Contacts of the helix formed by residues 1083 - 1093 (chain A) in PDB entry 4EI4
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 SER1083 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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965A LYS* 4.5 13.2 - - - +
1047A TRP* 5.4 3.4 - - - -
1073A GLU* 5.7 0.7 - - - -
1076A THR* 5.6 0.9 - - - -
1079A ASP 3.2 9.4 + - - -
1080A SER* 3.2 20.5 + - - -
1081A ASP 3.5 0.8 - - - -
1082A SER* 1.3 79.3 - - - +
1084A PRO* 1.3 68.4 - - - +
1085A MET* 3.8 14.0 + - - +
1086A ALA* 3.0 18.7 + - - +
1087A LEU* 2.8 26.2 + - - +
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Residues in contact with PRO1084 (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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1046A PHE* 4.2 9.6 - - - +
1047A TRP* 3.7 21.5 - - + -
1069A VAL* 3.4 36.1 - - + +
1072A HIS* 5.3 3.1 - - - +
1073A GLU* 3.8 23.6 - - + +
1082A SER 4.1 3.1 - - - +
1083A SER* 1.3 87.7 - - - +
1085A MET* 1.3 57.9 + - - +
1087A LEU* 4.0 0.4 - - + +
1088A PHE* 2.8 38.4 + - + -
1114A LEU* 4.2 22.0 - - + -
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Residues in contact with MET1085 (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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1046A PHE* 3.7 39.5 - - + +
1047A TRP* 4.4 10.6 - - + -
1083A SER* 3.2 12.3 - - - +
1084A PRO* 1.3 80.0 - - - +
1086A ALA* 1.3 60.1 + - + +
1088A PHE* 3.9 0.5 - - - +
1089A LEU* 2.9 50.7 + - + +
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Residues in contact with ALA1086 (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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1080A SER 3.8 12.8 - - - +
1081A ASP* 4.0 15.5 - - - +
1083A SER* 3.0 21.5 + - - +
1085A MET* 1.3 82.4 - - + +
1087A LEU* 1.3 62.5 + - - +
1089A LEU* 3.5 5.8 + - - +
1090A LYS* 3.1 42.1 + - - +
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Residues in contact with LEU1087 (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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1072A HIS* 3.6 24.9 - - + -
1081A ASP 4.3 13.2 - - - +
1082A SER* 3.2 27.8 - - - +
1083A SER 2.8 19.5 + - - +
1084A PRO 5.1 0.2 - - - -
1086A ALA* 1.3 74.0 - - - +
1088A PHE* 1.3 61.5 + - - +
1090A LYS* 3.5 12.9 + - + +
1091A MET* 3.1 26.7 + - - +
1114A LEU* 3.6 19.7 - - + -
1115A PRO* 4.2 20.4 - - + -
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Residues in contact with PHE1088 (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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1046A PHE* 3.5 50.5 - + + -
1065A TRP* 5.8 3.8 - + - -
1069A VAL* 5.4 3.8 - - + -
1084A PRO 2.8 30.8 + - - +
1085A MET 3.9 0.2 - - - +
1087A LEU* 1.3 71.4 - - - +
1089A LEU* 1.3 59.4 + - - +
1091A MET* 2.9 36.8 + - + +
1092A ILE* 2.9 36.7 + - + +
1104A LEU* 3.9 20.9 - - + -
1107A THR* 5.6 1.3 - - + -
1108A LEU* 4.3 21.5 - - + -
1113A ARG* 4.9 1.8 - - - -
1114A LEU* 3.7 34.1 - - + -
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Residues in contact with LEU1089 (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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1046A PHE* 3.8 23.6 - - + -
1085A MET* 2.9 40.9 + - + +
1086A ALA* 4.0 6.1 - - - +
1088A PHE* 1.3 74.1 - - - +
1090A LYS* 1.3 58.3 + - + +
1092A ILE* 4.1 9.4 - - + -
1093A GLY* 2.8 46.4 + - - +
1094A PRO* 3.2 30.8 - - + +
1100A THR* 4.4 9.6 - - + +
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Residues in contact with LYS1090 (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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1081A ASP* 5.0 10.9 + - - +
1086A ALA* 3.1 38.3 + - - +
1087A LEU* 3.5 16.2 - - + +
1088A PHE 3.1 0.4 - - - -
1089A LEU* 1.3 77.5 - - + +
1091A MET* 1.3 64.3 + - + +
1092A ILE 3.4 0.5 + - - -
1093A GLY* 4.0 3.6 + - - -
1094A PRO* 5.6 0.7 - - - -
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Residues in contact with MET1091 (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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1087A LEU* 3.1 13.9 + - - +
1088A PHE* 2.9 38.0 + - + +
1090A LYS* 1.3 79.1 - - + +
1092A ILE* 1.3 62.8 + - + +
1107A THR* 3.7 29.1 + - + +
1112A LYS* 3.8 22.8 - - + +
1113A ARG 4.0 19.5 - - - +
1114A LEU* 4.6 6.5 - - - -
1115A PRO* 5.0 5.6 - - + -
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Residues in contact with ILE1092 (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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1046A PHE* 4.4 10.1 - - + -
1088A PHE* 2.9 24.1 + - + +
1089A LEU* 4.1 9.4 - - + -
1090A LYS 4.6 0.4 - - - -
1091A MET* 1.3 82.7 - - + +
1093A GLY* 1.3 70.9 + - - +
1096A HIS* 2.9 21.1 + - + -
1100A THR* 4.0 38.8 - - + +
1103A ARG* 4.0 19.2 + - + +
1104A LEU* 4.2 9.2 - - + +
1107A THR* 3.1 32.5 - - + +
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Residues in contact with GLY1093 (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 LEU* 2.8 15.7 + - - +
1090A LYS 4.0 2.9 + - - -
1091A MET 3.8 0.4 - - - -
1092A ILE* 1.3 87.5 - - - +
1094A PRO* 1.3 72.6 - - - +
1095A THR* 3.3 3.4 - - - -
1096A HIS* 3.4 22.7 + - - +
1100A THR* 5.3 1.0 + - - -
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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