Contacts of the helix formed by residues 6 - 24 (chain A) 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 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS 3.3 4.3 + - - -
5A MET* 1.3 78.7 - - - +
7A GLN* 1.3 61.4 + - - +
8A LEU* 3.4 3.0 + - - +
9A GLU* 2.9 22.5 + - - +
10A ARG* 3.1 23.6 + - - +
44B ASP* 2.6 37.7 + - - -
46B GLN* 3.5 24.9 - - - +
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Residues in contact with GLN 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A MET 4.2 6.5 + - - -
6A SER* 1.3 76.7 + - - +
8A LEU* 1.3 65.0 + - - +
10A ARG* 3.3 14.8 + - - +
11A ASN* 2.5 42.9 + - - +
14B THR* 4.6 6.5 - - + -
44B ASP* 5.3 0.6 + - - -
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Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER* 3.3 7.3 + - - +
7A GLN* 1.3 79.1 - - - +
9A GLU* 1.3 63.1 + - - +
11A ASN* 3.3 2.3 + - - +
12A ILE* 2.9 41.6 + - + +
14B THR* 4.6 6.9 - - + +
15B ILE* 4.1 29.4 - - + +
18B THR* 4.1 30.5 + - + +
40B LEU* 4.0 23.1 - - + -
44B ASP* 4.0 17.6 + - + +
45B LEU* 3.9 22.4 - - + -
79B PHE* 4.6 11.4 - - + -
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Residues in contact with GLU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A MET* 3.4 7.5 - - + -
6A SER* 2.9 28.6 + - - +
8A LEU* 1.3 77.2 - - - +
10A ARG* 1.3 61.2 + - - +
12A ILE* 3.4 2.0 + - - +
13A GLU* 3.1 19.4 + - - +
44B ASP 3.3 10.5 - - - +
45B LEU* 3.1 18.8 - - + -
46B GLN* 3.6 2.5 - - - +
47B ASN* 2.7 56.3 + - - +
48B PHE* 2.8 46.9 + - + -
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Residues in contact with ARG 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A THR 4.7 4.8 + - - -
5A MET* 3.4 41.5 - - + +
6A SER 3.1 21.4 + - - +
7A GLN* 3.8 17.5 + - - +
8A LEU 3.3 0.2 - - - -
9A GLU* 1.3 76.1 - - - +
11A ASN* 1.3 61.1 + - - +
13A GLU* 3.4 19.3 + - - +
14A THR* 2.9 34.7 + - - +
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Residues in contact with ASN 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLN* 2.5 43.0 + - - +
8A LEU 3.8 2.9 - - - +
10A ARG* 1.3 77.6 - - - +
12A ILE* 1.3 64.2 + - - +
14A THR* 3.4 2.5 + - - -
15A ILE* 3.0 28.2 + - - +
10B ARG* 4.1 1.4 - - - +
11B ASN* 2.8 46.3 + - - +
14B THR* 3.4 33.9 + - + +
15B ILE* 4.6 6.1 - - + -
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 2.9 41.0 + - + +
9A GLU 3.7 3.8 - - - +
11A ASN* 1.3 74.9 - - - +
13A GLU* 1.3 66.2 + - - +
15A ILE* 3.1 6.0 + - - +
16A ILE* 3.0 33.3 + - + +
15B ILE* 3.9 22.9 - - + -
45B LEU* 4.3 16.4 - - + -
48B PHE* 3.9 18.6 - - + -
79B PHE* 6.1 4.0 - - + -
82B LEU* 6.2 3.6 - - + -
83B MET* 3.9 28.4 - - + +
86B LEU* 4.0 13.7 - - + -
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A MET* 3.7 22.2 - - - +
9A GLU 3.1 17.5 + - - +
10A ARG* 3.6 27.0 + - - +
12A ILE* 1.3 78.1 - - - +
14A THR* 1.3 60.8 + - - +
16A ILE* 3.4 8.6 + - - +
17A ASN* 2.9 52.3 + - - +
48B PHE* 4.5 10.7 - - + -
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Residues in contact with THR 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 2.9 22.4 + - - +
11A ASN 3.6 3.4 - - - -
12A ILE 3.2 0.2 - - - -
13A GLU* 1.3 78.2 + - - +
15A ILE* 1.3 58.1 + - - +
17A ASN* 3.8 6.5 - - + +
18A THR* 2.7 41.5 + - - +
7B GLN* 3.7 32.7 + - + +
11B ASN* 2.7 33.9 + - - +
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Residues in contact with ILE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ASN 3.0 11.3 + - - +
12A ILE* 3.1 7.8 + - - +
14A THR* 1.3 72.2 - - - +
16A ILE* 1.3 67.8 + - - +
18A THR* 3.3 5.3 + - - -
19A PHE* 3.0 23.0 + - - +
76A PHE* 4.0 21.8 - - + -
79A PHE* 5.2 8.8 - - + -
80A ILE* 4.6 9.4 - - + -
83A MET* 3.8 19.5 - - + -
8B LEU* 4.1 15.1 - - + +
11B ASN* 3.5 28.9 - - + +
12B ILE* 4.2 3.4 - - + +
15B ILE* 3.2 35.0 - - + -
83B MET* 4.7 4.3 - - - -
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Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.0 34.0 + - + +
13A GLU* 3.6 10.8 - - - +
15A ILE* 1.3 76.5 - - - +
17A ASN* 1.3 69.5 + - - +
19A PHE* 3.2 2.9 + - - +
20A HIS* 2.8 49.6 + - + +
76A PHE* 3.6 27.8 - - + -
48B PHE* 6.1 0.9 - - + -
83B MET 4.2 15.7 - - - +
86B LEU* 5.1 10.5 - - + +
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Residues in contact with ASN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU* 2.9 41.2 + - - +
14A THR* 3.9 7.1 - - - +
16A ILE* 1.3 83.6 - - - +
18A THR* 1.3 56.6 + - - +
20A HIS* 3.5 5.7 + - - +
21A GLN* 2.9 29.5 + - - +
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Residues in contact with THR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 2.7 31.7 + - - +
15A ILE 3.8 3.4 - - - -
17A ASN* 1.3 73.3 - - - +
19A PHE* 1.3 68.8 + - - +
21A GLN* 3.3 21.0 + - - +
22A TYR* 3.3 34.4 - - + -
40A LEU* 4.8 2.5 - - + -
44A ASP* 4.3 9.6 - - - +
7B GLN* 4.4 6.9 + - - -
8B LEU* 4.2 32.8 - - + +
11B ASN* 4.7 0.2 + - - -
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Residues in contact with PHE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE 3.0 14.0 + - - +
16A ILE 3.2 6.9 + - - +
18A THR* 1.3 76.4 - - - +
20A HIS* 1.3 82.2 + + - +
22A TYR* 3.1 6.9 + - - +
23A SER* 2.9 38.6 + - - -
30A ASP 3.3 27.6 - - - -
32A LEU* 3.6 26.7 - - + +
40A LEU* 4.6 8.7 - - - -
74A LEU 3.6 12.8 - - - -
76A PHE* 3.4 46.2 - + + -
79A PHE* 3.9 29.1 - + + -
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Residues in contact with HIS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 2.8 44.1 + - + +
17A ASN* 4.0 4.9 - - - +
19A PHE* 1.3 96.0 - + - +
21A GLN* 1.3 64.3 + - - +
23A SER* 3.3 15.9 - - - -
24A VAL* 3.1 30.0 + - + +
29A PRO 4.7 1.8 - - - +
30A ASP* 4.4 20.9 + - - +
76A PHE* 5.0 8.9 - + + +
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Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASN 2.9 18.2 + - - +
18A THR* 3.3 18.5 + - - +
19A PHE 3.2 0.2 - - - -
20A HIS* 1.3 78.3 - - - +
22A TYR* 1.3 87.7 + - + +
24A VAL* 3.8 8.6 - - - +
25A LYS* 3.7 21.9 - - - +
43A LYS* 4.5 7.3 - - - +
44A ASP* 4.7 3.0 + - - -
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Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A THR* 3.3 24.4 + - + -
19A PHE 3.1 4.1 + - - +
21A GLN* 1.3 93.4 + - - +
23A SER* 1.3 59.9 + - - +
24A VAL 3.3 2.2 - - - -
25A LYS* 3.4 28.4 + - + +
32A LEU* 3.7 17.5 - - + -
36A GLU* 3.1 28.5 - - - +
39A GLU* 3.8 17.7 - - + -
40A LEU* 3.6 43.7 - - + -
43A LYS* 2.9 42.6 + - - +
44A ASP* 2.6 30.1 + - - -
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Residues in contact with SER 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 2.9 25.4 + - - -
20A HIS* 3.3 17.3 + - - +
22A TYR* 1.3 77.5 - - - +
24A VAL* 1.3 58.2 + - - +
25A LYS 3.2 0.2 - - - -
28A HIS 3.0 9.9 - - - +
29A PRO 2.6 22.6 + - - +
30A ASP* 3.9 0.7 - - - -
31A THR 3.4 29.2 - - - -
32A LEU* 3.5 9.1 - - - +
36A GLU* 3.1 2.1 - - - +
187A CA 2.4 24.4 - - - -
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A HIS* 3.1 19.3 + - + +
21A GLN* 3.8 12.8 - - - +
23A SER* 1.3 77.5 + - - +
25A LYS* 1.3 72.2 + - + +
26A LEU* 3.5 1.8 + - - +
27A GLY 5.1 1.0 - - - +
29A PRO* 3.5 27.7 - - + +
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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
------------------------------------------------------------
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