Contacts of the helix formed by residues 61 - 76 (chain D) in PDB entry 1IRI
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 THR 61 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D TRP* 3.9 8.4 - - + -
23D GLU* 4.7 12.8 - - + +
24D LEU* 4.0 16.4 - - + -
29D LEU* 3.9 24.2 - - + -
36D ARG* 4.6 1.3 - - - +
40D PHE* 3.4 10.5 - - - -
60D VAL* 1.3 78.9 - - - +
62D GLU* 1.3 70.1 + - - +
63D ASP* 3.9 5.4 + - - +
64D VAL* 3.2 23.7 + - - +
65D MET* 3.0 21.7 + - - +
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Residues in contact with GLU 62 (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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33D ASN* 3.8 13.2 + - - -
36D ARG* 5.4 0.3 + - - -
39D HIS* 3.6 27.7 + - + +
40D PHE* 3.4 24.8 - - + -
61D THR* 1.3 77.6 - - - +
63D ASP* 1.3 67.9 + - - +
65D MET* 3.2 5.5 + - - +
66D ARG* 3.0 23.5 + - - +
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Residues in contact with ASP 63 (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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16D TRP* 4.5 18.0 + - + +
61D THR* 3.2 7.2 + - - +
62D GLU* 1.3 78.8 - - - +
64D VAL* 1.3 63.3 + - - +
66D ARG* 2.4 42.3 + - - +
67D MET* 2.9 31.6 + - + +
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Residues in contact with VAL 64 (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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13D LEU* 4.4 1.3 - - + +
16D TRP* 3.6 36.6 - - + -
24D LEU* 5.0 0.2 - - + -
60D VAL* 3.9 11.9 - - + -
61D THR* 3.2 30.4 + - + +
63D ASP* 1.3 75.2 - - - +
65D MET* 1.3 65.1 + - - +
67D MET* 3.3 10.9 + - + +
68D LEU* 3.0 39.2 + - + +
326D TRP* 3.8 33.0 - - + -
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Residues in contact with MET 65 (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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40D PHE* 3.5 22.4 - - + -
55D TYR* 3.8 25.8 - - + +
60D VAL* 3.8 24.2 - - + -
61D THR 3.0 14.6 + - - +
62D GLU* 3.6 7.4 - - - +
64D VAL* 1.3 76.3 - - - +
66D ARG* 1.3 63.7 + - - +
68D LEU* 3.1 23.1 + - + +
69D VAL* 3.0 29.3 + - + +
319D LEU* 4.0 28.5 - - + +
322D LEU* 5.7 1.6 - - + -
323D LEU* 4.5 10.3 - - + -
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Residues in contact with ARG 66 (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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12D LYS* 4.1 20.6 - - - +
62D GLU 3.0 12.2 + - - +
63D ASP* 2.4 52.5 + - - +
65D MET* 1.3 76.1 - - - +
67D MET* 1.3 66.9 + - - +
69D VAL* 3.3 9.1 + - - +
70D ASP* 3.1 32.4 + - - +
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Residues in contact with MET 67 (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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9D GLN* 4.6 7.2 - - - +
12D LYS* 3.9 49.1 - - + +
13D LEU* 3.7 25.0 - - + +
16D TRP* 3.3 49.6 - - + +
63D ASP* 2.9 16.0 + - + +
64D VAL* 3.8 24.7 - - + +
66D ARG* 1.3 83.5 - - - +
68D LEU* 1.3 62.8 + - - +
70D ASP* 3.0 11.2 + - - +
71D LEU* 2.9 22.3 + - - +
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Residues in contact with LEU 68 (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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13D LEU* 3.9 28.5 - - + -
60D VAL* 4.9 1.8 - - + -
64D VAL* 3.0 35.4 + - + +
65D MET* 3.1 26.2 + - + +
67D MET* 1.3 76.0 - - - +
69D VAL* 1.3 62.3 + - - +
71D LEU* 3.2 7.4 + - + +
72D ALA 3.1 15.8 + - - -
322D LEU* 3.2 61.8 - - + +
323D LEU* 4.9 1.8 - - - +
325D ILE* 4.8 4.7 - - + -
326D TRP* 4.2 18.2 - - + +
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Residues in contact with VAL 69 (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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65D MET* 3.0 19.1 + - + +
66D ARG* 3.7 9.9 - - - +
68D LEU* 1.3 77.7 - - - +
70D ASP* 1.3 63.2 + - - +
72D ALA* 2.9 14.6 + - - +
73D LYS* 2.9 36.3 + - - +
312D LEU* 4.0 23.1 - - + -
313D GLU* 4.1 31.4 - - + +
319D LEU* 4.7 7.4 - - + -
322D LEU* 3.9 15.0 - - + -
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Residues in contact with ASP 70 (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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9D GLN* 3.3 30.3 - - - +
12D LYS* 4.7 8.1 + - - -
66D ARG* 3.1 31.1 + - - +
67D MET* 3.0 10.1 + - - +
69D VAL* 1.3 77.3 - - - +
71D LEU* 1.3 51.5 + - - +
73D LYS* 3.1 24.0 + - - +
74D SER* 2.7 38.1 + - - -
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Residues in contact with LEU 71 (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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4D LEU* 3.9 20.2 - - + -
7D ASP* 3.8 23.1 - - - +
9D GLN* 4.0 8.9 - - + +
10D PHE* 3.9 15.7 - - + +
13D LEU* 4.9 7.0 - - + -
67D MET 2.9 11.2 + - - +
68D LEU* 3.2 17.3 - - + +
69D VAL 3.1 0.2 - - - -
70D ASP* 1.3 73.1 - - - +
72D ALA* 1.3 62.7 + - - +
74D SER* 4.4 0.4 - - - -
75D ARG* 2.8 53.7 + - + +
322D LEU* 4.7 8.7 - - + -
325D ILE* 4.2 26.0 - - + -
504D ILE* 4.3 8.1 - - + -
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Residues in contact with ALA 72 (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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68D LEU 3.1 7.6 + - - +
69D VAL 2.9 10.1 + - - +
71D LEU* 1.3 80.6 - - - +
73D LYS* 1.3 60.8 + - - +
76D GLY 3.1 4.0 + - - -
77D VAL* 3.0 51.6 + - + +
312D LEU* 3.8 16.3 - - + +
318D VAL* 4.8 5.4 - - + -
322D LEU* 4.3 18.8 - - + +
504D ILE* 4.6 5.6 - - + -
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Residues in contact with LYS 73 (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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69D VAL* 2.9 33.1 + - + +
70D ASP* 3.4 26.1 + - - +
72D ALA* 1.3 74.6 - - - +
74D SER* 1.3 66.6 + - - +
76D GLY* 3.0 15.8 + - - -
77D VAL 5.1 0.4 - - - +
78D GLU* 4.5 10.5 - - - +
312D LEU* 4.0 18.2 - - + -
313D GLU* 5.0 7.3 + - - -
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Residues in contact with SER 74 (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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7D ASP* 2.4 30.0 + - - +
8D PRO* 4.9 4.3 - - - +
9D GLN* 3.7 17.0 - - - +
70D ASP 2.7 19.6 + - - -
71D LEU 3.9 2.0 - - - -
73D LYS* 1.3 75.5 - - - +
75D ARG* 1.3 62.5 + - - +
76D GLY* 3.4 0.7 + - - -
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Residues in contact with ARG 75 (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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3D ALA* 3.8 16.0 - - - +
4D LEU* 4.4 8.3 - - - +
7D ASP* 3.7 25.1 - - - +
71D LEU* 2.8 41.8 + - + +
72D ALA 4.2 1.8 - - - +
74D SER* 1.3 74.5 + - - +
76D GLY* 1.3 62.1 + - - +
77D VAL* 3.5 1.1 - - + -
503D ILE* 3.2 24.6 + - - +
504D ILE* 3.1 40.9 + - + +
506D ASP* 3.0 42.2 + - - +
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Residues in contact with GLY 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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72D ALA 3.1 0.2 + - - -
73D LYS 3.0 14.8 + - - -
74D SER 3.2 1.7 - - - -
75D ARG* 1.3 79.9 - - - +
77D VAL* 1.3 65.8 + - - +
78D GLU 3.3 2.9 + - - -
79D ALA* 3.3 11.6 + - - +
80D ALA* 3.0 24.3 + - - +
83D ARG* 5.0 1.6 + - - -
503D ILE* 4.2 1.1 - - - +
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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