Contacts of the helix formed by residues 75 - 85 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.6 3.1 - - - -
30C ASP 4.3 2.2 - - - -
31C THR* 4.1 17.8 - - - +
73C GLN 4.0 0.4 - - - -
74C LEU* 1.3 77.7 - - - +
76C PHE* 1.3 65.2 + - - +
77C GLU* 3.7 11.6 - - - +
78C GLU* 2.6 37.8 + - - +
79C PHE* 2.9 18.5 + - - +
188C CA 4.3 0.4 - - - -
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Residues in contact with PHE 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 4.4 10.1 - - + -
16C ILE* 3.6 39.0 - - + -
19C PHE* 3.5 45.4 - + + -
20C HIS* 5.4 7.4 - - + +
30C ASP 4.5 1.8 + - - -
75C SER* 1.3 74.1 - - - +
77C GLU* 1.3 65.7 + - - +
79C PHE* 3.0 3.4 + + - +
80C ILE* 2.9 50.7 + - + +
83D MET* 3.7 38.4 - - + -
84D ALA* 3.8 15.7 - - + -
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Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C SER* 3.7 13.0 - - - +
76C PHE* 1.3 79.4 - - - +
78C GLU* 1.3 68.5 + - + +
80C ILE* 3.3 22.9 - - - +
81C MET* 3.6 12.5 - - - +
81D MET* 3.4 27.6 - - + +
84D ALA* 4.0 17.6 - - + +
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Residues in contact with GLU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 3.5 32.5 - - - +
67C ASP* 3.2 5.2 - - - +
68C THR* 3.9 15.9 + - - +
69C ASN* 2.9 17.2 + - - +
73C GLN 2.8 7.3 - - - +
74C LEU* 2.9 5.8 - - + -
75C SER* 2.6 41.8 + - - +
76C PHE 3.2 0.4 - - - -
77C GLU* 1.3 82.7 - - + +
79C PHE* 1.3 63.5 + - - +
81C MET* 3.4 19.5 - - - +
188C CA 2.6 30.6 - - - -
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Residues in contact with PHE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 5.1 11.2 - - + -
19C PHE* 3.6 32.3 - + + -
32C LEU* 3.8 15.0 - - + -
37C PHE* 4.2 14.8 - + - -
40C LEU* 4.1 35.7 - - + -
45C LEU* 5.2 0.9 - - + -
66C LEU* 5.2 1.3 - - + -
74C LEU* 4.6 11.2 - - + +
75C SER 2.9 18.3 + - - +
76C PHE* 3.0 3.8 + + - +
78C GLU* 1.3 74.2 - - - +
80C ILE* 1.3 74.0 + - + +
81C MET 3.1 2.5 - - - -
82C LEU* 2.9 56.1 + - + +
83C MET* 5.9 4.5 - - + -
8D LEU* 4.8 13.2 - - + -
12D ILE* 6.1 3.8 - - + -
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Residues in contact with ILE 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 4.9 1.6 - - + -
76C PHE* 2.9 52.7 + - + +
77C GLU* 3.3 24.5 - - - +
79C PHE* 1.3 77.3 - - + +
81C MET* 1.3 62.8 + - - +
82C LEU 2.8 5.8 - - - -
83C MET* 2.8 49.0 + - + +
80D ILE* 3.4 34.2 - - + +
81D MET* 4.0 22.0 - - + -
83D MET* 4.5 1.8 - - + -
84D ALA* 4.4 3.1 - - + -
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Residues in contact with MET 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LEU* 4.2 11.4 - - + -
77C GLU 3.6 16.4 - - - +
78C GLU* 3.4 13.2 - - - +
79C PHE 3.1 0.6 - - - -
80C ILE* 1.3 78.5 - - - +
82C LEU* 1.3 60.9 + - - +
83C MET 3.1 0.2 - - - -
84C ALA* 3.0 17.3 + - + +
85C ARG* 3.2 11.8 + - - +
77D GLU* 3.1 51.8 - - + +
80D ILE* 4.2 5.6 - - - -
81D MET* 4.0 21.1 - - - +
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C PHE* 4.2 18.2 - - + -
45C LEU* 3.7 29.4 - - + -
49C LEU* 4.7 11.9 - - + -
62C ILE* 4.1 21.8 - - + -
66C LEU* 4.0 13.9 - - + +
79C PHE* 2.9 36.8 + - + +
80C ILE 2.8 0.4 - - - -
81C MET* 1.3 79.4 - - - +
83C MET* 1.3 62.7 + - + +
84C ALA 3.4 0.2 + - - -
85C ARG* 3.4 27.9 + - + +
86C LEU* 3.5 13.2 + - + +
12D ILE* 6.3 2.9 - - + -
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Residues in contact with MET 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 4.1 17.7 - - + -
79C PHE* 5.9 4.3 - - + -
80C ILE* 2.8 51.1 + - + +
82C LEU* 1.3 78.9 - - + +
84C ALA* 1.3 63.0 + - - +
86C LEU* 3.4 18.7 + - - +
12D ILE* 3.7 49.1 - - + +
15D ILE* 4.7 6.1 - - - -
16D ILE* 4.4 8.1 - - - +
76D PHE* 4.0 18.5 - - + -
80D ILE* 4.6 9.6 - - + -
83D MET* 4.1 26.0 - - + -
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ILE 4.0 0.4 + - - -
81C MET* 3.0 13.4 + - + +
83C MET* 1.3 76.4 - - - +
85C ARG* 1.3 57.8 + - - +
86C LEU 2.8 17.1 + - - -
76D PHE* 4.0 17.2 - - + -
77D GLU* 4.0 36.3 - - + +
80D ILE* 4.2 5.1 - - + +
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Residues in contact with ARG 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LEU* 4.4 18.4 - - - +
52C GLU* 4.5 8.9 + - - -
58C VAL* 5.2 4.6 - - - +
62C ILE* 3.9 36.8 - - - +
65C ASP* 4.4 16.0 + - - -
66C LEU* 5.3 6.7 - - + -
81C MET 3.2 9.3 + - - +
82C LEU* 3.4 25.4 + - - +
84C ALA* 1.3 76.6 - - - +
86C LEU* 1.3 64.2 + - - +
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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