Contacts of the strand formed by residues 1189 - 1196 (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 PHE1189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1061B ALA* 3.5 24.9 - - + -
1063B TRP* 3.6 48.5 - + + -
1106B PHE* 3.4 32.1 - + - -
1182B PHE* 4.3 5.6 - + - -
1183B ILE* 3.9 32.5 - - + -
1186B HIS* 3.4 37.9 - + + -
1187B GLY 3.6 2.4 - - - -
1188B ASN* 1.3 76.1 - - - +
1190B LYS* 1.3 67.4 + - - +
1191B GLY 3.9 3.1 - - - +
1262B GLY 4.2 4.5 - - - +
1263B ILE* 3.7 38.1 - - + +
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Residues in contact with LYS1190 (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 PRO* 3.8 26.2 - - + -
1061B ALA 2.7 13.2 + - - +
1103B MET* 5.1 0.4 - - - -
1187B GLY 5.0 1.4 + - - -
1188B ASN* 2.9 35.8 + - - +
1189B PHE* 1.3 83.7 + - - +
1191B GLY* 1.3 55.1 + - - +
1263B ILE* 3.4 11.3 - - - +
1265B PHE* 3.6 24.3 + - - -
1304B VAL* 3.7 22.0 - - + -
1308B LEU* 3.9 12.1 - - + -
1309B TYR* 3.7 62.0 + - + +
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Residues in contact with GLY1191 (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 3.1 8.0 + - - +
1062B VAL* 3.4 15.6 - - - +
1063B TRP* 2.7 31.7 + - - +
1189B PHE* 3.9 4.7 - - - +
1190B LYS* 1.3 79.2 - - - +
1192B PHE* 1.3 57.7 - - - +
1193B ILE* 5.9 0.7 - - - -
1263B ILE* 3.6 7.1 - - - +
1265B PHE* 3.7 12.6 - - - -
1300B ILE* 6.5 0.2 - - - -
1304B VAL* 4.9 3.8 - - - -
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Residues in contact with PHE1192 (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* 3.4 21.5 - + + -
1065B ASN* 3.7 27.4 - - - -
1147B TRP* 4.1 15.5 - + - -
1183B ILE* 3.8 31.6 - - + -
1191B GLY* 1.3 72.8 - - - +
1193B ILE* 1.3 64.0 + - - +
1194B ASP* 4.2 2.5 - - + -
1254B SER* 3.4 39.5 - - - -
1255B ILE* 4.0 15.7 - - + -
1257B TRP* 4.6 2.7 - + - -
1258B ALA* 3.8 26.5 - - + -
1263B ILE* 3.9 10.0 - - + +
1265B PHE 3.2 7.5 + - - +
1266B ALA* 3.2 4.8 - - - -
1267B PHE 2.9 24.6 + - - -
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Residues in contact with ILE1193 (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* 4.8 7.6 - - + -
1063B TRP 2.9 12.5 + - - +
1064B LEU* 3.7 23.0 - - + +
1065B ASN* 3.2 28.3 + - - +
1191B GLY* 5.4 0.7 - - - -
1192B PHE* 1.3 83.9 - - - +
1194B ASP* 1.3 59.6 + - - +
1195B LEU* 4.0 8.3 + - + +
1265B PHE 4.6 1.3 - - - +
1267B PHE* 3.2 16.4 - - + +
1269B PHE* 3.6 30.5 - - + -
1297B LEU* 4.0 21.1 - - + +
1300B ILE* 3.6 37.9 - - + -
1301B MET* 4.9 2.5 - - + -
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Residues in contact with ASP1194 (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* 3.2 35.0 + - - +
1066B ALA* 4.4 1.0 + - - -
1068B ILE* 4.1 12.3 - - - +
1144B ASN* 3.6 4.7 - - - +
1192B PHE* 4.2 3.3 - - + -
1193B ILE* 1.3 72.4 - - - +
1195B LEU* 1.3 61.5 + - - +
1196B HIS* 3.1 28.8 + - + +
1254B SER* 3.0 29.1 + - - +
1255B ILE* 4.3 4.3 - - + -
1267B PHE 2.8 13.6 + - - +
1268B THR* 3.3 4.7 - - - +
1269B PHE* 2.7 34.0 + - - +
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Residues in contact with LEU1195 (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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1064B LEU* 6.2 6.1 - - + -
1065B ASN 3.0 16.9 + - - +
1066B ALA* 3.9 15.4 - - + -
1067B GLY 3.9 3.3 + - - -
1068B ILE 5.0 1.7 + - - -
1072B GLU* 4.7 0.3 - - - +
1075B SER* 3.4 33.2 - - - +
1078B THR* 4.0 26.0 - - + -
1079B ALA* 4.4 7.6 - - + +
1082B THR* 5.6 1.1 - - - +
1107B LEU* 5.9 2.7 - - + -
1193B ILE* 4.3 5.2 - - + +
1194B ASP* 1.3 74.1 + - - +
1196B HIS* 1.3 66.1 - - - +
1269B PHE* 3.5 33.9 - - + -
1271B LEU* 4.3 7.2 - - + -
1293B THR* 4.5 8.5 - - + -
1297B LEU* 4.3 20.4 - - + -
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Residues in contact with HIS1196 (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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1068B ILE* 3.3 14.5 - - + +
1069B HIS* 3.0 22.4 - + - -
1072B GLU* 3.1 7.1 + - - +
1075B SER* 4.4 6.5 - - - -
1144B ASN* 4.1 14.7 + - - -
1194B ASP* 3.1 33.5 + - + +
1195B LEU* 1.3 79.1 - - - +
1197B SER* 1.3 63.9 + - - +
1268B THR* 4.2 12.9 + - + +
1269B PHE 2.7 9.6 + - - +
1270B GLU* 3.1 26.4 + - - +
1271B LEU* 3.0 28.1 + - - +
1403B ZN 2.1 31.5 - - - -
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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