Contacts of the strand formed by residues 1189 - 1196 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1061A ALA* 3.4 22.0 - - + -
1062A VAL 3.8 1.8 - - - -
1063A TRP* 3.5 56.3 - + + -
1106A PHE* 3.4 25.4 - + - -
1182A PHE* 4.2 5.6 - + - -
1183A ILE* 4.0 25.5 + - + -
1186A HIS* 3.4 44.6 - + + -
1187A GLY 3.8 1.8 + - - -
1188A ASN* 1.3 76.2 - - - +
1190A LYS* 1.3 64.6 + - - +
1191A GLY 3.8 2.5 - - - +
1262A GLY 4.3 1.9 - - - +
1263A ILE* 3.4 37.3 - - + +
1309A TYR* 3.7 7.6 + - - -
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Residues in contact with LYS1190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060A PRO* 3.9 24.0 - - + +
1061A ALA 2.6 14.7 + - - +
1103A MET* 5.4 0.4 - - - -
1188A ASN* 2.9 37.2 + - - +
1189A PHE* 1.3 85.0 - - - +
1191A GLY* 1.3 55.3 + - - +
1263A ILE* 3.5 7.3 - - - +
1265A PHE* 3.4 29.5 + - - -
1304A VAL* 3.6 22.7 - - + -
1308A LEU* 3.9 14.6 - - + -
1309A TYR* 2.7 65.8 + - + +
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Residues in contact with GLY1191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061A ALA 3.1 6.1 + - - +
1062A VAL* 3.3 20.6 - - - +
1063A TRP* 2.7 31.5 + - - +
1189A PHE* 3.8 4.7 - - - -
1190A LYS* 1.3 81.0 - - - +
1192A PHE* 1.3 57.7 + - - +
1193A ILE* 5.6 0.9 - - - -
1263A ILE* 3.7 3.3 - - - +
1265A PHE* 3.6 13.0 - - - -
1300A ILE* 6.3 0.4 - - - -
1304A VAL* 4.8 3.6 - - - -
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Residues in contact with PHE1192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063A TRP* 3.3 25.1 - + + -
1065A ASN* 3.8 20.9 - - - -
1147A TRP* 4.1 19.5 - + - -
1179A VAL* 4.5 0.2 - - + -
1183A ILE* 3.7 31.4 - - + -
1191A GLY* 1.3 72.1 - - - +
1193A ILE* 1.3 63.7 + - - +
1194A ASP* 4.2 3.4 - - + -
1254A SER* 3.6 37.5 - - - -
1255A ILE* 4.1 10.8 - - + -
1257A TRP* 4.8 1.6 - + - -
1258A ALA* 3.6 30.3 - - + -
1263A ILE* 3.8 10.3 - - + +
1265A PHE 3.1 7.8 + - - +
1266A ALA* 3.2 4.8 - - - -
1267A PHE 3.0 23.6 + - - -
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Residues in contact with ILE1193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062A VAL* 4.5 6.1 - - + -
1063A TRP 2.7 9.1 + - - +
1064A LEU* 3.5 29.6 - - + -
1065A ASN* 3.1 29.2 + - - +
1191A GLY* 5.6 0.2 - - - -
1192A PHE* 1.3 82.7 - - - +
1194A ASP* 1.3 61.7 + - - +
1195A LEU* 4.0 10.1 + - + +
1265A PHE 4.8 0.7 - - - +
1267A PHE* 3.3 16.4 - - + +
1269A PHE* 3.9 16.6 - - + -
1297A LEU* 3.8 31.4 - - + -
1300A ILE* 3.6 35.7 - - + -
1301A MET* 4.7 5.2 - - + -
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Residues in contact with ASP1194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065A ASN* 3.2 25.6 + - - +
1066A ALA* 5.1 0.3 - - - -
1068A ILE* 4.6 8.9 + - - +
1144A ASN* 3.4 6.4 - - - +
1192A PHE* 4.2 2.1 + - + -
1193A ILE* 1.3 72.2 - - - +
1195A LEU* 1.3 62.3 + - - +
1196A HIS* 2.5 33.2 + - + -
1254A SER* 2.9 29.2 + - - +
1255A ILE* 3.8 13.5 - - + -
1267A PHE 2.8 7.9 + - - +
1268A THR* 3.4 6.0 + - - +
1269A PHE* 2.8 34.1 + - - +
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Residues in contact with LEU1195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064A LEU* 6.1 4.9 - - + -
1065A ASN 3.0 17.8 + - - +
1066A ALA* 3.8 13.1 - - + -
1067A GLY 3.7 12.1 + - - -
1068A ILE 5.1 0.7 + - - -
1072A GLU* 4.8 0.2 - - - +
1075A SER* 3.2 26.6 + - - +
1078A THR* 4.1 25.8 - - + -
1079A ALA* 4.8 7.6 - - + +
1082A THR* 5.5 0.9 - - - +
1107A LEU* 6.1 2.7 - - + -
1193A ILE* 4.0 15.3 - - + +
1194A ASP* 1.3 72.7 + - - +
1196A HIS* 1.3 65.3 + - - +
1269A PHE* 3.5 35.2 - - + -
1271A LEU* 4.4 10.5 - - + -
1293A THR* 4.9 2.0 - - + -
1297A LEU* 4.3 17.9 - - + -
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Residues in contact with HIS1196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068A ILE* 3.4 14.9 - - + +
1069A HIS* 3.2 19.1 - + - -
1072A GLU* 3.0 8.0 + - - +
1075A SER* 4.5 3.4 - - - -
1144A ASN* 4.0 9.3 + - - -
1194A ASP* 2.5 40.4 + - - -
1195A LEU* 1.3 75.1 - - - +
1197A SER* 1.3 62.6 + - - +
1268A THR* 3.9 17.9 - - + +
1269A PHE 2.7 12.9 + - - +
1270A GLU* 3.2 19.5 + - - +
1271A LEU* 2.9 33.3 + - - +
1402A ZN 2.1 33.5 - - - -
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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