Contacts of the helix formed by residues 91 - 100 (chain G) in PDB entry 1I43
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 LYS 91 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378E ASP* 3.6 20.0 - - + +
385E ILE* 3.9 7.0 - - - -
89G PHE* 3.3 3.4 - - - +
90G ASN* 1.3 84.6 - - + +
92G THR* 1.3 67.0 + - - +
93G SER* 4.2 18.2 - - - +
94G GLU* 2.8 41.4 + - + +
95G LEU* 3.2 9.4 + - - +
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Residues in contact with THR 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374E ALA* 3.4 29.1 - - + +
377E VAL* 3.1 20.8 - - - +
378E ASP* 2.8 24.8 + - - -
385E ILE* 4.1 5.6 - - - +
398E GLN* 3.9 2.6 + - - +
401E ILE* 3.7 25.1 - - + -
91G LYS* 1.3 70.4 - - - +
93G SER* 1.3 63.2 + - - +
95G LEU* 3.3 15.2 + - + +
96G ILE* 3.1 29.5 + - + +
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Residues in contact with SER 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378E ASP* 4.5 2.7 + - - -
91G LYS* 3.0 20.7 - - - +
92G THR* 1.3 79.9 - - - +
94G GLU* 1.3 61.9 + - - +
96G ILE* 3.2 14.4 + - - +
97G ASP* 3.0 33.4 + - - +
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Residues in contact with GLU 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G PHE* 4.5 6.1 - - + -
90G ASN* 3.1 48.5 + - - +
91G LYS* 2.8 27.7 + - + +
93G SER* 1.3 81.4 + - - +
95G LEU* 1.3 60.9 + - - +
97G ASP* 3.0 13.4 + - - +
98G PHE* 2.8 29.8 + - - +
103G ARG* 3.7 42.5 + - - +
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Residues in contact with LEU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E ILE* 4.5 16.2 - - + -
398E GLN* 5.5 4.0 - - + +
401E ILE* 3.9 25.8 - - + -
402E MET* 3.8 36.3 - - + -
89G PHE* 3.7 46.3 - - + -
91G LYS 3.2 5.0 + - - +
92G THR* 3.5 18.4 - - + +
94G GLU* 1.3 78.5 - - - +
96G ILE* 1.3 58.7 + - - +
98G PHE* 3.4 8.0 + - + +
99G LYS* 3.0 30.3 + - + +
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Residues in contact with ILE 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E LEU* 4.9 11.0 - - + -
371E LEU* 6.1 2.2 - - + -
401E ILE* 4.0 25.8 - - + -
405E TRP* 4.3 17.0 - - + +
92G THR* 3.1 29.4 + - + +
93G SER* 3.4 11.0 - - - +
95G LEU* 1.3 72.9 - - - +
97G ASP* 1.3 56.5 + - - +
99G LYS* 2.9 7.3 + - - -
100G GLU* 2.7 63.7 + - + +
102G ARG* 4.2 5.8 - - - +
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Residues in contact with ASP 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93G SER* 3.0 21.5 + - - +
94G GLU* 3.0 18.4 + - - +
96G ILE* 1.3 75.8 - - - +
98G PHE* 1.3 60.5 + - - +
100G GLU 3.1 7.6 + - - -
102G ARG* 2.8 64.8 + - + +
103G ARG* 3.9 21.9 + - + +
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Residues in contact with PHE 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G PHE* 3.9 23.3 - + + -
94G GLU 2.8 11.8 + - - +
95G LEU* 3.6 11.0 - - + +
97G ASP* 1.3 75.3 - - - +
99G LYS* 1.3 82.0 + - + +
101G LYS* 3.3 14.6 + - - +
103G ARG* 3.6 33.1 - - + +
105G SER* 3.1 37.5 - - - -
106G PHE 5.1 0.2 - - - -
107G GLU* 3.5 40.4 - - + -
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Residues in contact with LYS 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401E ILE* 3.8 18.6 + - + +
402E MET* 2.7 33.3 + - - +
403E SER* 4.7 3.6 - - - +
405E TRP* 3.8 27.6 - - + +
604E PMC 4.7 1.6 + - - -
95G LEU* 3.0 24.8 + - + +
96G ILE* 2.9 10.8 + - - +
98G PHE* 1.3 90.2 - - + +
100G GLU* 1.3 58.0 + - - +
101G LYS* 3.3 13.7 + - - +
107G GLU* 3.0 25.6 + - - -
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Residues in contact with GLU 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405E TRP* 3.1 25.0 + - + +
96G ILE* 2.7 34.0 + - + +
97G ASP 3.1 0.8 + - - +
99G LYS* 1.3 80.0 - - - +
101G LYS* 1.3 71.1 + - - +
102G ARG* 3.0 48.6 + - - +
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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