Contacts of the helix formed by residues 1092 - 1102 (chain A) in PDB entry 4N78
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 MET1092 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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926A ILE* 4.9 5.6 - - + -
927A ALA* 6.4 0.9 - - - -
930A MET* 3.5 44.6 - - + +
1011A GLU* 2.8 40.5 + - + +
1014A LEU* 4.2 18.2 - - + -
1086A LEU* 4.5 19.1 - - + -
1091A SER* 1.3 77.7 - - - +
1093A PHE* 1.3 66.9 + - - +
1094A GLU 3.0 2.5 - - - -
1095A VAL* 2.8 21.7 + - + +
1096A ILE* 2.9 16.9 + - + +
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Residues in contact with PHE1093 (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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930A MET* 6.4 0.2 - - - -
1004A ILE* 3.5 45.3 - - + -
1007A CYS* 4.5 8.3 - - + -
1008A LEU* 3.6 43.3 - - + -
1011A GLU* 3.0 18.9 + - - +
1091A SER* 4.9 1.3 - - - -
1092A MET* 1.3 75.0 - - - +
1094A GLU* 1.3 61.7 + - - +
1096A ILE* 3.4 9.5 + - + +
1097A LEU* 3.1 48.2 + - + +
1159A TRP* 4.6 3.6 - + - -
1221A ILE* 5.3 0.4 - - + -
1222A LEU* 4.2 12.6 - - + -
1225A TYR* 3.7 44.4 - + + -
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Residues in contact with GLU1094 (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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1091A SER* 2.7 30.8 + - - +
1092A MET 3.0 0.6 - - - -
1093A PHE* 1.3 77.2 - - - +
1095A VAL* 1.3 64.2 + - + +
1097A LEU* 3.4 10.1 + - - +
1098A THR* 2.9 29.1 + - - +
1225A TYR* 3.1 39.1 - - + +
1226A LEU* 4.6 3.6 - - + +
1227A LYS* 3.1 34.4 + - - +
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Residues in contact with VAL1095 (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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1091A SER 4.4 12.8 - - - +
1092A MET* 2.8 13.9 + - + +
1094A GLU* 1.3 73.2 - - + +
1096A ILE* 1.3 69.8 + - + +
1098A THR* 3.6 6.6 - - - -
1099A ARG* 3.0 46.9 + - + +
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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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930A MET* 4.2 29.8 - - + -
934A LEU* 3.9 29.2 - - + +
1004A ILE* 4.1 24.7 - - + -
1007A CYS* 4.4 27.6 - - + -
1092A MET* 2.9 26.0 + - + +
1093A PHE* 3.4 15.9 - - + +
1095A VAL* 1.3 80.7 - - + +
1097A LEU* 1.3 62.7 + - - +
1099A ARG* 3.4 3.2 + - - +
1100A ILE* 3.1 26.6 + - + +
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Residues in contact with LEU1097 (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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1004A ILE* 4.4 8.7 - - + -
1093A PHE* 3.1 44.9 + - + +
1094A GLU* 3.7 5.4 - - - +
1096A ILE* 1.3 78.3 - - - +
1098A THR* 1.3 63.5 + - - +
1100A ILE* 2.9 16.4 + - - +
1101A ARG* 3.0 11.3 + - - +
1163A MET* 4.2 25.6 - - + -
1167A LEU* 3.8 15.2 - - + +
1222A LEU* 4.1 35.7 - - + +
1225A TYR* 4.5 5.4 - - + -
1226A LEU* 3.8 26.5 - - + -
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Residues in contact with THR1098 (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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1094A GLU* 2.9 20.7 + - - +
1095A VAL* 3.6 9.1 - - + -
1097A LEU* 1.3 76.8 - - - +
1099A ARG* 1.3 64.7 + - + +
1100A ILE 3.5 0.2 + - - -
1101A ARG* 3.6 35.7 + - - +
1102A SER* 3.7 10.0 + - - -
1226A LEU* 4.6 6.0 - - - +
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Residues in contact with ARG1099 (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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931A GLU* 3.3 36.6 + - - -
934A LEU* 3.4 32.5 - - + +
935A LYS* 5.9 1.2 - - - +
1095A VAL* 3.0 39.3 + - + +
1096A ILE 3.9 3.6 - - - +
1098A THR* 1.3 78.6 - - + +
1100A ILE* 1.3 62.9 + - - +
1102A SER* 2.3 27.7 + - - +
1103A PHE* 3.3 20.5 - - + -
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Residues in contact with ILE1100 (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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934A LEU* 3.7 16.2 - - + -
937A VAL* 3.9 18.4 - - + -
941A LEU* 3.8 24.2 - - + -
1004A ILE* 3.2 34.8 - - + -
1096A ILE* 3.1 19.9 + - + +
1097A LEU* 2.9 9.0 + - - +
1099A ARG* 1.3 74.4 - - - +
1101A ARG* 1.3 60.2 + - - +
1102A SER 3.1 1.8 - - - -
1103A PHE* 2.8 33.4 + - + +
1104A LEU* 3.9 5.5 + - + +
1163A MET* 4.1 10.8 - - + -
1167A LEU* 3.7 15.9 - - + -
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Residues in contact with ARG1101 (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 LEU 3.0 10.5 + - - +
1098A THR* 3.8 34.4 + - - +
1099A ARG 3.4 0.2 - - - -
1100A ILE* 1.3 76.2 - - - +
1102A SER* 1.3 57.3 + - - +
1103A PHE 3.0 0.2 - - - -
1104A LEU* 3.0 29.7 + - + +
1105A ASP* 4.5 2.1 - - - +
1110A ARG* 4.6 13.1 + - - +
1166A VAL 5.4 0.6 + - - -
1167A LEU* 3.1 48.7 + - + +
1226A LEU* 3.9 29.9 - - - +
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Residues in contact with SER1102 (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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942A GLN* 4.4 3.8 + - - -
1098A THR 3.7 6.7 + - - -
1099A ARG* 2.3 32.9 + - - +
1101A ARG* 1.3 77.5 - - - +
1103A PHE* 1.3 66.3 + - - +
1104A LEU 3.2 2.0 - - - -
1105A ASP* 3.1 27.2 - - - +
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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