Contacts of the helix formed by residues 75 - 86 (chain G) in PDB entry 1IRJ
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 SER 75 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19G PHE* 3.8 2.2 - - - -
30G ASP 4.5 1.1 - - - -
31G THR* 4.2 16.5 - - - +
73G GLN* 4.0 0.8 - - - +
74G LEU* 1.3 77.2 - - - +
76G PHE* 1.3 59.8 + - - +
77G GLU* 3.6 8.6 + - - +
78G GLU* 2.8 36.6 + - - +
79G PHE* 2.9 26.9 + - - +
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Residues in contact with PHE 76 (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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15G ILE* 4.2 6.5 - - + -
16G ILE* 3.5 41.5 - - + -
19G PHE* 3.5 47.4 - + + -
20G HIS* 5.5 6.3 - + + +
30G ASP 4.5 1.6 + - - +
75G SER* 1.3 74.4 - - - +
77G GLU* 1.3 62.2 + - - +
79G PHE* 3.2 1.9 + + - +
80G ILE* 3.0 51.7 + - + +
83H MET* 3.9 18.8 - - + -
84H ALA* 3.9 39.3 - - + -
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Residues in contact with GLU 77 (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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75G SER* 3.2 8.1 + - - +
76G PHE* 1.3 79.4 - - + +
78G GLU* 1.3 62.6 + - + +
80G ILE* 3.2 21.1 - - + +
81G MET* 3.7 15.9 - - - +
81H MET* 3.0 21.8 - - + +
84H ALA* 3.2 25.2 - - + +
85H ARG* 2.3 48.1 + - - -
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Residues in contact with GLU 78 (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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66G LEU* 3.4 29.9 - - - +
67G ASP* 3.9 2.0 - - - -
68G THR* 3.2 29.4 + - - +
69G ASN* 3.1 17.9 + - - +
73G GLN 3.0 4.5 - - - +
74G LEU* 3.1 5.4 - - + -
75G SER* 2.8 43.4 + - - +
77G GLU* 1.3 76.1 - - + +
79G PHE* 1.3 67.1 + - - +
81G MET* 3.3 20.2 + - - +
188G CA 2.5 30.6 - - - -
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Residues in contact with PHE 79 (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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15G ILE* 4.6 17.9 - - + -
18G THR* 6.4 0.2 - - + -
19G PHE* 3.9 32.8 - + + -
32G LEU* 3.7 15.5 - - + -
37G PHE* 4.0 22.2 - + - -
40G LEU* 3.9 40.6 - - + -
45G LEU* 5.4 0.2 - - + -
66G LEU* 4.3 1.2 - - - +
74G LEU* 4.6 10.9 - - + +
75G SER 2.9 17.8 + - - +
76G PHE* 3.5 4.0 - + - +
78G GLU* 1.3 77.2 - - - +
80G ILE* 1.3 70.2 + - + +
82G LEU* 2.8 44.1 + - + +
83G MET* 6.3 2.5 - - + -
8H LEU* 4.6 12.6 - - + -
12H ILE* 5.8 5.4 - - + -
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Residues in contact with ILE 80 (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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15G ILE* 4.8 3.8 - - + -
76G PHE* 3.0 50.1 + - + +
77G GLU* 3.2 25.4 - - - +
79G PHE* 1.3 83.8 - - + +
81G MET* 1.3 59.1 + - + +
82G LEU 2.9 0.9 - - - -
83G MET* 2.9 49.6 + - + +
80H ILE* 3.6 44.3 - - + +
81H MET* 4.5 5.8 - - - +
83H MET* 4.7 4.9 - - + -
84H ALA* 4.9 2.2 - - + -
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Residues in contact with MET 81 (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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66G LEU* 4.1 8.7 - - + +
68G THR* 6.2 4.5 - - + -
77G GLU 3.7 16.4 - - - +
78G GLU* 3.3 12.5 + - - +
79G PHE 2.9 1.6 + - - -
80G ILE* 1.3 79.9 - - + +
82G LEU* 1.3 62.9 + - - +
83G MET 3.0 0.4 - - - -
84G ALA* 3.0 13.9 + - + +
85G ARG* 3.1 26.7 + - - +
77H GLU* 3.5 52.9 - - + +
80H ILE* 4.0 16.8 - - + -
81H MET* 3.7 26.5 - - + -
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Residues in contact with LEU 82 (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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37G PHE* 4.3 21.3 - - + -
45G LEU* 3.7 30.7 - - + -
49G LEU* 4.6 10.5 - - + -
62G ILE* 4.1 22.9 - - + -
66G LEU* 3.7 14.8 - - + +
79G PHE* 2.8 27.1 + - + +
81G MET* 1.3 79.7 - - - +
83G MET* 1.3 63.1 + - + +
85G ARG* 3.0 21.2 + - + -
86G LEU* 3.3 25.7 + - + +
489G CPS 4.8 7.4 - - + -
12H ILE* 5.9 4.7 - - + -
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Residues in contact with MET 83 (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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15G ILE* 4.0 12.8 - - + -
79G PHE* 6.3 2.0 - - + -
80G ILE* 2.9 33.1 + - + +
82G LEU* 1.3 79.0 - - + +
84G ALA* 1.3 60.7 + - - +
85G ARG 3.3 0.5 + - - -
86G LEU* 3.4 28.2 + - - +
12H ILE* 3.8 47.3 - - + +
15H ILE* 4.3 12.6 - - + -
16H ILE* 4.0 6.5 - - + +
76H PHE* 3.8 16.3 - - + -
80H ILE* 4.1 15.7 - - + -
83H MET* 3.9 29.6 - - + -
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Residues in contact with ALA 84 (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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80G ILE 4.0 0.4 + - - -
81G MET* 3.0 14.3 + - - +
83G MET* 1.3 78.8 - - - +
85G ARG* 1.3 64.3 + - - +
86G LEU 3.3 2.7 + - - -
76H PHE* 3.7 23.0 - - + -
77H GLU* 3.3 41.7 - - + +
80H ILE* 4.8 2.0 - - + -
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Residues in contact with ARG 85 (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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51B LYS* 4.5 4.7 - - - +
65G ASP* 2.4 57.3 + - - +
66G LEU* 4.0 17.9 - - + +
68G THR* 5.0 8.3 - - - +
81G MET* 3.1 26.0 + - - +
82G LEU* 3.0 18.0 + - + +
84G ALA* 1.3 82.7 - - - +
86G LEU* 1.3 66.3 + - - +
489G CPS 4.2 32.4 + - + +
77H GLU* 5.3 8.7 + - - -
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Residues in contact with LEU 86 (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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48G PHE* 3.8 34.3 - - + -
49G LEU* 4.9 5.8 - - + -
82G LEU* 3.3 28.5 - - + +
83G MET* 3.5 18.4 - - - +
84G ALA 3.3 4.7 - - - -
85G ARG* 1.3 84.1 - - - +
489G CPS 2.6 55.9 - - + +
12H ILE* 3.8 22.0 - - + -
16H ILE* 4.2 9.4 - - + -
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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