Contacts of the helix formed by residues 75 - 81 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D PHE* 3.7 1.6 - - - -
30D ASP 4.5 1.1 - - - -
31D THR* 4.2 15.7 - - - +
73D GLN 3.9 0.6 + - - -
74D LEU* 1.3 77.7 - - - +
76D PHE* 1.3 66.2 + - - +
77D GLU* 3.6 10.5 + - - +
78D GLU* 2.7 39.1 + - - +
79D PHE* 2.9 20.8 + - - +
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Residues in contact with PHE 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C MET* 4.0 25.4 - - + -
84C ALA* 4.0 19.1 - - + -
15D ILE* 3.7 16.8 - - + -
16D ILE* 3.4 48.5 - - + -
19D PHE* 3.4 45.3 - + + -
20D HIS* 5.4 6.5 - + + -
30D ASP 4.5 1.8 + - - +
75D SER* 1.3 72.1 - - - +
77D GLU* 1.3 61.9 + - - +
79D PHE* 3.2 2.8 + + - +
80D ILE* 3.0 50.1 + - + +
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Residues in contact with GLU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C MET* 3.1 34.5 - - + +
84C ALA* 4.0 17.8 - - + +
75D SER* 3.6 9.8 + - - +
76D PHE* 1.3 80.3 - - - +
78D GLU* 1.3 64.9 + - + +
80D ILE* 3.2 21.1 - - - +
81D MET* 3.4 11.4 - - - +
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Residues in contact with GLU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LEU* 3.4 31.4 - - - +
67D ASP* 4.1 1.1 - - - -
68D THR* 3.3 30.4 + - - +
69D ASN* 2.8 14.1 + - - +
73D GLN 3.0 3.9 - - - +
74D LEU* 3.2 4.2 - - + -
75D SER* 2.7 39.2 + - - +
77D GLU* 1.3 80.8 - - + +
79D PHE* 1.3 66.2 + - - +
81D MET* 3.3 22.8 + - - +
188D CA 2.5 30.4 - - - -
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Residues in contact with PHE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 4.7 12.6 - - + -
12C ILE* 6.0 3.1 - - + -
15D ILE* 4.4 19.5 - - + -
18D THR* 6.0 0.2 - - + -
19D PHE* 3.8 32.8 - + + -
32D LEU* 3.7 13.7 - - + -
37D PHE* 4.0 24.5 - + - -
40D LEU* 3.7 37.7 - - + -
45D LEU* 5.4 0.2 - - + -
66D LEU* 4.5 1.9 - - + +
74D LEU* 4.4 10.7 - - + +
75D SER 2.9 16.7 + - - +
76D PHE* 3.5 3.8 - + - +
78D GLU* 1.3 79.2 - - - +
80D ILE* 1.3 69.3 + - + +
82D LEU* 2.9 43.4 + - + +
83D MET* 5.5 1.8 - - + -
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Residues in contact with ILE 80 (chain D).
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* 3.4 38.3 - - + +
81C MET* 4.2 9.4 - - - -
83C MET* 4.6 8.3 - - + -
84C ALA* 4.2 12.8 - - + +
15D ILE* 4.3 0.4 - - + -
76D PHE* 3.0 40.9 + - + +
77D GLU* 3.2 28.9 - - - +
79D PHE* 1.3 81.9 - - + +
81D MET* 1.3 60.2 + - - +
82D LEU 2.9 0.9 - - - -
83D MET* 2.9 50.7 + - + +
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Residues in contact with MET 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C GLU* 3.4 42.0 - - + +
80C ILE* 4.0 14.1 - - + -
81C MET* 4.0 24.9 - - - +
66D LEU* 4.3 8.3 - - + -
68D THR* 6.3 2.9 - - + -
77D GLU* 3.4 15.3 - - + +
78D GLU* 3.4 13.2 - - - +
79D PHE 3.0 0.8 + - - -
80D ILE* 1.3 77.3 - - - +
82D LEU* 1.3 61.0 + - - +
83D MET 3.0 0.4 - - - -
84D ALA* 3.0 23.7 + - + +
85D ARG* 3.5 14.7 + - - +
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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