Contacts of the strand formed by residues 1104 - 1108 (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 ASP1104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1051A LYS* 3.7 19.1 - - + -
1052A PHE 3.2 4.7 - - - +
1053A SER* 2.6 34.8 + - - -
1054A THR 4.6 0.3 + - - -
1057A VAL 4.1 5.2 - - - +
1058A ARG* 4.8 1.4 - - - -
1059A ARG* 3.5 31.5 + - + +
1060A PRO 3.0 10.0 + - - +
1061A ALA* 3.3 4.6 - - + -
1062A VAL 2.9 25.6 + - - -
1103A MET* 1.3 78.1 - - - +
1105A ILE* 1.3 62.6 + - - +
1106A PHE* 3.9 20.8 - - + -
1186A HIS* 5.1 1.0 + - - -
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Residues in contact with ILE1105 (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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1050A LEU 3.5 1.2 - - - +
1051A LYS* 3.4 1.9 - - - -
1052A PHE* 2.6 57.1 + - + +
1062A VAL* 3.6 11.0 - - + +
1064A LEU* 3.8 26.5 - - + -
1086A ILE* 4.4 13.0 - - + -
1096A ILE* 3.9 24.5 - - + -
1099A ILE* 3.9 13.9 - - + -
1100A LEU* 3.9 15.3 - - + -
1103A MET* 4.2 1.3 + - + -
1104A ASP* 1.3 77.2 - - - +
1106A PHE* 1.3 69.3 + - - +
1107A LEU* 4.7 1.6 - - + +
1301A MET* 3.8 28.7 - - + -
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Residues in contact with PHE1106 (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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1036A VAL* 5.4 2.0 - - + -
1049A VAL* 3.8 19.7 - - + -
1050A LEU 3.2 4.0 - - - -
1051A LYS* 3.5 42.6 - - + -
1061A ALA* 4.0 9.2 - - + -
1062A VAL 3.0 7.6 + - - +
1063A TRP* 3.6 22.8 - + + -
1064A LEU* 2.9 28.9 + - - +
1104A ASP* 3.9 19.7 - - + -
1105A ILE* 1.3 77.8 - - - +
1107A LEU* 1.3 60.9 + - - +
1182A PHE* 3.4 35.2 - + - -
1186A HIS* 4.1 14.1 - + - -
1189A PHE* 3.4 25.8 - + - -
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Residues in contact with LEU1107 (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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1049A VAL* 3.1 5.9 - - - +
1050A LEU* 2.7 42.3 + - + +
1052A PHE* 4.2 9.0 - - + -
1064A LEU* 3.2 30.3 - - + +
1065A ASN* 5.2 0.4 - - - -
1079A ALA* 3.5 45.3 - - + +
1082A THR* 4.0 14.4 - - + -
1083A ALA* 3.6 28.3 - - + +
1086A ILE* 4.2 9.6 - - + -
1105A ILE* 4.1 2.2 - - + -
1106A PHE* 1.3 72.5 - - - +
1108A LEU* 1.3 62.0 + - - +
1109A PRO* 3.2 13.3 - - + +
1195A LEU* 6.1 2.2 - - + -
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Residues in contact with LEU1108 (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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1019A TYR* 6.4 0.4 - - + -
1038A ILE* 4.5 3.1 - - + -
1047A MET* 4.3 11.7 - - + -
1048A TYR 3.1 37.0 - - - +
1049A VAL* 3.7 12.6 - - + -
1063A TRP* 3.9 10.3 - - + -
1064A LEU 2.8 10.1 + - - -
1065A ASN* 3.8 11.2 - - + -
1066A ALA 2.8 26.3 + - - +
1106A PHE 4.2 0.2 - - - -
1107A LEU* 1.3 73.8 - - - +
1109A PRO* 1.3 62.8 - - - +
1110A VAL 3.7 17.0 - - - +
1111A ALA* 3.6 30.3 - - + -
1179A VAL* 3.8 26.9 - - + -
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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