Contacts of the helix formed by residues 9 - 27 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ILE* 1.3 82.1 - - - +
10F ASN* 1.3 64.6 + - - +
11F ASP* 3.7 10.5 + - - +
12F ALA* 3.1 24.1 + - - +
13F TYR* 3.0 19.4 + - - +
2G ALA* 4.8 0.2 - - - -
44G GLU* 3.6 16.6 + - - -
20P T 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 10 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F SER* 1.3 73.7 - - - +
11F ASP* 1.3 64.3 + - - +
13F TYR* 3.6 7.9 - - + +
14F GLU* 3.0 39.6 + - + +
2G ALA* 4.1 19.2 + - - +
19P C 5.7 3.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 11 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F SER* 3.2 9.3 + - - +
10F ASN* 1.3 77.7 - - - +
12F ALA* 1.3 60.2 + - - +
14F GLU* 3.3 12.0 + - - +
15F LYS* 3.0 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ILE* 4.2 17.7 - - + -
9F SER* 3.1 21.1 + - - +
11F ASP* 1.3 77.9 - - - +
13F TYR* 1.3 63.7 + - - +
15F LYS* 3.4 4.6 + - - +
16F ILE* 3.0 30.8 + - + +
43G LEU* 5.7 2.0 - - + -
44G GLU* 4.4 13.7 - - + -
47G LEU* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 13 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ILE* 3.8 10.5 - - + +
9F SER 3.0 17.0 + - - +
10F ASN* 3.6 9.2 - - + +
12F ALA* 1.3 76.5 - - - +
14F GLU* 1.3 70.1 + - + +
16F ILE* 3.4 6.2 + - - +
17F ASN* 3.2 45.2 + - - -
35F PHE* 3.6 32.2 - + - -
2G ALA* 4.3 14.1 - - + -
3G LYS 5.5 2.0 - - - -
4G VAL* 4.1 17.0 - - + -
4Q C 4.7 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F ASN* 3.0 29.2 + - + +
11F ASP* 3.9 12.1 - - - +
13F TYR* 1.3 84.0 - - + +
15F LYS* 1.3 60.9 + - + +
17F ASN* 3.4 7.1 + - - +
18F ALA* 2.8 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ASP* 3.0 34.5 + - + +
12F ALA* 3.7 5.2 - - - +
14F GLU* 1.3 76.0 - - + +
16F ILE* 1.3 63.4 + - - +
18F ALA* 3.3 9.0 + - + +
19F ILE* 3.1 28.9 + - - +
47G LEU* 4.2 24.8 - - + +
48G ARG* 6.3 0.6 - - - +
51G GLU* 3.7 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ILE* 4.3 8.3 - - + -
12F ALA* 3.0 18.6 + - + +
13F TYR 3.7 4.3 - - - +
15F LYS* 1.3 73.7 - - - +
17F ASN* 1.3 64.6 + - - +
19F ILE* 3.1 19.0 + - + +
20F ILE* 3.1 14.5 + - + +
35F PHE* 3.6 36.8 - - + -
38F THR* 3.7 22.0 - - - +
39F ALA* 3.9 15.7 - - + +
42F LEU* 4.1 16.4 - - + -
43G LEU* 3.8 30.1 - - + -
47G LEU* 4.6 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 17 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F TYR* 3.2 49.0 + - - -
14F GLU* 3.7 9.9 - - - +
16F ILE* 1.3 77.9 - - - +
18F ALA* 1.3 61.8 + - - +
20F ILE* 3.3 10.3 + - - +
21F GLU* 3.0 40.0 + - + +
35F PHE* 3.4 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F GLU 2.8 18.1 + - - +
15F LYS* 3.3 11.4 - - - +
16F ILE 3.2 0.2 - - - -
17F ASN* 1.3 76.8 - - - +
19F ILE* 1.3 61.8 + - + +
21F GLU* 3.6 10.8 + - - +
22F LYS* 3.2 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F LYS 3.1 16.5 + - - +
16F ILE* 3.1 9.6 + - + +
18F ALA* 1.3 75.6 - - + +
20F ILE* 1.3 62.2 + - + +
22F LYS* 2.9 18.9 + - + +
23F ARG* 2.9 55.2 + - + +
38F THR* 5.2 10.5 - - - -
41F MET* 5.6 2.7 - - + -
42F LEU* 4.1 27.4 - - + -
47G LEU* 4.2 9.2 - - + -
50G HIS* 3.8 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ILE* 3.1 15.2 + - + +
17F ASN* 3.7 11.2 - - - +
19F ILE* 1.3 75.6 - - - +
21F GLU* 1.3 59.2 + - + +
23F ARG* 3.2 8.4 + - - +
24F ARG* 2.9 46.0 + - + +
33F VAL* 3.3 20.4 - - + +
34F SER 3.9 2.7 - - - +
35F PHE* 3.7 37.2 - - + +
38F THR* 3.6 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F ASN* 3.0 30.9 + - + +
18F ALA* 3.9 8.9 - - - +
20F ILE* 1.3 78.1 - - + +
22F LYS* 1.3 61.2 + - + +
24F ARG* 3.9 5.6 + - - +
25F GLN* 3.2 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F ALA* 3.2 26.9 + - - +
19F ILE* 2.9 19.4 + - + +
21F GLU* 1.3 77.3 - - + +
23F ARG* 1.3 60.9 + - + +
25F GLN* 3.1 8.2 + - - +
26F GLU* 2.8 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ILE* 2.9 35.4 + - + +
20F ILE* 3.2 8.9 + - - +
22F LYS* 1.3 77.1 - - - +
24F ARG* 1.3 55.5 + - - +
25F GLN 3.0 0.2 - - - -
26F GLU* 4.1 16.3 + - - -
27F GLY 2.7 31.0 + - - -
28F ALA* 3.2 9.8 - - + +
33F VAL* 3.9 28.7 - - + +
38F THR* 5.3 5.5 - - + +
41F MET* 3.9 21.2 - - - +
50G HIS* 3.6 27.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ILE* 2.9 31.0 + - + +
21F GLU* 4.1 6.7 - - - +
23F ARG* 1.3 75.6 - - - +
25F GLN* 1.3 57.7 + - - +
27F GLY 3.1 13.1 - - - +
28F ALA* 3.7 13.3 + - + +
30F GLU* 4.4 12.0 - - - +
31F LYS* 3.1 35.5 - - - +
33F VAL* 3.7 28.3 + - + +
34F SER* 5.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F GLU* 3.2 23.6 + - - +
22F LYS* 3.1 8.7 + - - +
23F ARG 3.0 0.8 - - - -
24F ARG* 1.3 80.1 - - - +
26F GLU* 1.3 66.9 + - + +
27F GLY 3.6 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F LYS* 2.8 27.5 + - - +
23F ARG* 3.9 22.6 + - - +
25F GLN* 1.3 77.0 - - + +
27F GLY* 1.3 66.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ARG 2.7 13.7 + - - -
24F ARG 3.1 13.4 - - - +
25F GLN 3.6 3.6 - - - +
26F GLU* 1.3 80.5 - - - +
28F ALA* 1.3 61.3 + - - -
----------------------------------------------------------
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