Contacts of the helix formed by residues 7 - 21 (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 ASP 7 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D ALA 3.0 13.7 + - - +
4D LEU* 3.2 17.7 + - - +
6D ARG* 1.3 76.4 - - - +
8D PRO* 1.3 72.1 - - - +
9D GLN* 2.3 34.4 + - - +
10D PHE* 2.6 14.6 + - + +
11D GLN* 3.1 20.3 + - - +
71D LEU* 3.8 9.4 - - + +
74D SER* 2.4 32.3 + - - +
75D ARG* 3.7 16.4 - - - -
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Residues in contact with PRO 8 (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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6D ARG 3.0 8.5 - - - +
7D ASP* 1.3 86.4 - - - +
9D GLN* 1.3 68.8 + - + +
11D GLN* 3.2 12.9 + - + +
12D LYS* 2.9 28.2 + - - +
74D SER* 4.9 4.0 - - - +
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Residues in contact with GLN 9 (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* 2.3 21.0 + - - +
8D PRO* 1.3 79.4 - - + +
10D PHE* 1.3 53.9 + - - +
12D LYS* 3.2 25.4 + - - +
13D LEU* 2.9 28.3 + - - +
67D MET* 4.6 7.4 - - - +
70D ASP* 3.3 31.1 - - - +
71D LEU* 4.0 21.1 - - + +
74D SER* 3.7 23.8 - - - +
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Residues in contact with PHE 10 (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* 3.1 58.1 - - + +
5D THR* 3.7 25.1 - - + -
7D ASP* 2.6 13.4 + - - +
9D GLN* 1.3 71.8 - - - +
11D GLN* 1.3 58.5 + - - +
13D LEU* 2.9 14.3 + - + +
14D GLN* 2.8 69.6 + - + +
71D LEU* 3.9 13.1 - - + +
325D ILE* 5.2 2.7 - - + -
329D ASN* 3.8 33.2 - - + -
330D CYS* 4.7 7.9 - - - -
373D HIS* 5.4 3.6 - - + -
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Residues in contact with GLN 11 (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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1D MET* 6.1 0.3 - - - +
5D THR 3.2 19.5 - - - +
6D ARG* 3.2 23.1 - - - +
7D ASP 3.1 9.1 + - - +
8D PRO* 3.4 11.7 - - - +
10D PHE* 1.3 79.0 - - + +
12D LYS* 1.3 56.9 + - - +
14D GLN* 3.3 17.3 + - - +
15D GLN* 2.9 30.1 + - - +
18D ARG* 4.9 1.4 + - - -
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Residues in contact with LYS 12 (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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8D PRO 2.9 13.4 + - - +
9D GLN* 3.5 29.4 + - - +
10D PHE 3.2 0.2 - - - -
11D GLN* 1.3 76.5 - - - +
13D LEU* 1.3 58.4 + - - +
15D GLN* 3.4 18.1 + - - +
16D TRP* 2.9 28.8 + - - +
66D ARG* 4.1 14.3 - - - +
67D MET* 3.9 31.2 - - + +
70D ASP* 4.7 6.9 + - - -
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Residues in contact with LEU 13 (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 2.9 13.6 + - - +
10D PHE* 3.0 25.4 - - + +
12D LYS* 1.3 76.7 - - - +
14D GLN* 1.3 60.6 + - - +
16D TRP* 3.0 5.5 + - - +
17D TYR* 2.9 20.8 + - - +
64D VAL* 4.4 2.5 - - + +
67D MET* 3.7 41.2 - - + +
68D LEU* 3.9 26.2 - - + -
71D LEU* 4.9 9.0 - - + -
325D ILE* 5.2 2.2 - - + -
326D TRP* 3.5 42.5 - - + -
330D CYS* 3.7 14.6 - - - -
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Residues in contact with GLN 14 (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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5D THR* 5.0 2.4 - - - +
10D PHE* 2.8 59.3 + - + +
11D GLN* 3.6 22.4 - - - +
13D LEU* 1.3 68.6 - - - +
15D GLN* 1.3 68.7 + - - +
17D TYR* 3.0 11.4 + - - +
18D ARG* 2.9 42.2 + - + +
329D ASN 5.0 4.9 + - - +
330D CYS* 4.4 8.7 - - - -
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Residues in contact with GLN 15 (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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11D GLN 2.9 18.4 + - - +
12D LYS* 3.5 20.0 - - - +
14D GLN* 1.3 76.4 - - - +
16D TRP* 1.3 63.9 + - - +
18D ARG* 3.2 29.5 + - - +
19D GLU* 3.0 48.1 + - + +
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Residues in contact with TRP 16 (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 2.9 12.4 + - - +
13D LEU 3.0 9.2 + - - +
15D GLN* 1.3 76.8 + - - +
17D TYR* 1.3 67.5 + - - +
19D GLU* 3.1 2.8 + - - -
20D HIS* 3.0 63.9 + + + -
21D ARG 4.8 0.2 - - - -
23D GLU* 3.4 22.9 - - - -
24D LEU* 3.9 31.0 - - + -
61D THR* 3.9 15.5 - - - -
63D ASP* 4.5 13.2 + - + +
64D VAL* 3.6 24.9 - - + -
67D MET* 3.3 33.6 - - + +
326D TRP* 4.0 8.7 - + + -
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Residues in contact with TYR 17 (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 2.9 11.2 + - - +
14D GLN* 3.1 13.9 - - - +
16D TRP* 1.3 85.3 - - - +
18D ARG* 1.3 67.7 + - + +
21D ARG* 2.9 51.7 + - + +
24D LEU* 5.4 0.2 - - + -
326D TRP* 4.1 18.8 - + + -
330D CYS* 3.4 35.4 - - + -
331D PHE* 3.3 57.0 + + - -
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Residues in contact with ARG 18 (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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11D GLN 4.9 1.0 + - - -
14D GLN* 2.9 29.3 + - + +
15D GLN* 3.5 45.2 - - - +
17D TYR* 1.3 87.5 - - + +
19D GLU* 1.3 65.1 + - + +
21D ARG* 4.8 3.0 + - - +
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Residues in contact with GLU 19 (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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15D GLN* 3.0 41.8 + - + +
16D TRP* 5.7 0.3 - - - -
18D ARG* 1.3 84.5 + - + +
20D HIS* 1.3 83.8 + - + +
21D ARG 4.0 0.2 - - - -
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Residues in contact with HIS 20 (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* 3.0 68.5 + + + -
19D GLU* 1.3 102.2 + - + +
21D ARG* 1.3 69.0 + - - +
22D SER* 2.6 7.2 + - - -
23D GLU* 2.7 36.9 + - - +
24D LEU* 3.9 2.4 + - - +
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Residues in contact with ARG 21 (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* 4.4 0.8 + - - -
17D TYR* 2.9 50.9 + - + +
18D ARG 4.8 2.6 + - - +
20D HIS* 1.3 75.9 - - - +
22D SER* 1.3 62.7 + - - +
24D LEU* 2.7 64.4 + - - +
59D LEU* 4.3 4.8 - - - +
331D PHE* 4.1 21.1 - - + -
401D MET* 4.8 8.9 - - - +
471D ASN* 3.1 16.8 - - - +
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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