Contacts of the helix formed by residues 1074 - 1088 (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 ASP1074 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1031B TYR* 3.2 24.7 + - - +
1038B ARG* 5.0 0.3 + - - -
1072B ALA 3.6 1.6 + - - -
1073B ILE* 1.3 75.2 - - - +
1075B SER* 1.3 68.5 + - - +
1076B GLN* 3.2 33.8 + - - +
1077B VAL* 3.5 18.4 - - + +
1078B LEU* 3.1 28.2 + - - +
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Residues in contact with SER1075 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073B ILE 3.5 4.5 + - - -
1074B ASP* 1.3 75.1 + - - +
1076B GLN* 1.3 61.3 + - - +
1078B LEU* 4.5 4.0 - - - -
1079B CYS* 2.9 42.2 + - - +
1135B ILE* 4.8 13.2 + - - +
1139B GLN* 3.4 29.9 + - - +
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Residues in contact with GLN1076 (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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1038B ARG* 3.4 14.7 + - - +
1074B ASP* 3.2 20.1 + - - +
1075B SER* 1.3 80.1 - - - +
1077B VAL* 1.3 57.1 + - + +
1079B CYS* 5.2 0.2 - - - -
1080B GLY* 3.0 25.1 + - - -
1139B GLN* 4.9 11.0 + - - +
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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
----------------------------------------------------------
1031B TYR* 4.4 2.5 - - + +
1035B LEU* 4.0 30.7 - - + -
1038B ARG* 3.2 41.3 + - + +
1060B VAL* 6.1 2.7 - - + -
1064B PHE* 4.7 15.3 - - + -
1074B ASP* 3.5 29.5 + - + +
1075B SER 3.3 0.4 - - - -
1076B GLN* 1.3 76.3 - - - +
1078B LEU* 1.3 67.7 + - - +
1080B GLY* 3.4 0.9 + - - -
1081B ALA* 3.3 19.9 + - - +
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Residues in contact with LEU1078 (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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1060B VAL* 6.2 0.4 - - + -
1061B VAL* 3.9 20.9 - - + -
1064B PHE* 4.0 22.4 - - + -
1065B SER* 3.8 22.7 - - - +
1068B VAL* 4.7 0.7 - - + -
1073B ILE* 4.2 18.8 - - + -
1074B ASP 3.1 16.0 + - - +
1075B SER* 4.2 3.4 - - - +
1077B VAL* 1.3 82.2 - - - +
1079B CYS* 1.3 62.0 + - - +
1081B ALA* 3.4 8.6 + - - +
1082B VAL* 3.3 18.4 + - - +
1132B ALA* 4.8 3.4 - - + -
1135B ILE* 3.6 44.2 - - + -
1136B CYS* 4.4 6.5 - - - -
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Residues in contact with CYS1079 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075B SER* 2.9 21.1 + - - +
1076B GLN* 5.2 0.4 - - - -
1078B LEU* 1.3 74.6 - - - +
1080B GLY* 1.3 59.4 + - - +
1082B VAL* 3.2 4.5 + - - +
1083B LYS* 2.9 31.9 + - - +
1135B ILE* 3.8 7.6 - - - -
1136B CYS* 2.0 54.3 - - + -
1139B GLN* 3.2 28.5 - - + +
1140B VAL* 4.0 10.6 - - + +
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Residues in contact with GLY1080 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038B ARG* 4.6 8.1 - - - -
1041B SER 3.5 16.4 - - - +
1076B GLN 3.0 22.9 + - - -
1077B VAL 3.4 2.0 + - - -
1078B LEU 3.2 0.6 - - - -
1079B CYS* 1.3 79.6 - - - +
1081B ALA* 1.3 58.6 + - - +
1083B LYS* 3.8 15.2 + - - +
1084B TRP* 3.4 14.2 + - - +
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Residues in contact with ALA1081 (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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1041B SER* 4.5 4.3 - - - +
1057B THR* 3.7 24.1 - - + +
1060B VAL* 5.9 4.7 - - + -
1061B VAL* 4.1 13.9 - - + -
1077B VAL 3.3 11.3 + - - +
1078B LEU* 3.8 7.9 - - - +
1079B CYS 3.2 0.6 - - - -
1080B GLY* 1.3 74.3 - - - +
1082B VAL* 1.3 65.2 + - - +
1084B TRP* 3.2 8.5 + - - +
1085B LEU* 3.1 29.1 + - - +
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Residues in contact with VAL1082 (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* 4.1 25.4 - - + -
1078B LEU 3.3 15.9 - - - +
1079B CYS* 3.2 12.3 + - - +
1081B ALA* 1.3 78.1 - - - +
1083B LYS* 1.3 62.8 + - - +
1084B TRP 3.3 0.3 + - - -
1085B LEU* 3.4 5.2 + - - +
1086B ILE* 3.2 34.5 + - + +
1129B LEU* 3.7 28.0 - - + +
1132B ALA* 4.4 12.1 - - + +
1136B CYS* 4.5 9.4 - - + -
1140B VAL* 4.8 8.7 - - + -
1143B LEU* 4.3 12.3 - - + -
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Residues in contact with LYS1083 (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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1079B CYS 2.9 16.1 + - - +
1080B GLY* 4.0 15.1 - - - +
1082B VAL* 1.3 76.5 - - - +
1084B TRP* 1.3 60.4 - - - +
1086B ILE* 3.7 2.9 + - - +
1087B LEU* 3.3 44.4 + - + +
1139B GLN 5.7 2.9 - - - +
1140B VAL* 4.2 25.5 - - + +
1142B SER* 5.3 2.0 - - - +
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Residues in contact with TRP1084 (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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1041B SER* 2.9 36.5 + - - +
1052B PRO* 3.8 32.5 - - + +
1053B SER 4.0 12.1 - - - -
1054B THR* 4.5 0.7 - - - -
1057B THR* 3.9 23.1 - - + -
1080B GLY 3.4 11.7 + - - +
1081B ALA* 3.2 7.8 + - - +
1082B VAL 3.1 0.8 - - - -
1083B LYS* 1.3 78.1 - - - +
1085B LEU* 1.3 95.6 + - + +
1086B ILE 3.1 2.2 - - - -
1087B LEU* 5.4 0.2 - - - -
1088B GLU* 2.9 69.8 + - + +
1089B LYS* 3.4 38.8 - - + -
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Residues in contact with LEU1085 (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* 3.8 30.5 - - + +
1057B THR* 4.2 7.0 - - + +
1058B ALA* 3.9 25.6 - - - +
1061B VAL* 4.8 5.4 - - + -
1081B ALA 3.1 20.2 + - - +
1082B VAL 3.4 4.2 + - - +
1084B TRP* 1.3 107.3 - - + +
1086B ILE* 1.3 59.2 + - - +
1089B LYS* 3.4 20.7 - - + +
1090B GLN* 3.6 0.5 - - - +
1096B PHE* 3.3 26.4 - - + -
1125B VAL* 4.0 16.4 - - + -
1128B SER* 6.1 0.7 - - - -
1129B LEU* 4.3 15.3 - - + -
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Residues in contact with ILE1086 (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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1082B VAL* 3.2 20.6 + - + +
1083B LYS* 4.0 4.5 - - - +
1084B TRP 3.1 0.8 - - - -
1085B LEU* 1.3 79.2 - - - +
1087B LEU* 1.3 66.1 + - + +
1090B GLN* 3.0 40.1 - - - +
1096B PHE* 4.9 0.4 - - - -
1129B LEU* 4.7 10.3 - - + -
1140B VAL* 4.2 8.3 - - + -
1142B SER* 3.6 39.9 - - - +
1143B LEU* 3.8 28.9 - - + -
1146B SER* 3.6 20.2 - - - +
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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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1083B LYS* 3.3 35.8 + - + +
1084B TRP* 4.6 0.7 - - - +
1086B ILE* 1.3 81.5 - - + +
1088B GLU* 1.3 72.8 + - + +
1090B GLN 5.8 0.9 - - - -
1142B SER* 4.3 24.9 - - - +
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Residues in contact with GLU1088 (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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1084B TRP* 2.9 54.0 + - + +
1086B ILE 3.3 0.2 - - - -
1087B LEU* 1.3 91.5 - - + +
1089B LYS* 1.3 71.5 + - + +
1090B GLN 3.1 12.3 + - - +
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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