Contacts of the helix formed by residues 3 - 22 (chain A) in PDB entry 2OLM
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 3 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 1.3 60.7 + - - +
5A ALA* 3.4 15.4 + - - +
6A LYS* 3.5 33.6 + - - +
7A ARG* 2.9 50.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 4 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 1.3 71.5 + - - +
5A ALA* 1.3 57.3 + - - +
6A LYS 3.2 0.2 - - - -
7A ARG* 3.3 18.3 + - - +
8A LYS* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 3.4 8.2 + - - +
4A SER* 1.3 75.1 - - - +
6A LYS* 1.3 64.6 + - - +
8A LYS* 3.4 10.6 + - - +
9A GLN* 3.3 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 3.5 34.4 + - - +
4A SER 3.2 0.2 - - - -
5A ALA* 1.3 75.3 - - - +
7A ARG* 1.3 66.3 + - + +
8A LYS 3.3 0.2 + - - -
9A GLN* 3.3 6.5 + - - +
10A GLU* 3.0 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 2.9 37.8 + - - +
4A SER* 3.5 15.2 + - - +
6A LYS* 1.3 77.2 - - + +
8A LYS* 1.3 62.5 + - - +
10A GLU* 3.2 14.9 + - - +
11A GLU* 2.9 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 2.8 20.4 + - - +
5A ALA* 3.6 11.0 - - - +
6A LYS 3.3 0.2 - - - -
7A ARG* 1.3 71.8 - - - +
9A GLN* 1.3 75.3 + - - +
11A GLU* 3.5 4.6 + - - +
12A LYS* 3.0 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ALA 3.3 12.1 + - - +
6A LYS* 3.9 6.5 - - - +
8A LYS* 1.3 99.4 - - - +
10A GLU* 1.3 61.9 + - + +
12A LYS* 3.3 22.7 + - - +
13A HIS* 2.9 47.2 + - + -
75A GLN* 4.3 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LYS* 3.0 54.6 + - + +
7A ARG* 3.6 15.9 - - - +
9A GLN* 1.3 77.4 - - + +
11A GLU* 1.3 70.9 + - - +
13A HIS* 3.3 10.4 + - - +
14A LEU* 3.2 26.3 + - + +
72A THR* 3.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 2.9 30.3 + - + +
8A LYS* 4.1 4.0 - - - +
10A GLU* 1.3 82.3 - - - +
12A LYS* 1.3 60.3 + - - +
14A LEU* 3.2 25.3 + - - +
15A LYS* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 3.0 22.8 + - + +
9A GLN* 3.5 26.5 - - - +
11A GLU* 1.3 76.7 - - - +
13A HIS* 1.3 58.3 + - + +
15A LYS* 3.2 11.4 + - + +
16A MET* 2.9 50.5 + - + +
75A GLN* 5.0 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 2.9 38.2 + - + +
10A GLU* 3.7 9.5 - - - +
11A GLU 3.2 0.2 - - - -
12A LYS* 1.3 79.2 - - + +
14A LEU* 1.3 58.0 + - + +
16A MET* 3.3 17.3 + - - +
17A LEU* 2.8 29.6 + - - +
73A PHE* 3.4 22.1 + - + +
75A GLN* 2.6 56.5 + - + -
78A ILE* 3.7 20.8 - - + +
1002A UNX 3.7 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 3.2 14.7 + - + +
11A GLU* 3.2 32.1 + - - +
13A HIS* 1.3 75.4 - - + +
15A LYS* 1.3 65.5 + - - +
17A LEU* 3.3 23.2 + - + +
18A ARG* 2.9 34.8 + - - +
68A ILE 4.8 5.4 - - - +
69A SER* 5.7 4.0 - - - +
71A THR 5.0 10.5 - - - +
73A PHE* 5.6 1.8 - - + -
1009A UNX 4.6 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU 2.9 14.6 + - - +
12A LYS* 3.2 14.1 + - + +
14A LEU* 1.3 76.6 - - - +
16A MET* 1.3 59.5 + - + +
18A ARG* 3.3 6.3 + - - +
19A ASP* 2.9 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 2.9 36.2 + - + +
13A HIS* 3.5 18.8 - - - +
15A LYS* 1.3 77.4 - - + +
17A LEU* 1.3 62.5 + - - +
19A ASP* 3.3 10.3 + - - +
20A MET* 3.2 26.6 + - - +
75A GLN* 3.8 21.1 - - - +
78A ILE* 3.5 26.9 - - + -
79A GLU* 4.9 1.3 - - + -
82A GLN* 3.4 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A HIS 2.8 19.8 + - - +
14A LEU* 3.5 20.2 - - + +
16A MET* 1.3 73.9 - - - +
18A ARG* 1.3 62.5 + - - +
20A MET* 3.0 17.2 + - + +
21A THR* 2.8 33.7 + - + +
40A VAL* 4.8 2.0 - - + -
47A PHE* 4.2 22.7 - - + -
68A ILE* 3.6 39.5 - - + +
73A PHE* 3.9 23.8 - - + -
78A ILE* 4.2 14.3 - - + +
81A LEU* 4.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 2.9 22.7 + - - +
15A LYS* 3.9 4.9 - - - +
17A LEU* 1.3 79.3 - - + +
19A ASP* 1.3 64.8 + - - +
21A THR* 3.2 27.7 + - - +
22A GLY* 3.4 3.8 + - - -
68A ILE* 3.7 33.1 + - - +
69A SER* 4.5 18.0 - - - +
1008A UNX 2.8 18.2 - - - -
1009A UNX 3.0 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS* 2.9 13.7 + - + +
16A MET* 3.4 14.0 - - - +
18A ARG* 1.3 76.3 - - - +
20A MET* 1.3 66.3 + - - +
22A GLY 3.6 5.5 + - - -
23A LEU* 3.6 22.5 + - - +
82A GLN* 5.8 3.0 + - - +
1008A UNX 3.9 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A MET 3.2 18.6 + - - +
17A LEU* 3.0 24.4 + - + +
19A ASP* 1.3 78.0 - - - +
21A THR* 1.3 64.2 + - - +
22A GLY 3.1 3.7 + - - -
23A LEU* 3.1 24.1 + - + +
26A ASN* 2.9 25.0 + - - +
47A PHE* 4.0 16.2 - - + -
78A ILE* 3.9 22.2 - - + +
81A LEU* 3.5 27.4 - - + +
82A GLN* 3.4 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 2.8 23.9 + - + +
18A ARG* 3.2 44.3 + - - +
20A MET* 1.3 72.3 - - - +
22A GLY* 1.3 57.9 + - - +
23A LEU 3.4 0.4 - - - -
26A ASN* 4.0 17.3 - - - +
27A ARG* 3.9 14.9 - - - +
37A PRO* 6.0 2.2 - - + -
47A PHE* 3.9 24.2 - - + -
68A ILE* 4.4 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG 3.4 5.8 + - - -
19A ASP 3.6 1.5 + - - -
20A MET 3.1 1.4 - - - -
21A THR* 1.3 80.0 + - - +
23A LEU* 1.3 60.8 + - - +
27A ARG* 2.8 33.9 + - - -
1008A UNX 3.9 16.6 - - - -
----------------------------------------------------------
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