - - +
1086A VAL* 1.3 64.5 + - + +
1088A ARG* 3.4 34.4 + - - +
1089A LYS* 3.9 11.1 - - - +
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Residues in contact with VAL1086 (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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1032A PHE* 3.3 28.9 - - + -
1033A ILE* 4.4 20.6 - - + +
1036A ASP* 3.5 34.5 - - + +
1037A PHE* 3.9 22.4 - - + -
1082A GLU 3.2 14.2 + - - +
1083A LEU* 3.1 11.7 + - + +
1085A ARG* 1.3 76.8 - - + +
1087A LEU* 1.3 61.4 + - - +
1089A LYS* 3.1 25.2 + - - +
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Residues in contact with LEU1087 (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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1029A LEU* 4.6 6.5 - - + -
1032A PHE* 4.4 8.7 - - + -
1033A ILE* 4.1 27.1 - - + -
1083A LEU* 3.0 37.1 + - + +
1084A ALA 3.2 4.9 + - - +
1086A VAL* 1.3 76.4 - - - +
1088A ARG* 1.3 62.5 + - - +
1089A LYS 3.1 0.2 - - - -
1090A HIS* 3.2 19.7 + - - +
1093A LEU* 4.0 18.9 - - + +
1096A ILE* 3.9 22.5 - - + +
1107A VAL* 4.0 17.0 - - + -
1109A PHE* 3.7 31.4 - - + -
1120A ILE* 4.2 3.8 - - + -
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Residues in contact with ARG1088 (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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1081A GLU 4.8 0.4 + - - -
1084A ALA* 3.1 24.9 + - - +
1085A ARG* 3.6 45.1 - - - +
1086A VAL 3.2 0.8 - - - -
1087A LEU* 1.3 76.2 - - - +
1089A LYS* 1.3 60.7 + - + +
1090A HIS 3.3 3.8 + - - +
1096A ILE* 3.7 30.1 + - + +
1098A PRO* 4.0 27.3 - - - +
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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