Contacts of the helix formed by residues 4 - 29 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ASP* 1.4 81.7 - - - +
5D VAL* 1.3 66.9 + - - +
6D LEU* 3.8 18.6 - - - -
7D ASP* 3.0 38.5 + - - +
8D VAL* 3.1 13.4 + - - +
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Residues in contact with VAL 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ASP 3.5 5.1 + - - +
4D CYS* 1.3 71.5 - - - +
6D LEU* 1.4 57.8 + - - +
8D VAL* 3.2 10.5 + - + +
9D MET* 2.9 53.1 + - + +
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Residues in contact with LEU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D CYS* 3.3 13.3 - - - -
5D VAL* 1.4 76.9 - - - +
7D ASP* 1.3 53.4 + - - +
9D MET* 3.3 23.7 + - + +
10D HIS* 2.8 67.6 + - + +
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Residues in contact with ASP 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ASP* 4.6 10.3 - - + +
4D CYS* 3.0 32.8 + - + +
6D LEU* 1.3 73.6 - - - +
8D VAL* 1.4 65.8 + - + +
10D HIS* 3.2 17.8 + - - +
11D ALA* 3.1 23.0 + - - +
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Residues in contact with VAL 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ASP* 3.9 24.7 - - + +
4D CYS 3.1 15.9 + - - +
5D VAL* 3.5 11.0 - - + +
7D ASP* 1.4 72.9 - - + +
9D MET* 1.3 62.7 + - + +
11D ALA* 3.3 9.3 + - - +
12D ILE* 3.1 41.0 + - + +
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Residues in contact with MET 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 2.9 36.3 + - + +
6D LEU* 3.4 27.4 - - + +
8D VAL* 1.3 73.5 - - + +
10D HIS* 1.4 60.3 + - - +
12D ILE* 3.3 13.6 + - + +
13D TYR* 2.9 30.0 + - - +
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Residues in contact with HIS 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 2.8 57.1 + - + +
7D ASP* 3.2 19.9 + - - +
9D MET* 1.4 72.0 - - - +
11D ALA* 1.4 58.2 + - - +
13D TYR* 3.3 12.6 + - - +
14D GLN* 2.9 33.0 + - - +
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Residues in contact with ALA 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ASP 3.1 11.6 + - - +
8D VAL* 3.3 11.6 + - - +
10D HIS* 1.4 73.3 - - - +
12D ILE* 1.3 64.1 - - + +
14D GLN* 3.5 6.0 + - - +
15D GLN* 2.9 35.2 + - - +
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Residues in contact with ILE 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 3.1 35.5 + - + +
9D MET* 3.3 12.5 + - + +
11D ALA* 1.3 73.6 - - + +
13D TYR* 1.4 64.9 + - - +
15D GLN* 3.4 6.6 + - + +
16D ASN* 2.8 44.5 + - - +
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Residues in contact with TYR 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D MET 2.9 17.2 + - - +
10D HIS* 3.4 13.7 - - - +
12D ILE* 1.4 76.5 - - - +
14D GLN* 1.3 65.8 + - - +
16D ASN* 3.2 9.4 + - + +
17D LYS* 2.8 64.3 + - + +
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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
----------------------------------------------------------
10D HIS 2.9 16.4 + - - +
11D ALA* 3.6 9.0 - - - +
12D ILE 3.3 0.2 - - - -
13D TYR* 1.3 95.3 - - - +
15D GLN* 1.3 65.6 + - - +
17D LYS* 3.4 29.2 + - - +
18D GLU* 3.2 24.4 + - - +
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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
----------------------------------------------------------
11D ALA* 2.9 32.6 + - - +
12D ILE* 3.7 10.3 - - - +
13D TYR 3.3 0.2 - - - -
14D GLN* 1.3 80.5 - - - +
16D ASN* 1.3 60.2 + - - +
18D GLU* 3.6 8.7 + - - +
19D HIS* 3.2 25.3 + - - +
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Residues in contact with ASN 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ILE* 2.8 40.0 + - - +
13D TYR* 3.6 11.7 - - + +
15D GLN* 1.3 78.0 - - - +
17D LYS* 1.4 58.4 + - - +
19D HIS* 3.5 10.7 + - - +
20D PHE* 3.1 26.9 + - - +
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Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D TYR* 2.8 45.2 + - + +
14D GLN* 3.4 29.4 + - - +
16D ASN* 1.4 73.6 - - - +
18D GLU* 1.3 58.5 + - - +
20D PHE* 3.2 13.1 + - + +
21D GLN* 3.0 59.3 + - + +
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Residues in contact with GLU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLN* 3.2 13.8 + - - +
15D GLN* 3.7 9.6 - - - +
17D LYS* 1.3 74.3 - - - +
19D HIS* 1.3 59.6 + - - +
21D GLN* 3.3 9.6 + - - +
22D ASP* 2.9 42.6 + - - +
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Residues in contact with HIS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLN 3.2 11.9 + - - +
16D ASN* 3.5 15.3 - - - +
17D LYS 3.3 0.2 - - - -
18D GLU* 1.3 79.1 - - - +
20D PHE* 1.3 55.6 + - - +
22D ASP* 3.9 7.2 - - - +
23D GLU* 3.0 53.1 + - + +
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Residues in contact with PHE 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASN 3.1 14.1 + - - +
17D LYS* 3.2 19.7 + - + +
19D HIS* 1.3 76.4 - - - +
21D GLN* 1.3 64.7 + - + +
23D GLU* 3.3 10.9 + - + +
24D CYS* 3.1 44.1 + - - -
49D TRP* 3.8 31.9 - + - -
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Residues in contact with GLN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LYS* 3.0 49.3 + - - +
18D GLU* 3.8 8.6 - - - +
20D PHE* 1.3 82.3 - - + +
22D ASP* 1.3 61.4 + - - +
24D CYS 3.4 1.4 + - - -
25D THR* 3.0 33.9 + - - +
49D TRP* 3.6 64.9 + - + +
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Residues in contact with ASP 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU* 2.9 27.7 + - - +
19D HIS* 3.9 6.8 - - - +
21D GLN* 1.3 78.7 - - - +
23D GLU* 1.3 56.7 - - - +
25D THR* 2.9 21.1 + - - +
26D LYS* 2.9 19.8 + - - +
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Residues in contact with GLU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D HIS* 3.0 42.7 + - + +
20D PHE* 3.3 10.2 + - + +
22D ASP* 1.3 77.2 - - - +
24D CYS* 1.3 59.7 + - - +
26D LYS* 3.8 6.2 - - + +
27D LEU* 3.2 23.4 + - - +
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Residues in contact with CYS 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D PHE* 3.1 44.7 + - - +
23D GLU* 1.3 74.7 - - - +
25D THR* 1.4 58.4 + - - +
27D LEU* 3.3 8.2 + - - +
28D LEU* 2.9 48.0 + - + +
47D VAL* 5.3 0.7 - - + -
49D TRP* 3.6 25.1 - - + -
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Residues in contact with THR 25 (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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21D GLN 3.0 15.5 + - - +
22D ASP* 2.9 25.7 + - - +
24D CYS* 1.4 72.2 - - - +
26D LYS* 1.4 59.1 + - - +
28D LEU 3.1 0.7 + - - +
29D VAL* 2.9 46.5 + - + +
46D ASP* 5.1 4.5 - - - +
47D VAL* 4.0 22.9 - - + +
49D TRP* 3.4 22.7 - - + +
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Residues in contact with LYS 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ASP 2.9 19.3 + - - +
23D GLU* 3.8 7.0 - - + +
25D THR* 1.4 75.9 + - - +
27D LEU* 1.3 62.4 + - - +
28D LEU 3.5 0.2 + - - -
29D VAL* 4.1 10.5 - - - +
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLU 3.2 16.7 + - - +
24D CYS* 3.5 9.6 - - - +
25D THR 3.3 0.2 - - - -
26D LYS* 1.3 80.0 - - - +
28D LEU* 1.3 65.0 + - + +
29D VAL 4.9 1.1 - - - +
31D ASN* 4.3 6.9 + - - +
115D MET* 3.8 32.9 - - + +
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D CYS* 2.9 39.6 + - + +
25D THR 4.2 0.7 - - - +
27D LEU* 1.3 81.2 - - + +
29D VAL* 1.3 66.8 + - - +
30D GLY 3.2 0.3 + - - -
31D ASN* 3.0 22.7 + - - +
33D VAL* 4.6 2.9 - - + -
44D ILE* 3.7 39.7 - - + +
47D VAL* 4.7 10.1 - - + -
87D LEU* 4.6 20.2 - - + -
115D MET* 4.2 30.1 - - + -
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Residues in contact with VAL 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D THR* 2.9 37.4 + - - +
26D LYS* 4.1 9.3 - - - +
27D LEU 4.9 1.2 - - - +
28D LEU* 1.3 69.7 - - - +
30D GLY* 1.3 60.0 + - - +
31D ASN 3.8 0.3 + - - -
44D ILE* 3.6 7.2 - - + +
45D ASP* 3.5 28.3 - - - +
46D ASP* 3.9 20.6 - - - +
47D VAL* 5.1 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
------------------------------------------------------------
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