Contacts of the helix formed by residues 4 - 29 (chain A) in PDB entry 3QIR
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 CYS 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 1.4 73.1 - - - +
5A VAL* 1.3 65.3 + - - +
6A LEU* 3.3 3.8 - - + +
7A ASP* 3.0 39.7 + - - +
8A VAL* 3.1 12.7 + - - +
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Residues in contact with VAL 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP 3.8 4.6 + - - +
4A CYS* 1.3 70.9 - - - +
6A LEU* 1.3 57.2 + - - +
8A VAL* 3.3 8.8 + - + +
9A MET* 2.9 30.5 + - + +
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A CYS* 3.3 3.5 - - + +
5A VAL* 1.3 78.2 - - - +
7A ASP* 1.3 54.9 + - - +
9A MET* 3.3 11.2 + - + +
10A HIS* 2.8 69.0 + - + +
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Residues in contact with ASP 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 5.6 3.1 - - + -
4A CYS* 3.0 35.0 + - + +
6A LEU* 1.3 74.2 - - - +
8A VAL* 1.4 63.5 + - - +
10A HIS* 3.2 16.1 + - - +
11A ALA* 3.1 22.9 + - - +
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Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 5.4 8.0 - - + +
4A CYS 3.1 10.4 + - - +
5A VAL* 3.3 12.1 + - - +
7A ASP* 1.4 73.2 - - - +
9A MET* 1.3 63.1 + - - +
11A ALA* 3.3 9.6 + - - +
12A ILE* 3.2 32.6 + - + +
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Residues in contact with MET 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 2.9 19.6 + - + +
6A LEU* 3.4 16.4 - - + +
8A VAL* 1.3 74.0 - - - +
10A HIS* 1.4 59.6 + - - +
12A ILE* 3.3 12.5 + - - +
13A TYR* 2.9 30.0 + - - +
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Residues in contact with HIS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 2.8 58.3 + - + +
7A ASP* 3.2 17.0 + - - +
9A MET* 1.4 72.4 - - - +
11A ALA* 1.4 57.2 + - - +
13A TYR* 3.3 12.7 + - - +
14A GLN* 2.9 31.6 + - - +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASP 3.1 12.5 + - - +
8A VAL* 3.3 11.4 + - - +
10A HIS* 1.4 73.1 - - - +
12A ILE* 1.3 64.7 + - + +
14A GLN* 3.5 7.8 + - - +
15A GLN* 3.2 21.3 + - - +
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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
----------------------------------------------------------
8A VAL* 3.2 27.2 + - + +
9A MET* 3.7 9.4 - - - +
11A ALA* 1.3 74.0 - - + +
13A TYR* 1.3 63.6 + - - +
15A GLN* 3.4 6.2 + - + +
16A ASN* 2.8 46.1 + - - +
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Residues in contact with TYR 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A MET 2.9 17.9 + - - +
10A HIS* 3.3 13.4 + - - +
12A ILE* 1.3 75.6 - - - +
14A GLN* 1.3 70.1 + - - +
16A ASN* 3.2 8.5 + - + +
17A LYS* 2.9 51.3 + - + +
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Residues in contact with GLN 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS 2.9 16.7 + - - +
11A ALA* 3.7 8.7 - - - +
12A ILE 3.3 0.2 - - - -
13A TYR* 1.3 90.4 - - - +
15A GLN* 1.4 63.3 + - - +
17A LYS* 3.5 14.6 + - - +
18A GLU* 3.3 48.2 + - - +
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Residues in contact with GLN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 3.2 13.4 + - - +
12A ILE* 3.8 9.9 - - + +
13A TYR 3.3 0.2 - - - -
14A GLN* 1.4 76.3 - - - +
16A ASN* 1.3 63.2 + - - +
18A GLU* 3.6 11.8 + - - +
19A HIS* 3.2 21.0 + - - +
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Residues in contact with ASN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 2.8 40.4 + - - +
13A TYR* 3.6 10.5 - - + +
15A GLN* 1.3 79.3 - - - +
17A LYS* 1.4 58.4 + - - +
19A HIS* 3.5 9.9 + - - +
20A PHE* 3.1 27.2 + - - +
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Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 2.9 40.6 + - + +
14A GLN* 3.8 20.2 - - - +
15A GLN 3.4 0.2 - - - -
16A ASN* 1.4 68.7 - - - +
18A GLU* 1.4 60.0 + - - +
20A PHE* 3.2 11.7 + - + +
21A GLN* 3.0 59.5 + - + +
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Residues in contact with GLU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN* 3.3 36.7 + - - +
15A GLN* 3.7 11.3 - - - +
16A ASN 3.4 0.2 - - - -
17A LYS* 1.4 77.6 - - + +
19A HIS* 1.4 56.0 + - - +
21A GLN* 3.3 10.5 + - - +
22A ASP* 2.9 33.5 + - - +
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Residues in contact with HIS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN 3.2 12.8 + - - +
16A ASN* 3.6 14.1 - - - +
17A LYS 3.3 0.2 - - - -
18A GLU* 1.4 78.6 - - - +
20A PHE* 1.3 58.4 + - - +
22A ASP* 3.8 5.8 - - - +
23A GLU* 3.0 37.2 + - + +
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Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN 3.1 13.5 + - - +
17A LYS* 3.2 12.8 + - + +
19A HIS* 1.3 80.5 - - + +
21A GLN* 1.3 67.7 + - + +
23A GLU* 3.2 7.4 + - + +
24A CYS* 3.0 44.3 + - - +
49A TRP* 3.7 32.8 - + - -
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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
----------------------------------------------------------
17A LYS* 3.0 41.6 + - - +
18A GLU* 3.8 9.2 - - - +
20A PHE* 1.3 85.1 - - + +
22A ASP* 1.4 56.0 + - - +
24A CYS 3.4 0.9 + - - -
25A THR* 3.1 36.4 + - - +
49A TRP* 3.6 61.2 + - + +
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Residues in contact with ASP 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU 2.9 18.0 + - - +
19A HIS* 3.9 5.8 - - - +
21A GLN* 1.4 73.2 - - - +
23A GLU* 1.3 58.5 + - - +
25A THR* 3.4 17.1 + - - -
26A LYS* 3.4 14.9 + - - +
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A HIS* 3.0 27.1 + - + +
20A PHE* 3.2 8.9 + - + +
22A ASP* 1.3 77.4 - - - +
24A CYS* 1.4 62.7 + - - +
26A LYS* 3.6 4.9 + - - +
27A LEU* 3.2 24.1 + - - +
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Residues in contact with CYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.0 44.4 + - - +
21A GLN 3.6 4.9 - - - +
23A GLU* 1.4 73.1 - - - +
25A THR* 1.4 60.5 + - - +
27A LEU* 3.3 6.6 + - - +
28A LEU* 2.9 33.6 + - + +
47A VAL* 6.1 0.7 - - + -
49A TRP* 3.6 20.9 - - + -
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN 3.1 19.1 + - - +
22A ASP* 3.4 13.2 + - - -
24A CYS* 1.4 72.9 - - - +
26A LYS* 1.4 66.6 + - - +
28A LEU* 3.2 2.4 + - - +
29A VAL* 2.9 36.6 + - - +
46A ASP* 4.3 15.5 - - - +
47A VAL* 4.3 16.4 - - + +
49A TRP* 3.7 20.6 - - + +
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP 3.4 16.0 + - - +
23A GLU* 3.8 7.0 - - - +
24A CYS 3.4 0.4 - - - -
25A THR* 1.4 82.8 + - - +
27A LEU* 1.3 60.4 + - - +
29A VAL* 4.2 9.4 - - - +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU 3.2 15.9 + - - +
24A CYS* 3.6 6.5 - - - +
25A THR 3.3 0.2 - - - -
26A LYS* 1.3 80.5 - - - +
28A LEU* 1.4 57.6 + - + +
29A VAL 4.8 1.0 - - - +
31A ASN* 5.4 3.5 - - - +
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A CYS* 2.9 20.7 + - + +
25A THR* 4.3 2.0 - - - +
27A LEU* 1.4 73.3 - - + +
29A VAL* 1.4 66.8 + - - +
30A GLY 3.3 0.3 + - - -
31A ASN* 3.2 24.6 + - - +
44A ILE* 3.7 29.3 - - + +
87A LEU* 5.7 4.7 - - + -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 2.9 26.5 + - - +
26A LYS* 4.2 9.1 - - - +
27A LEU 4.8 1.0 - - - +
28A LEU* 1.4 70.8 - - - +
30A GLY* 1.3 57.8 + - - +
31A ASN 3.9 0.5 + - - -
44A ILE* 3.4 16.7 - - + +
45A ASP* 4.5 15.3 - - - +
46A ASP* 4.9 3.6 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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