Contacts of the helix formed by residues 1083 - 1091 (chain B) in PDB entry 3ETA
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081B HIS 4.1 0.7 - - - +
1082B GLY* 1.3 75.4 - - - -
1084B LEU* 1.3 61.0 + - - +
1085B LYS* 3.1 17.0 + - - +
1086B SER* 2.8 44.0 + - - -
1087B TYR* 3.2 18.5 + - - +
1136B ARG* 3.2 25.0 - - - +
1138B CYS 3.3 5.8 - - - +
1139B MET* 4.4 0.2 - - - +
1140B VAL* 4.4 0.2 - - - -
1151B PHE* 3.7 18.4 - - + -
1155B ARG* 3.9 11.0 + - - -
1157B ILE* 4.0 6.2 - - - +
1158B TYR* 3.4 9.6 - - - -
2001B 351 4.9 5.8 + - - -
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Residues in contact with LEU1084 (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 GLY 3.9 0.4 + - - -
1083B ASP* 1.3 70.6 - - - +
1085B LYS* 1.3 60.3 + - - +
1087B TYR* 4.0 19.7 - - + -
1088B LEU* 2.9 40.0 + - + +
1112B MET* 3.9 23.3 - - - -
1116B ILE* 4.1 26.5 - - + -
1135B ALA* 3.2 24.4 + - + +
1138B CYS* 2.7 25.6 + - + +
1140B VAL* 4.0 16.4 - - + +
1146B VAL* 4.4 7.4 - - + -
1198B VAL* 4.7 1.1 - - + -
1202B ILE* 4.3 16.8 - - + -
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Residues in contact with LYS1085 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083B ASP* 3.1 10.8 + - - +
1084B LEU* 1.3 77.1 - - - +
1086B SER* 1.3 55.5 + - - +
1088B LEU* 3.4 1.9 + - - +
1089B ARG* 3.0 56.9 + - - +
1135B ALA* 3.2 14.2 + - + -
1136B ARG* 3.7 17.9 - - + +
1158B TYR* 3.6 28.7 - - + +
1161B ASP* 2.9 29.7 + - - +
1175B TRP* 4.1 8.9 - - - -
1201B GLU* 4.1 10.0 + - - +
1206B ALA* 3.9 17.4 + - + -
1207B GLU 4.8 2.0 + - - -
1208B GLN* 2.7 25.9 + - - -
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Residues in contact with SER1086 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081B HIS 5.9 1.1 - - - -
1083B ASP* 2.8 33.1 + - - -
1085B LYS* 1.3 72.3 - - - +
1087B TYR* 1.3 61.1 + - - +
1089B ARG* 3.3 4.8 + - - +
1090B SER* 3.0 30.0 + - - -
1097B ASN* 5.0 3.9 + - - -
1157B ILE* 4.1 7.6 - - - +
1158B TYR* 2.6 24.0 + - - -
2001B 351 5.9 0.2 + - - -
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Residues in contact with TYR1087 (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 HIS* 4.5 15.4 + + + +
1083B ASP 3.2 15.1 + - - +
1084B LEU* 3.7 24.9 - - + +
1086B SER* 1.3 77.9 - - - +
1088B LEU* 1.3 65.3 + - + +
1090B SER* 2.7 27.0 + - - -
1091B LEU* 3.3 43.3 + - + +
1099B PRO* 5.2 5.2 - - + -
1101B ARG* 3.8 22.9 + - - -
1112B MET* 5.2 12.8 - - + -
1140B VAL* 4.4 16.4 - - + -
1144B PHE* 3.8 37.9 - + + +
1146B VAL* 6.5 0.2 - - + -
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Residues in contact with LEU1088 (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 LEU* 2.9 47.2 + - + +
1085B LYS 3.7 3.6 - - - +
1087B TYR* 1.3 79.4 - - + +
1089B ARG* 1.3 62.5 + - - +
1091B LEU* 3.1 12.6 + - + +
1092B ARG 3.7 2.1 + - - -
1104B PRO* 3.9 27.6 - - + -
1112B MET* 4.9 2.9 - - - -
1135B ALA* 4.4 5.2 - - + -
1201B GLU 3.8 8.1 - - - +
1202B ILE* 3.8 42.6 - - + +
1205B LEU* 3.5 31.2 - - + +
1206B ALA* 4.2 13.7 - - + -
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Residues in contact with ARG1089 (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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1085B LYS* 3.0 35.8 + - - +
1086B SER* 3.8 5.8 - - - +
1087B TYR 3.3 0.4 - - - -
1088B LEU* 1.3 73.9 - - - +
1090B SER* 1.3 62.9 + - - +
1092B ARG* 3.4 34.7 + - - +
1095B ALA* 3.3 16.1 - - - +
1097B ASN* 5.1 0.7 - - - -
1158B TYR* 4.0 23.5 - - - +
1205B LEU 3.8 15.3 - - - +
1206B ALA* 2.8 25.0 + - + +
1207B GLU* 4.1 0.4 - - - +
1208B GLN* 2.8 38.4 + - - +
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Residues in contact with SER1090 (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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1086B SER 3.0 14.5 + - - -
1087B TYR* 2.7 26.3 + - - -
1089B ARG* 1.3 76.1 - - - +
1091B LEU* 1.3 57.2 + - - +
1092B ARG 3.2 1.7 + - - -
1095B ALA* 3.7 3.8 - - - +
1097B ASN* 3.7 40.6 - - - -
1098B ASN* 3.2 31.0 + - - +
1099B PRO* 3.4 14.1 - - - +
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Residues in contact with LEU1091 (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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1087B TYR* 3.4 46.2 - - + +
1088B LEU* 3.1 14.6 + - - +
1090B SER* 1.3 76.1 + - - +
1092B ARG* 1.3 63.5 + - - +
1093B PRO* 3.5 2.3 - - - +
1098B ASN* 3.9 6.0 + - - +
1099B PRO* 3.9 14.1 - - + -
1101B ARG* 3.6 31.8 - - + +
1102B PRO 3.5 20.4 - - - +
1103B PRO* 3.8 29.8 - - + +
1104B PRO* 3.8 27.1 - - + -
1205B LEU* 4.3 5.4 - - + -
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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
------------------------------------------------------------
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