Contacts of the helix formed by residues 1075 - 1088 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1073B GLY 3.5 4.0 + - - +
1074B LEU* 1.3 70.9 - - - +
1076B CYS* 1.3 58.5 + - - +
1077B VAL* 3.1 27.4 - - - +
1078B ARG* 3.2 32.0 + - + +
1079B THR* 2.8 31.5 + - - -
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Residues in contact with CYS1076 (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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1071B ALA* 4.1 25.4 - - - -
1074B LEU* 3.0 26.9 + - - -
1075B ASP* 1.3 70.2 + - - +
1077B VAL* 1.3 63.5 + - + +
1079B THR* 3.2 2.0 + - - -
1080B ILE* 2.8 35.1 + - + +
1105B PRO* 5.2 12.1 - - + -
1122B LEU* 4.0 22.4 - - + -
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Residues in contact with VAL1077 (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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1075B ASP* 3.1 20.9 - - - +
1076B CYS* 1.3 78.5 - - + +
1078B ARG* 1.3 62.7 + - - +
1080B ILE* 3.3 7.7 + - - +
1081B GLU* 3.0 35.7 + - - +
1100B THR* 4.3 30.7 - - + +
1105B PRO* 5.4 7.9 - - + -
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Residues in contact with ARG1078 (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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1075B ASP* 3.2 34.6 + - + +
1077B VAL* 1.3 82.7 - - + +
1079B THR* 1.3 62.5 + - - +
1081B GLU* 3.5 9.9 + - - +
1082B GLU* 3.1 23.6 + - + +
1085B ARG* 4.9 3.4 + - - +
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Residues in contact with THR1079 (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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1037B PHE* 4.3 19.7 - - + -
1063B MET* 5.0 7.4 - - + -
1065B ILE* 5.1 7.2 - - + -
1074B LEU* 3.7 21.0 - - + +
1075B ASP 2.8 19.2 + - - -
1076B CYS 3.2 4.2 + - - -
1078B ARG* 1.3 75.0 - - - +
1080B ILE* 1.3 60.1 + - - +
1082B GLU* 3.4 5.6 + - - +
1083B LEU* 2.9 29.1 + - + +
1122B LEU* 3.6 30.7 - - + -
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Residues in contact with ILE1080 (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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1076B CYS* 2.8 25.9 + - + +
1077B VAL* 3.6 6.5 - - - +
1079B THR* 1.3 72.4 - - - +
1081B GLU* 1.3 58.0 + - - +
1083B LEU* 3.2 16.2 + - + +
1084B ALA* 3.0 26.2 + - - +
1098B PRO* 4.1 9.2 - - + -
1100B THR* 4.1 18.4 - - + -
1105B PRO* 4.2 31.9 - - + +
1106B ILE 4.0 21.1 - - - +
1107B VAL* 4.6 4.2 - - + +
1120B ILE 4.4 13.2 - - - +
1121B SER* 4.9 0.4 - - - -
1122B LEU* 3.8 26.7 - - + +
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Residues in contact with GLU1081 (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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1077B VAL* 3.0 25.4 + - - +
1078B ARG* 4.1 7.8 - - - +
1080B ILE* 1.3 76.8 - - + +
1082B GLU* 1.3 62.3 + - - +
1084B ALA* 3.3 8.4 + - - +
1085B ARG* 3.2 51.4 + - - +
1088B ARG* 4.8 0.3 + - - -
1098B PRO* 5.1 8.5 - - + -
1100B THR* 4.1 23.4 + - + +
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Residues in contact with GLU1082 (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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1036B ASP* 5.5 1.4 - - + +
1037B PHE* 3.4 24.9 - - + -
1078B ARG* 3.1 18.7 + - + +
1079B THR* 3.8 4.7 - - - +
1081B GLU* 1.3 73.6 - - - +
1083B LEU* 1.3 65.4 + - - +
1085B ARG* 3.2 31.9 + - - +
1086B VAL* 3.0 32.8 + - + +
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Residues in contact with LEU1083 (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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1033B ILE* 3.8 42.0 - - + -
1037B PHE* 4.1 14.7 - - + -
1063B MET* 4.0 15.7 - - - -
1079B THR* 2.9 15.9 + - + +
1080B ILE* 3.2 18.4 + - + +
1082B GLU* 1.3 77.2 - - - +
1084B ALA* 1.3 61.7 + - - +
1086B VAL* 3.2 4.8 + - + +
1087B LEU* 3.0 33.9 + - + +
1107B VAL* 3.4 29.8 - - + -
1120B ILE* 3.8 21.3 - - + -
1122B LEU* 5.5 2.2 - - + -
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Residues in contact with ALA1084 (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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1080B ILE 3.0 13.3 + - - +
1081B GLU* 3.6 8.3 - - - +
1082B GLU 3.3 0.4 - - - -
1083B LEU* 1.3 75.6 - - - +
1085B ARG* 1.3 62.5 + - - +
1087B LEU* 3.3 2.1 + - - +
1088B ARG* 3.2 36.0 + - - +
1096B ILE* 3.6 22.5 - - + +
1098B PRO* 3.9 26.7 - - + -
1107B VAL* 4.1 10.7 - - + +
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Residues in contact with ARG1085 (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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1078B ARG* 4.9 3.2 + - - +
1081B GLU* 3.2 31.5 + - - +
1082B GLU* 3.2 53.8 + - - +
1084B ALA* 1.3 77.2 - - - +
1086B VAL* 1.3 62.7 + - - +
1088B ARG* 3.3 36.8 + - - +
1089B LYS* 4.0 9.2 + - - +
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Residues in contact with VAL1086 (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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1032B PHE* 3.3 26.7 - - + -
1033B ILE* 4.8 14.1 - - + +
1036B ASP* 3.2 49.4 - - + +
1037B PHE* 4.1 10.8 - - + -
1082B GLU* 3.0 26.7 + - - +
1083B LEU* 3.2 9.2 + - + +
1085B ARG* 1.3 75.4 - - - +
1087B LEU* 1.3 63.3 + - + +
1089B LYS* 3.0 26.0 + - - +
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Residues in contact with LEU1087 (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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1029B LEU* 4.6 8.1 - - + -
1032B PHE* 4.1 12.3 - - + -
1033B ILE* 4.1 26.9 - - + -
1083B LEU* 3.0 35.0 + - + +
1084B ALA 3.3 4.7 + - - +
1086B VAL* 1.3 75.7 - - + +
1088B ARG* 1.3 57.4 + - - +
1090B HIS* 3.1 25.5 + - - +
1093B LEU* 3.8 27.0 - - + +
1096B ILE* 4.1 13.5 - - + +
1107B VAL* 4.0 21.1 - - + -
1109B PHE* 3.7 26.0 - - + -
1120B ILE* 4.3 2.7 - - + -
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Residues in contact with ARG1088 (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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1081B GLU 4.8 0.2 + - - -
1084B ALA* 3.2 27.3 + - - +
1085B ARG* 3.5 46.6 - - - +
1086B VAL 3.1 1.0 - - - -
1087B LEU* 1.3 76.6 - - - +
1089B LYS* 1.3 60.5 + - + +
1090B HIS 3.3 4.2 + - - +
1096B ILE* 3.8 30.6 + - + +
1098B PRO* 4.1 19.0 - - - +
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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