Contacts of the helix formed by residues 9 - 27 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 1.3 82.3 - - - +
10B ASN* 1.3 64.1 + - - +
11B ASP* 3.7 10.0 + - - +
12B ALA* 3.1 24.5 + - - +
13B TYR* 3.0 19.8 + - - +
44C GLU* 3.4 17.2 + - - -
8Q T 5.6 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE 3.9 0.2 + - - -
9B SER* 1.3 72.1 - - - +
11B ASP* 1.3 67.0 + - - +
13B TYR* 3.6 7.9 - - + +
14B GLU* 3.0 40.1 + - + +
2C ALA* 4.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER* 3.2 9.3 + - - +
10B ASN* 1.3 76.5 - - - +
12B ALA* 1.3 59.3 + - - +
14B GLU* 3.3 12.8 + - - +
15B LYS* 3.0 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.2 17.3 - - + -
9B SER* 3.1 20.3 + - - +
11B ASP* 1.3 78.9 - - - +
13B TYR* 1.3 62.3 + - - +
15B LYS* 3.4 4.6 + - - +
16B ILE* 3.0 30.4 + - + +
43C LEU* 5.6 2.2 - - + -
44C GLU* 4.3 16.2 - - + +
47C LEU* 4.0 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.8 10.3 - - + +
9B SER 3.0 16.6 + - - +
10B ASN* 3.6 9.2 - - - +
12B ALA* 1.3 77.6 - - - +
14B GLU* 1.3 72.0 + - + +
16B ILE* 3.4 6.0 + - - +
17B ASN* 3.2 43.7 + - - -
35B PHE* 3.6 32.2 - + - -
2C ALA* 4.3 15.5 - - + -
3C LYS 5.5 1.3 - - - -
4C VAL* 4.1 16.6 - - + -
16P C 5.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASN* 3.0 28.7 + - + +
11B ASP* 3.9 11.6 - - - +
13B TYR* 1.3 86.5 - - + +
15B LYS* 1.3 59.2 + - + +
17B ASN* 3.4 8.2 + - - +
18B ALA* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP* 3.0 33.5 + - - +
12B ALA* 3.7 5.4 - - - +
14B GLU* 1.3 76.3 - - + +
16B ILE* 1.3 63.6 + - - +
18B ALA* 3.3 9.7 + - - +
19B ILE* 3.1 28.5 + - - +
47C LEU* 4.2 24.6 - - + +
48C ARG* 6.1 2.0 - - - +
51C GLU* 3.6 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.3 7.9 - - + -
12B ALA 3.0 18.4 + - - +
13B TYR 3.7 4.3 - - - +
14B GLU 3.3 0.2 - - - -
15B LYS* 1.3 74.5 - - - +
17B ASN* 1.3 64.4 + - - +
19B ILE* 3.1 19.3 + - + +
20B ILE* 3.1 14.3 + - + +
35B PHE* 3.6 37.5 - - + -
38B THR* 3.7 21.8 - - - +
39B ALA* 3.9 15.5 - - + +
42B LEU* 4.1 15.9 - - + -
43C LEU* 3.7 31.0 - - + -
47C LEU* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TYR* 3.2 46.9 + - - -
14B GLU* 3.7 10.1 - - - +
16B ILE* 1.3 78.8 - - - +
18B ALA* 1.3 62.5 + - - +
20B ILE* 3.3 11.0 + - - +
21B GLU* 3.0 40.2 + - + +
35B PHE* 3.4 22.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU 2.8 18.3 + - - +
15B LYS* 3.3 11.2 - - - +
16B ILE 3.2 0.2 - - - -
17B ASN* 1.3 75.5 - - - +
19B ILE* 1.3 61.3 + - + +
21B GLU* 3.6 10.8 + - - +
22B LYS* 3.2 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS 3.1 16.0 + - - +
16B ILE* 3.1 9.4 + - + +
18B ALA* 1.3 75.6 - - + +
20B ILE* 1.3 63.0 + - + +
22B LYS* 3.0 20.0 + - + +
23B ARG* 2.9 55.9 + - + +
38B THR* 5.3 9.4 - - - -
41B MET* 5.6 3.1 - - + -
42B LEU* 4.1 27.1 - - + -
47C LEU* 4.2 9.4 - - + -
50C HIS* 3.7 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE 3.1 15.0 + - - +
17B ASN* 3.7 12.3 - - - +
19B ILE* 1.3 75.0 - - - +
21B GLU* 1.3 58.8 + - + +
23B ARG* 3.2 8.0 + - - +
24B ARG* 2.9 45.7 + - + +
33B VAL* 3.3 21.5 - - + +
34B SER 3.9 2.5 - - - +
35B PHE* 3.7 36.6 - - + +
38B THR* 3.6 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASN* 3.0 29.8 + - + +
18B ALA* 3.9 8.5 - - - +
20B ILE* 1.3 77.9 - - + +
22B LYS* 1.3 61.7 + - + +
24B ARG* 4.1 5.6 - - - +
25B GLN* 3.2 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA* 3.2 26.9 + - - +
19B ILE* 3.0 19.1 + - + +
21B GLU* 1.3 77.6 - - + +
23B ARG* 1.3 59.7 + - + +
25B GLN* 3.1 9.2 + - - +
26B GLU* 2.8 45.1 + - - +
50C HIS* 6.3 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 2.9 35.1 + - + +
20B ILE* 3.6 8.5 - - - +
22B LYS* 1.3 77.9 - - - +
24B ARG* 1.3 55.5 + - - +
26B GLU* 3.9 16.3 + - - +
27B GLY 2.7 31.0 + - - -
28B ALA* 3.2 9.9 - - + +
33B VAL* 3.9 28.3 - - + -
38B THR* 5.3 5.5 - - + +
41B MET* 3.9 21.1 - - - +
50C HIS* 3.7 27.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 2.9 28.6 + - + +
21B GLU* 4.1 6.7 - - - +
23B ARG* 1.3 75.0 - - - +
25B GLN* 1.3 57.3 + - - +
27B GLY 3.1 12.4 - - - +
28B ALA* 3.7 13.6 + - + +
30B GLU* 4.2 12.6 - - - +
31B LYS* 3.1 35.0 - - - +
33B VAL* 3.7 28.1 + - + +
34B SER* 5.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU* 3.2 22.3 + - - +
22B LYS* 3.1 8.2 + - - +
23B ARG 3.0 0.4 - - - -
24B ARG* 1.3 79.1 - - - +
26B GLU* 1.3 66.1 + - + +
27B GLY 3.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 2.8 26.4 + - + +
23B ARG* 3.9 22.0 + - - +
25B GLN* 1.3 76.2 - - + +
27B GLY* 1.3 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG 2.7 12.9 + - - -
24B ARG 3.1 14.7 - - - +
25B GLN 3.6 3.6 - - - +
26B GLU* 1.3 80.0 - - - +
28B ALA* 1.3 61.2 + - - -
----------------------------------------------------------
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