Contacts of the helix formed by residues 1053 - 1067 (chain B) in PDB entry 2WIN
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 SER1053 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046B ALA 5.5 5.0 - - - +
1050B ARG* 6.1 1.6 - - - -
1051B ALA 3.5 2.3 + - - -
1052B PRO* 1.3 73.2 - - - +
1054B THR* 1.3 65.0 + - - +
1056B LEU* 3.5 26.2 + - - +
1057B THR* 2.8 30.9 + - - -
1084B TRP* 4.0 3.8 - - - -
1098B GLU* 3.4 9.7 + - - -
1100B ALA* 2.9 25.2 + - - -
1101B PRO 5.1 0.2 - - - -
1102B VAL* 3.5 19.4 - - - +
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Residues in contact with THR1054 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052B PRO 4.1 1.3 + - - -
1053B SER* 1.3 71.3 - - - +
1055B TRP* 1.3 64.4 + - - +
1058B ALA* 3.2 22.1 + - - +
1084B TRP* 4.5 6.5 - - - -
1085B LEU* 3.8 17.6 - - + +
1089B LYS* 3.5 24.9 - - + +
1096B PHE* 4.7 7.4 - - + -
1097B GLN 3.0 28.9 + - - +
1098B GLU* 3.0 22.7 + - - -
1099B ASP* 4.0 4.2 + - - +
1100B ALA 5.1 0.2 - - - +
1121B LEU* 4.8 4.9 - - + -
1125B VAL* 4.5 15.5 - - + -
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Residues in contact with TRP1055 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053B SER* 3.6 2.3 + - - +
1054B THR* 1.3 77.7 - - - +
1056B LEU* 1.3 89.9 + - + +
1058B ALA* 3.0 7.5 + - - +
1059B TYR* 2.8 36.3 + + + +
1098B GLU* 3.7 17.0 + - - +
1102B VAL* 3.8 13.2 - - + -
1107B MET* 3.5 50.9 - - + -
1108B ILE* 3.4 30.1 + - + +
1111B LEU* 3.3 34.6 - - + +
1121B LEU* 4.4 12.5 - - + +
1124B PHE* 3.5 28.1 - + - -
1248B GLN* 3.0 28.0 - - - -
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Residues in contact with LEU1056 (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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989B GLY 4.8 2.5 - - - -
990B GLU* 4.3 28.9 - - + +
993B MET* 4.4 16.2 - - + -
1034B GLN* 5.2 3.6 - - - +
1046B ALA* 3.1 38.4 - - + +
1053B SER* 3.5 20.5 + - - +
1054B THR 3.5 0.2 - - - -
1055B TRP* 1.3 99.7 - - + +
1057B THR* 1.3 58.4 + - - +
1059B TYR* 3.2 5.5 + - + +
1060B VAL* 3.0 38.5 + - + +
1102B VAL* 3.8 10.8 - - + -
1107B MET* 4.5 3.8 - - + -
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Residues in contact with THR1057 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041B SER* 5.5 2.4 + - - +
1052B PRO* 5.3 2.1 - - - +
1053B SER 2.8 25.8 + - - -
1054B THR 4.0 2.9 - - - -
1055B TRP 3.3 0.4 - - - -
1056B LEU* 1.3 79.2 - - - +
1058B ALA* 1.3 61.7 + - - +
1060B VAL* 3.4 14.0 + - + +
1061B VAL* 3.4 17.7 + - - +
1081B ALA* 3.7 26.2 - - + -
1084B TRP* 3.9 27.5 - - + -
1085B LEU* 4.2 7.9 - - + -
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Residues in contact with ALA1058 (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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1054B THR 3.2 18.4 + - - +
1055B TRP 3.0 5.9 + - - +
1057B THR* 1.3 77.9 - - - +
1059B TYR* 1.3 60.7 + - - +
1061B VAL* 3.5 3.6 + - - +
1062B LYS 3.4 5.2 + - - -
1085B LEU* 3.9 16.3 - - + +
1124B PHE* 4.2 8.1 - - + -
1125B VAL* 3.8 33.2 - - + -
1128B SER* 2.9 28.5 + - - +
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Residues in contact with TYR1059 (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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993B MET* 4.0 21.1 - - + -
997B THR* 2.7 43.2 + - - +
1055B TRP* 2.8 33.4 + + + +
1056B LEU* 3.2 6.3 + - + +
1058B ALA* 1.3 75.4 - - - +
1060B VAL* 1.3 64.3 + - - +
1062B LYS* 3.0 28.2 + - + +
1063B VAL* 3.1 31.1 + - + +
1107B MET* 4.7 5.6 - - + -
1124B PHE* 3.7 19.3 - + + -
1247B THR* 3.2 15.4 - - + +
1248B GLN* 3.0 31.0 - - - -
1251B PHE* 3.9 9.4 - + - +
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Residues in contact with VAL1060 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993B MET* 4.3 16.6 - - + -
1034B GLN* 3.9 25.6 - - + +
1056B LEU* 3.0 29.0 + - + +
1057B THR* 3.6 11.9 - - + +
1059B TYR* 1.3 77.6 - - - +
1061B VAL* 1.3 59.3 + - + +
1063B VAL* 4.0 0.2 - - - -
1064B PHE* 2.9 66.5 + - + +
1077B VAL* 6.1 2.9 - - + -
1078B LEU* 6.2 0.9 - - + -
1081B ALA* 5.9 4.7 - - + -
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Residues in contact with VAL1061 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057B THR 3.4 16.4 - - - +
1058B ALA* 3.6 9.6 - - - +
1059B TYR 3.2 0.2 - - - -
1060B VAL* 1.3 77.8 - - + +
1062B LYS* 1.3 56.9 + - - +
1065B SER* 2.8 46.0 + - - +
1078B LEU* 3.9 16.8 - - + -
1081B ALA* 4.1 20.6 - - + -
1082B VAL* 4.1 16.4 - - + +
1085B LEU* 4.8 6.5 - - + -
1128B SER* 3.3 27.6 - - - +
1129B LEU* 5.5 0.9 - - + -
1132B ALA* 3.8 10.3 - - + -
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Residues in contact with LYS1062 (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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1058B ALA 3.4 3.1 + - - +
1059B TYR* 3.0 23.4 + - + +
1061B VAL* 1.3 81.7 - - - +
1063B VAL* 1.3 59.9 + - - +
1065B SER* 4.1 2.8 - - - -
1066B LEU* 3.5 20.1 + - - +
1124B PHE* 3.7 29.3 + - + -
1127B ILE* 3.5 32.9 - - - +
1128B SER* 3.5 25.7 + - - +
1131B GLU* 4.2 20.3 + - - +
1213B TYR* 4.3 10.0 + - - -
1248B GLN* 5.0 0.4 - - - +
1251B PHE* 3.5 33.1 - - + -
1252B MET* 4.4 10.4 - - - +
1255B GLN* 5.0 0.8 + - - +
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Residues in contact with VAL1063 (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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993B MET* 4.1 15.0 - - + -
996B MET* 5.3 4.0 - - + +
997B THR* 4.7 5.2 - - - +
1000B VAL* 4.0 32.2 - - + +
1059B TYR* 3.1 48.0 + - + +
1060B VAL 4.1 2.7 - - - +
1062B LYS* 1.3 73.3 - - - +
1064B PHE* 1.3 72.5 + - + +
1066B LEU* 3.2 4.7 + - - +
1067B ALA* 3.0 21.8 + - + +
1251B PHE* 3.9 19.3 - - + -
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Residues in contact with PHE1064 (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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993B MET* 4.6 11.7 - - + -
1031B TYR* 3.3 45.1 - + + -
1034B GLN* 4.1 25.8 - - + -
1035B LEU* 5.2 1.8 - - + -
1060B VAL* 2.9 51.2 + - + +
1063B VAL* 1.3 84.4 - - + +
1065B SER* 1.3 61.8 + - - +
1067B ALA* 3.1 14.3 + - - +
1068B VAL* 3.1 16.1 + - - +
1073B ILE* 3.7 22.9 - - + +
1077B VAL* 4.7 16.8 - - + -
1078B LEU* 4.0 20.4 - - + -
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Residues in contact with SER1065 (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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1061B VAL* 2.8 24.8 + - - +
1062B LYS* 4.1 3.6 - - - -
1064B PHE* 1.3 77.8 - - - +
1066B LEU* 1.3 56.5 + - - +
1068B VAL* 3.2 29.5 - - - +
1078B LEU* 3.8 7.3 - - - +
1128B SER 5.4 0.2 - - - -
1131B GLU* 3.8 30.3 - - - +
1132B ALA* 3.3 24.9 - - - +
1135B ILE* 4.4 5.4 - - - +
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Residues in contact with LEU1066 (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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1000B VAL* 4.2 17.0 - - + -
1001B ILE* 4.2 13.0 - - + -
1004B HIS* 3.5 49.8 + - + +
1062B LYS 3.5 10.8 + - - +
1063B VAL 3.2 7.4 + - - +
1064B PHE 3.1 0.6 - - - -
1065B SER* 1.3 78.9 - - - +
1067B ALA* 1.3 58.7 + - - +
1068B VAL* 3.3 6.9 + - - +
1069B ASN* 4.6 5.0 + - - +
1070B LEU* 4.7 5.1 - - + +
1131B GLU* 5.7 3.1 + - - +
1251B PHE* 3.6 23.6 - - + -
1255B GLN* 4.1 25.1 - - + +
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Residues in contact with ALA1067 (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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1000B VAL* 3.9 21.3 - - + -
1027B ILE* 4.7 10.5 - - + -
1063B VAL* 3.0 17.2 + - + +
1064B PHE* 3.1 8.7 + - - +
1066B LEU* 1.3 76.5 - - - +
1068B VAL* 1.3 59.6 + - - +
1069B ASN 3.4 2.5 - - - -
1070B LEU* 3.9 19.5 - - + -
1071B ILE* 3.5 17.5 + - + +
1073B ILE* 3.3 14.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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