Contacts of the helix formed by residues 9 - 27 (chain G) in PDB entry 4QPQ
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 9 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F ALA* 4.9 0.2 - - - -
44F GLU* 3.4 16.0 + - - -
8G ILE* 1.3 82.6 - - - +
10G ASN* 1.3 64.9 + - - +
11G ASP* 3.7 10.4 + - - +
12G ALA* 3.1 24.3 + - - +
13G TYR* 3.0 19.6 + - - +
1Q G 5.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 10 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F ALA* 4.1 21.1 + - - +
9G SER* 1.3 70.6 - - - +
11G ASP* 1.3 67.3 + - - +
13G TYR* 3.5 8.1 + - + +
14G GLU* 3.0 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 11 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G SER* 3.2 10.2 + - - +
10G ASN* 1.3 77.5 - - - +
12G ALA* 1.3 60.5 + - - +
14G GLU* 3.3 12.5 + - - +
15G LYS* 3.0 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F LEU* 5.8 2.0 - - + -
44F GLU* 4.2 17.5 - - + +
47F LEU* 4.1 21.9 - - + +
8G ILE* 4.2 17.3 - - + -
9G SER* 3.1 21.3 + - - +
11G ASP* 1.3 79.2 - - - +
13G TYR* 1.3 63.4 + - - +
15G LYS* 3.4 4.6 + - - +
16G ILE* 3.0 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 13 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F ALA* 4.1 20.0 - - + -
3F LYS 5.4 1.6 - - - -
4F VAL* 4.0 17.0 - - + -
8G ILE* 3.8 10.3 - - + +
9G SER 3.0 16.4 + - - +
10G ASN* 3.6 6.7 - - + +
11G ASP 3.2 0.2 - - - -
12G ALA* 1.3 77.2 - - - +
14G GLU* 1.3 71.4 + - + +
16G ILE* 3.4 6.0 + - - +
17G ASN* 3.2 44.9 + - - -
35G PHE* 3.6 30.9 - + - -
23P C 5.5 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ASN* 3.0 29.1 + - + +
11G ASP* 3.9 11.4 - - - +
13G TYR* 1.3 85.4 - - + +
15G LYS* 1.3 61.3 + - + +
17G ASN* 3.4 7.9 + - - +
18G ALA* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F LEU* 4.3 23.6 - - + -
48F ARG* 6.2 2.2 - - - +
51F GLU* 4.0 22.6 + - - +
11G ASP* 3.0 33.4 + - - +
12G ALA* 3.7 5.8 - - - +
13G TYR 3.3 0.2 - - - -
14G GLU* 1.3 76.1 - - + +
16G ILE* 1.3 64.4 + - - +
18G ALA* 3.3 8.8 + - - +
19G ILE* 3.1 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F LEU* 3.8 30.7 - - + -
47F LEU* 4.5 4.0 - - + -
8G ILE* 4.3 8.1 - - + -
12G ALA 3.0 18.4 + - - +
13G TYR 3.7 4.9 - - - +
15G LYS* 1.3 74.1 - - - +
17G ASN* 1.3 64.7 + - - +
19G ILE* 3.1 18.3 + - + +
20G ILE* 3.1 14.9 + - + +
35G PHE* 3.6 36.6 - - + -
38G THR* 3.7 22.0 - - - +
39G ALA* 4.0 14.8 - - + +
42G LEU* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 17 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G TYR* 3.2 47.8 + - - -
14G GLU* 3.7 10.6 - - - +
16G ILE* 1.3 78.3 - - - +
18G ALA* 1.3 61.9 + - - +
20G ILE* 3.3 11.5 + - - +
21G GLU* 3.0 39.9 + - + +
35G PHE* 3.4 21.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G GLU 2.8 17.9 + - - +
15G LYS* 3.3 11.7 - - + +
16G ILE 3.2 0.2 - - - -
17G ASN* 1.3 77.6 - - - +
19G ILE* 1.3 61.9 + - + +
21G GLU* 3.6 11.2 + - - +
22G LYS* 3.2 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F LEU* 4.0 21.8 - - + -
50F HIS* 3.8 35.2 - - + +
15G LYS 3.1 15.8 + - - +
16G ILE* 3.1 9.2 + - + +
18G ALA* 1.3 75.2 - - + +
20G ILE* 1.3 62.0 + - + +
22G LYS* 3.0 19.4 + - + +
23G ARG* 2.9 54.4 + - + +
38G THR* 5.3 9.9 - - - -
41G MET* 5.6 2.7 - - + -
42G LEU* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ILE* 3.1 14.7 + - + +
17G ASN* 3.3 12.3 + - - +
19G ILE* 1.3 75.8 - - - +
21G GLU* 1.3 58.6 + - + +
23G ARG* 3.2 8.4 + - - +
24G ARG* 2.9 45.9 + - + +
33G VAL* 3.3 21.5 - - + +
34G SER 3.9 2.7 - - - +
35G PHE* 3.7 36.8 - - + +
38G THR* 3.6 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ASN* 3.0 30.2 + - + +
18G ALA* 3.9 8.8 - - - +
20G ILE* 1.3 78.8 - - + +
22G LYS* 1.3 60.7 + - + +
24G ARG* 4.1 5.7 - - - +
25G GLN* 3.2 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ALA* 3.2 27.3 + - - +
19G ILE* 3.0 18.4 + - + +
21G GLU* 1.3 77.4 - - + +
23G ARG* 1.3 60.8 + - + +
25G GLN* 3.1 8.4 + - - +
26G GLU* 2.8 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F HIS* 3.4 30.7 + - - -
19G ILE* 2.9 35.7 + - + +
20G ILE* 3.6 8.3 - - - +
22G LYS* 1.3 76.6 - - - +
24G ARG* 1.3 54.7 + - - +
26G GLU* 4.1 17.0 + - - -
27G GLY 2.7 30.3 + - - -
28G ALA* 3.2 9.9 - - + +
33G VAL* 3.9 29.1 - - + +
38G THR* 5.3 5.7 - - + +
41G MET* 3.9 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ILE* 2.9 29.3 + - + +
21G GLU* 4.1 6.3 - - - +
23G ARG* 1.3 75.3 - - - +
25G GLN* 1.3 57.0 + - - +
27G GLY 3.1 13.5 - - - +
28G ALA* 3.7 13.0 + - + +
30G GLU* 4.2 12.8 - - - +
31G LYS* 3.1 35.3 - - - +
33G VAL* 3.7 27.9 + - + +
34G SER* 5.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G GLU* 3.2 22.9 + - - +
22G LYS* 3.1 9.1 + - - +
23G ARG 3.0 0.8 - - - -
24G ARG* 1.3 79.3 - - - +
26G GLU* 1.3 67.1 + - + +
27G GLY 3.6 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LYS* 2.8 29.1 + - - +
23G ARG* 3.9 22.0 + - - +
25G GLN* 1.3 76.5 - - + +
27G GLY* 1.3 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G ARG 2.7 14.4 + - - -
24G ARG 3.1 14.2 - - - +
25G GLN 3.6 3.3 - - - +
26G GLU* 1.3 82.1 - - - +
28G ALA* 1.3 62.4 + - - -
----------------------------------------------------------
Back to top of page
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