Contacts of the helix formed by residues 1093 - 1103 (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 ASP1093 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1089A ASP* 3.1 34.1 + - - +
1092A ARG* 1.3 77.6 - - - +
1094A PRO* 1.3 67.5 - - - +
1095A ALA* 3.3 8.5 + - - +
1096A ILE* 3.2 19.9 + - - +
1097A THR* 2.6 36.8 + - - -
1294A TRP* 5.1 0.3 + - - -
1298A LYS* 3.1 33.6 + - - +
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Residues in contact with PRO1094 (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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1092A ARG 3.6 8.3 - - - +
1093A ASP* 1.3 93.6 - - - +
1095A ALA* 1.3 55.9 + - - +
1097A THR* 4.1 6.1 - - - -
1098A SER* 3.1 27.8 + - - -
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Residues in contact with ALA1095 (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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1093A ASP* 3.2 4.6 + - - +
1094A PRO* 1.3 78.3 - - - +
1096A ILE* 1.3 61.7 + - - +
1099A ILE* 2.8 35.4 + - - +
1298A LYS* 3.8 24.2 - - + +
1302A GLU* 3.3 27.4 - - + +
1305A ARG* 3.3 9.9 + - - +
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Residues in contact with ILE1096 (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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1086A ILE* 4.3 18.2 - - + +
1089A ASP* 3.0 43.1 - - + +
1090A TYR* 4.3 1.6 - - - +
1093A ASP* 3.2 20.4 + - - +
1095A ALA* 1.3 74.5 - - - +
1097A THR* 1.3 65.7 + - - +
1099A ILE* 3.9 11.4 - - + +
1100A LEU* 3.0 26.9 + - + +
1105A ILE* 3.9 26.5 - - + -
1294A TRP* 3.7 35.2 - - + -
1298A LYS* 4.7 1.7 - - + +
1301A MET* 3.9 9.6 - - + -
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Residues in contact with THR1097 (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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1089A ASP 3.6 1.0 + - - -
1090A TYR* 3.8 21.4 - - + +
1091A GLN* 2.8 42.2 + - + +
1092A ARG 3.5 1.2 + - - -
1093A ASP 2.6 24.7 + - - -
1094A PRO* 4.1 6.7 - - - -
1096A ILE* 1.3 81.3 - - - +
1098A SER* 1.3 56.5 + - - +
1100A LEU* 3.3 3.3 + - - +
1101A GLU* 3.1 43.1 + - - +
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Residues in contact with SER1098 (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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1094A PRO 3.1 19.0 + - - -
1095A ALA 3.7 0.2 - - - -
1097A THR* 1.3 76.6 - - - +
1099A ILE* 1.3 63.5 + - - +
1101A GLU* 3.6 26.9 + - - +
1102A LYS* 3.7 5.4 + - - +
1305A ARG* 2.6 42.3 + - - -
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Residues in contact with ILE1099 (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* 6.2 0.2 - - + -
1095A ALA 2.8 30.3 + - - +
1096A ILE* 3.2 20.8 + - + +
1098A SER* 1.3 73.3 - - - +
1100A LEU* 1.3 58.2 + - - +
1101A GLU 3.2 0.4 - - - -
1102A LYS* 3.1 3.3 + - - -
1103A MET* 2.9 46.9 + - + +
1105A ILE* 3.9 27.8 - - + -
1298A LYS* 4.1 11.0 - - + +
1301A MET* 3.7 37.7 - - + +
1302A GLU* 4.0 14.1 - - + -
1305A ARG* 4.0 15.7 - - - +
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Residues in contact with LEU1100 (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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1032A LEU* 4.1 11.7 - - + -
1052A PHE* 3.7 40.2 - - + +
1053A SER* 4.1 2.9 - - - +
1054A THR* 2.7 37.2 + - + +
1059A ARG* 3.6 2.9 + - - -
1086A ILE* 3.7 23.8 - - + -
1090A TYR* 3.7 25.6 - - + -
1096A ILE* 3.0 19.2 + - + +
1097A THR 3.7 4.3 - - - +
1099A ILE* 1.3 74.1 - - - +
1101A GLU* 1.3 55.6 + - - +
1102A LYS 3.3 0.2 - - - -
1103A MET 3.3 18.6 - - - +
1105A ILE* 3.9 19.7 - - + -
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Residues in contact with GLU1101 (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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1054A THR* 3.7 8.2 + - - +
1059A ARG* 3.3 22.2 + - - -
1090A TYR* 5.0 8.1 - - - +
1097A THR* 3.1 35.4 + - + +
1098A SER* 3.6 18.2 + - - +
1099A ILE 3.2 0.4 - - - -
1100A LEU* 1.3 79.3 - - - +
1102A LYS* 1.3 67.0 + - + +
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Residues in contact with LYS1102 (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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1059A ARG* 3.5 13.8 - - - +
1060A PRO* 3.5 18.3 - - + +
1098A SER 3.7 3.7 + - - +
1099A ILE 3.1 6.3 + - - +
1101A GLU* 1.3 90.0 - - + +
1103A MET* 1.3 66.9 + - + +
1305A ARG* 4.2 23.6 - - + +
1308A LEU* 4.3 20.2 - - + -
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Residues in contact with MET1103 (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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1052A PHE 4.3 0.2 - - - +
1053A SER* 4.9 0.2 - - - -
1059A ARG* 4.4 2.9 - - - -
1060A PRO* 3.2 24.9 - - + +
1061A ALA 4.8 0.2 - - - +
1062A VAL* 4.2 11.9 - - + -
1099A ILE* 2.9 37.6 + - + +
1100A LEU* 3.3 30.9 - - - +
1101A GLU 3.7 0.4 - - - -
1102A LYS* 1.3 86.6 - - + +
1104A ASP* 1.3 73.7 + - - +
1105A ILE* 5.6 0.4 - - + -
1190A LYS* 5.4 0.7 - - - -
1301A MET 3.6 7.6 - - - +
1304A VAL* 3.6 29.6 - - - -
1305A ARG* 3.6 33.4 - - + -
1308A LEU* 4.3 7.9 - - + -
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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