Contacts of the helix formed by residues 1098 - 1109 (chain A) in PDB entry 4BHW
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 ASP1098 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1075A PHE* 3.4 13.5 - - - +
1077A GLN 3.6 5.2 - - - +
1078A PRO* 3.1 37.8 - - + +
1079A VAL* 4.7 3.4 - - + +
1097A MET* 1.3 78.6 - - - +
1099A LEU* 1.3 63.3 + - - +
1100A SER* 2.7 40.0 + - - -
1101A THR* 2.4 24.9 + - - -
1102A ILE* 3.4 23.0 + - - +
1124A MET* 3.7 11.7 - - - -
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Residues in contact with LEU1099 (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 LEU* 3.4 34.0 - - + +
1065A LEU* 4.3 15.0 - - + -
1066A TYR* 3.9 29.1 + - + +
1072A SER* 4.2 23.1 - - - -
1075A PHE* 2.5 33.4 + - + +
1076A ARG* 3.8 19.3 - - + -
1098A ASP* 1.3 71.7 - - - +
1100A SER* 1.3 58.9 + - - +
1102A ILE* 3.5 5.2 + - + +
1103A LYS* 3.0 25.5 + - - +
1121A ILE* 5.1 0.7 - - + -
1124A MET* 3.9 18.1 - - + -
1145A LEU* 5.5 1.6 - - + -
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Residues in contact with SER1100 (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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1066A TYR* 4.0 9.9 - - - -
1076A ARG 3.5 13.1 + - - -
1077A GLN* 3.8 1.9 - - - +
1078A PRO* 3.2 17.8 - - - +
1098A ASP* 2.7 23.3 + - - -
1099A LEU* 1.3 72.5 - - - +
1101A THR* 1.3 56.9 + - - +
1103A LYS* 3.6 5.8 - - - +
1104A ARG* 2.7 36.8 + - - +
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Residues in contact with THR1101 (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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1078A PRO* 4.1 6.8 - - - +
1097A MET* 3.6 27.3 - - + -
1098A ASP* 2.4 35.9 + - - -
1099A LEU 3.4 0.2 - - - -
1100A SER* 1.3 76.4 + - - +
1102A ILE* 1.3 63.2 + - - +
1104A ARG* 3.4 6.1 + - - +
1105A LYS* 3.2 30.5 + - + +
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Residues in contact with ILE1102 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1062A LEU* 3.9 14.8 - - + -
1097A MET* 3.5 31.2 - - + -
1098A ASP 3.4 14.7 + - - +
1099A LEU* 3.7 7.4 - - - +
1100A SER 3.2 0.4 - - - -
1101A THR* 1.3 81.0 - - - +
1103A LYS* 1.3 61.7 + - - +
1105A LYS* 3.4 3.5 + - - +
1106A LEU* 3.1 20.4 + - - +
1111A TYR* 3.9 8.7 - - - +
1117A TYR* 3.5 34.5 - - + -
1120A ASP* 3.8 21.3 - - + +
1121A ILE* 3.7 22.7 - - + +
1124A MET* 4.3 9.6 - - + -
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Residues in contact with LYS1103 (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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1055A ARG* 5.5 1.2 - - - +
1059A MET* 4.2 19.4 - - + +
1062A LEU* 3.7 17.9 - - + -
1063A GLU* 5.9 4.3 - - - -
1066A TYR* 4.5 20.6 - - + +
1099A LEU 3.0 18.2 + - - +
1100A SER* 3.1 7.8 + - - +
1102A ILE* 1.3 74.6 - - - +
1104A ARG* 1.3 61.4 + - - +
1106A LEU* 3.1 4.3 + - - +
1107A ASP* 2.7 55.5 + - - +
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Residues in contact with ARG1104 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1100A SER 2.7 20.1 + - - +
1101A THR* 3.7 7.2 - - - +
1102A ILE 3.4 0.2 - - - -
1103A LYS* 1.3 72.8 - - - +
1105A LYS* 1.3 56.0 + - + +
1107A ASP* 3.1 5.2 + - - +
1108A THR* 2.8 46.3 + - + +
1110A GLN* 4.8 2.2 - - - +
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Residues in contact with LYS1105 (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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1097A MET* 4.3 8.0 - - + +
1101A THR* 3.2 21.4 + - + +
1102A ILE 3.8 4.7 - - - +
1104A ARG* 1.3 80.3 - - + +
1106A LEU* 1.3 57.9 + - - +
1108A THR* 3.8 6.7 - - - -
1109A GLY* 3.0 7.8 + - - -
1110A GLN* 2.8 67.4 + - + +
1111A TYR* 3.7 28.5 + - + +
1116A GLN* 5.9 0.8 - - - +
1120A ASP* 3.2 29.0 + - - +
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Residues in contact with LEU1106 (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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1051A PRO 4.3 7.0 - - - +
1054A LEU* 4.6 6.5 - - + -
1055A ARG* 3.8 33.1 - - + +
1058A LEU* 3.9 21.1 - - + -
1059A MET* 3.8 49.6 - - + +
1062A LEU* 4.6 4.3 - - + -
1102A ILE 3.1 14.5 + - - +
1103A LYS* 3.1 7.0 + - - +
1105A LYS* 1.3 80.0 - - - +
1107A ASP* 1.3 60.4 + - - +
1109A GLY* 4.2 4.4 + - - -
1111A TYR* 3.7 22.8 - - + -
1117A TYR* 4.1 16.2 - - + -
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Residues in contact with ASP1107 (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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1055A ARG* 3.2 37.2 + - - +
1059A MET* 3.4 7.8 - - - +
1103A LYS* 2.7 48.8 + - - +
1104A ARG* 3.8 5.5 - - - +
1106A LEU* 1.3 77.8 - - - +
1108A THR* 1.3 67.2 + - + +
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Residues in contact with THR1108 (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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1051A PRO* 4.9 3.2 - - - +
1104A ARG* 2.8 30.9 + - + +
1105A LYS 3.6 0.5 + - - -
1107A ASP* 1.3 77.4 - - + +
1109A GLY* 1.3 59.4 + - - +
1110A GLN* 2.9 36.1 + - - +
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Residues in contact with GLY1109 (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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1051A PRO* 3.7 34.5 - - - +
1105A LYS 3.0 6.0 + - - -
1106A LEU* 4.5 5.2 - - - -
1107A ASP 3.4 1.4 - - - -
1108A THR* 1.3 79.9 + - - +
1110A GLN* 1.3 58.9 + - - +
1111A TYR 3.2 10.7 + - - +
1112A GLN* 4.2 7.6 + - - -
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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