Contacts of the strand formed by residues 1061 - 1066 (chain B) in PDB entry 2BOA
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 ALA1061 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059B ARG 3.9 1.1 - - - +
1060B PRO* 1.3 76.2 - - - +
1062B VAL* 1.3 65.2 + - - +
1103B MET* 5.0 0.7 - - - -
1104B ASP* 3.2 9.4 - - + +
1106B PHE* 3.8 8.5 - - + -
1186B HIS* 3.6 25.6 - - + +
1188B ASN 3.0 6.6 + - - +
1189B PHE* 3.5 26.4 - - + -
1190B LYS* 2.7 32.5 + - - +
1191B GLY 3.1 4.9 + - - -
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Residues in contact with VAL1062 (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 ALA* 1.3 76.3 - - - +
1063B TRP* 1.3 63.4 + - - +
1064B LEU* 3.6 27.6 - - + -
1103B MET* 3.7 32.3 - - + -
1104B ASP 2.9 12.2 + - - +
1105B ILE* 3.3 9.3 - - + +
1106B PHE* 2.8 27.2 + - - -
1189B PHE* 3.8 3.4 - - - -
1191B GLY* 3.4 13.9 - - - +
1193B ILE* 4.8 6.3 - - + -
1301B MET* 4.0 22.9 - - + -
1304B VAL* 4.3 13.0 - - + -
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Residues in contact with TRP1063 (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 ILE* 3.9 13.2 - - + -
1049B VAL* 3.7 19.7 - - + -
1062B VAL* 1.3 71.9 - - - +
1064B LEU* 1.3 68.3 + - - +
1065B ASN* 3.2 39.1 + - - +
1106B PHE* 3.6 26.0 - + + -
1108B LEU* 3.7 30.1 - - + -
1179B VAL* 3.8 19.1 - - + +
1182B PHE* 3.6 29.4 - + + -
1183B ILE* 4.0 14.4 - - + -
1189B PHE* 3.6 23.6 - + + -
1191B GLY 2.7 16.2 + - - +
1192B PHE* 3.4 21.8 - + + -
1193B ILE 2.9 27.7 + - - -
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Residues in contact with LEU1064 (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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1062B VAL* 3.6 29.8 - - + -
1063B TRP* 1.3 74.9 - - - +
1065B ASN* 1.3 54.5 + - - +
1082B THR* 4.5 18.6 - - + -
1086B ILE* 4.8 5.8 - - + -
1105B ILE* 3.5 21.3 - - + -
1106B PHE 2.6 12.7 + - - +
1107B LEU* 3.0 27.4 - - + +
1108B LEU 2.7 31.5 + - - -
1193B ILE* 3.7 25.4 - - + +
1195B LEU* 6.2 6.1 - - + -
1297B LEU* 4.9 15.5 - - + -
1301B MET* 4.6 13.0 - - + -
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Residues in contact with ASN1065 (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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1063B TRP* 3.2 29.3 + - - +
1064B LEU* 1.3 73.1 - - - +
1066B ALA* 1.3 62.6 + - - +
1068B ILE* 4.0 15.9 - - - +
1107B LEU* 5.5 0.4 - - - -
1108B LEU* 3.4 21.9 - - + +
1111B ALA* 4.5 4.7 - - + +
1147B TRP* 4.7 3.8 - - - -
1179B VAL* 5.2 2.1 - - - +
1192B PHE* 3.7 18.5 - - - -
1193B ILE 3.2 13.7 + - - +
1194B ASP* 3.2 28.9 + - - +
1195B LEU* 3.0 29.7 + - - +
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Residues in contact with ALA1066 (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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1065B ASN* 1.3 76.1 - - - +
1067B GLY* 1.3 56.5 + - - +
1068B ILE 3.3 2.9 - - - -
1075B SER* 3.4 27.4 - - - +
1079B ALA* 3.4 14.6 - - + -
1108B LEU 2.9 3.6 + - - +
1109B PRO 3.2 17.7 - - - +
1111B ALA* 2.8 34.4 + - - +
1194B ASP* 4.6 0.4 - - - -
1195B LEU* 3.9 14.6 - - + -
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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