Contacts of the helix formed by residues 5 - 21 (chain M) in PDB entry 2ZQK
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 5 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M ALA* 1.3 67.2 + - - +
7M THR* 3.1 12.8 + - - -
8M GLU* 3.2 27.0 + - - +
9M THR* 3.2 26.5 + - - -
58M GLY* 4.6 13.5 + - - -
61M ALA* 4.9 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 6 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M SER* 1.3 73.4 + - - +
7M THR* 1.3 57.9 + - - +
9M THR* 4.2 4.6 - - - +
10M ALA* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 7 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M SER* 3.1 7.4 + - - -
6M ALA* 1.3 75.6 - - - +
8M GLU* 1.3 65.6 + - - +
10M ALA* 3.8 3.1 - - - +
11M THR* 2.8 32.0 + - - +
57M ALA* 3.2 38.1 - - + +
58M GLY* 4.4 1.1 - - - -
61M ALA* 3.5 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 8 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M SER* 3.2 26.9 + - - +
7M THR* 1.3 80.0 - - - +
9M THR* 1.3 54.2 + - - +
11M THR* 3.1 4.4 + - - -
12M ARG* 2.7 58.4 + - - +
51M GLU* 4.0 3.6 - - - +
54M ALA* 3.5 28.2 - - + +
55M LYS* 3.6 28.4 + - - +
58M GLY* 4.3 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 9 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M SER 3.2 15.7 + - - -
6M ALA* 4.2 5.2 - - - -
8M GLU* 1.3 80.9 + - - +
10M ALA* 1.3 64.4 + - - +
12M ARG* 3.2 21.1 + - - +
13M ASP* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M ALA 3.0 21.6 + - - +
7M THR* 3.8 3.8 - - - +
9M THR* 1.3 75.7 - - - +
11M THR* 1.3 65.2 - - - +
13M ASP* 3.1 12.7 + - - +
14M GLN* 3.0 22.6 + - - +
10N ALA* 4.7 20.9 - - + +
13N ASP* 4.3 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 11 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M THR* 2.8 26.5 + - - +
8M GLU 3.3 4.0 - - - -
10M ALA* 1.3 76.0 - - - +
12M ARG* 1.3 64.3 + - - +
14M GLN* 2.9 14.6 + - + +
15M LEU* 2.8 50.6 + - + +
53M GLN* 4.3 1.6 - - + +
54M ALA* 3.7 15.3 - - - +
57M ALA* 3.3 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M GLU* 2.7 43.5 + - - +
9M THR* 3.4 24.0 + - - +
11M THR* 1.3 73.4 - - - +
13M ASP* 1.3 60.1 + - - +
15M LEU* 4.1 0.5 - - - +
16M THR* 2.7 44.3 + - - +
50M ILE* 4.2 17.6 - - - +
51M GLU* 3.3 39.3 + - - -
54M ALA* 3.9 11.7 - - + +
17N LYS* 5.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 13 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M THR* 2.9 31.8 + - - +
10M ALA* 3.3 10.9 - - - +
12M ARG* 1.3 78.1 - - - +
14M GLN* 1.3 58.3 + - - +
16M THR* 3.6 4.3 - - - -
17M LYS* 2.8 31.5 + - - +
10N ALA* 4.3 4.5 - - - +
13N ASP* 3.5 19.9 - - + +
14N GLN* 3.8 23.9 + - - +
17N LYS* 2.9 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 14 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M ALA 3.0 11.1 + - - +
11M THR* 2.9 14.7 + - - +
13M ASP* 1.3 78.0 - - - +
15M LEU* 1.3 67.1 + - - +
17M LYS* 3.6 5.6 - - - +
18M GLU* 2.8 62.7 + - - +
13N ASP* 3.6 26.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M THR* 2.8 45.4 + - + +
14M GLN* 1.3 80.4 - - - +
16M THR* 1.3 60.0 + - - +
18M GLU* 3.8 16.7 - - + +
19M ALA* 2.9 31.7 + - - +
50M ILE* 3.7 25.9 - - + +
53M GLN* 3.5 50.7 - - + +
54M ALA 4.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 16 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M ARG* 2.7 35.5 + - - +
13M ASP* 3.6 3.6 - - - -
15M LEU* 1.3 77.2 - - - +
17M LYS* 1.3 65.0 + - - +
19M ALA* 3.1 4.4 + - - +
20M PHE* 3.1 46.4 + - + -
42M LEU* 3.9 8.6 - - + +
50M ILE* 3.9 17.4 - - - +
17N LYS* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 17 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M ASP 2.8 17.9 + - - +
14M GLN* 3.6 6.4 + - - +
16M THR* 1.3 77.0 - - - +
18M GLU* 1.3 93.2 + - - +
20M PHE* 3.2 15.7 + - - +
21M GLN* 3.4 29.8 + - - +
12N ARG* 5.4 9.3 - - + +
13N ASP* 3.3 33.6 + - - +
16N THR* 3.4 35.2 - - + +
17N LYS* 4.8 4.7 - - - +
20N PHE* 4.0 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M GLN* 2.8 52.5 + - - +
15M LEU* 3.8 15.7 - - + +
17M LYS* 1.3 89.7 + - - +
19M ALA* 1.3 56.3 + - - +
21M GLN* 2.9 39.1 + - - +
22M ASN* 3.9 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M LEU 2.9 19.6 + - - +
16M THR 3.1 4.0 + - - +
18M GLU* 1.3 76.0 - - - +
20M PHE* 1.3 61.2 + - - +
22M ASN* 3.2 11.5 + - - +
25M ASN* 2.9 38.1 + - - +
42M LEU* 4.3 6.3 - - + -
46M VAL* 3.9 23.8 - - + -
50M ILE* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 20 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M THR* 3.1 34.0 + - + -
17M LYS* 3.6 2.5 - - - +
18M GLU 3.2 0.6 - - - -
19M ALA* 1.3 73.5 - - - +
21M GLN* 1.3 62.3 + - - +
22M ASN 3.0 10.0 + - - -
26M GLN* 3.7 41.9 - - + +
40M GLY 3.6 24.5 - - - -
42M LEU* 3.2 39.0 - - + -
17N LYS* 5.1 4.0 - - - -
20N PHE* 3.3 67.9 - + + -
21N GLN* 4.7 4.3 - - + -
40N GLY* 3.4 15.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 21 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M LYS* 3.4 33.6 - - - +
18M GLU* 2.9 33.6 + - - +
20M PHE* 1.3 78.1 - - - +
22M ASN* 1.3 55.7 + - - +
23M PRO* 3.5 9.7 - - - +
16N THR* 5.7 1.2 - - - +
20N PHE* 4.2 8.1 - - + -
39N SER 4.4 1.6 - - - +
40N GLY* 3.5 24.7 - - - +
----------------------------------------------------------
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