Contacts of the helix formed by residues 12 - 25 (chain A) in PDB entry 2O8C
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 GLU 12 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 1.3 79.3 - - - +
13A SER* 1.3 61.2 + - - +
14A ALA* 3.2 8.5 - - + +
15A ALA* 3.8 15.9 + - + +
16A GLU* 2.9 29.6 + - - +
112A SER* 4.1 11.1 + - - -
113A LYS* 3.4 39.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 3.9 0.8 + - - -
12A GLU* 1.3 73.0 - - - +
14A ALA* 1.3 63.6 + - - +
15A ALA 3.6 0.2 + - - -
16A GLU* 3.7 8.9 + - - +
17A VAL* 3.4 26.0 + - - +
68A GLY 5.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.2 8.8 - - + +
13A SER* 1.3 81.0 + - - +
15A ALA* 1.3 59.4 + - - +
16A GLU 3.5 0.2 - - - -
17A VAL* 4.3 8.0 - - - +
18A GLY* 3.9 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.4 12.7 - - + +
12A GLU* 3.1 28.2 + - + +
14A ALA* 1.3 76.9 - - - +
16A GLU* 1.3 63.8 + - - +
17A VAL 3.4 0.9 - - - -
18A GLY* 3.7 9.4 + - - +
19A PHE* 3.8 8.7 + - - +
113A LYS* 3.9 37.2 - - + +
115A ASN* 4.0 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 5.6 1.2 - - - +
11A LEU* 4.7 15.9 + - + +
12A GLU 2.9 17.1 + - - +
13A SER* 3.9 8.7 - - - +
14A ALA 3.5 0.2 - - - -
15A ALA* 1.3 77.6 - - - +
17A VAL* 1.3 64.7 + - - +
19A PHE* 3.3 13.7 + - - +
20A VAL* 3.3 16.3 + - - +
66A TYR 4.6 0.3 - - - +
67A MET* 3.4 36.1 - - + +
68A GLY 2.9 19.5 + - - +
73A LYS* 2.8 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER 3.4 18.1 + - - +
14A ALA* 4.4 7.0 - - - +
15A ALA 3.4 0.2 - - - -
16A GLU* 1.3 75.6 - - - +
18A GLY* 1.3 64.1 + - - +
20A VAL* 3.0 20.9 + - + +
21A ARG* 3.3 24.2 + - + +
68A GLY 4.0 2.5 - - - +
69A PRO* 3.9 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 3.9 7.6 + - - -
15A ALA* 3.7 9.8 + - - -
16A GLU 3.3 1.0 - - - -
17A VAL* 1.3 79.7 - - - +
19A PHE* 1.3 56.2 + - - +
21A ARG* 4.9 1.7 - - - +
22A PHE* 3.5 18.4 + - - +
115A ASN* 3.4 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.9 2.9 - - + -
15A ALA 3.8 3.9 + - - +
16A GLU 3.3 8.8 + - - +
17A VAL 3.1 0.4 - - - -
18A GLY* 1.3 75.3 - - - +
20A VAL* 1.3 67.1 + - - +
21A ARG 3.4 0.7 - - - -
22A PHE* 3.1 8.5 + + - +
23A PHE* 2.9 26.8 + + + +
37A PHE* 3.9 27.4 - + - -
39A ARG* 3.7 19.7 - - - +
46A HIS* 3.4 46.4 - + + -
67A MET* 3.9 20.9 - - + -
75A LEU* 4.6 8.7 - - + -
115A ASN* 3.3 12.5 - - - +
117A TRP* 3.6 36.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU 3.3 15.9 - - - +
17A VAL* 3.0 10.9 + - + +
19A PHE* 1.3 78.4 - - - +
21A ARG* 1.3 65.5 + - + +
23A PHE* 3.4 8.3 + - - +
24A GLN* 3.4 33.6 + - - +
67A MET* 3.8 20.0 - - + +
68A GLY* 3.6 29.6 - - - +
69A PRO* 5.2 4.5 - - + -
75A LEU* 4.0 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.3 20.5 + - + +
18A GLY* 5.1 1.8 - - - +
20A VAL* 1.3 80.6 - - + +
22A PHE* 1.3 63.0 + - - +
23A PHE 3.4 0.2 - - - -
24A GLN* 3.3 37.3 + - - +
25A GLY* 3.5 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 3.5 16.5 + - - +
19A PHE* 3.1 18.4 + + - +
21A ARG* 1.3 77.2 - - - +
23A PHE* 1.3 62.8 + - - +
25A GLY* 2.9 19.6 + - - -
26A MET* 3.3 41.0 + - + +
37A PHE* 4.8 1.6 - + - -
103A TYR* 6.3 0.2 - + - -
115A ASN* 4.3 16.6 - - + -
116A ASP* 5.6 0.4 - - - -
117A TRP* 3.4 57.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 2.9 21.4 + + + +
20A VAL 3.7 5.8 - - - +
22A PHE* 1.3 78.8 - - - +
24A GLN* 1.3 64.0 + - + +
26A MET* 3.5 39.0 + - + +
29A LYS* 5.4 11.7 - - + -
35A ARG* 5.3 12.0 + - + -
37A PHE* 3.9 23.1 - + - -
46A HIS* 3.5 36.8 - - + -
47A GLY* 4.3 6.1 - - - -
48A GLU 5.3 1.1 - - - -
49A ASP* 6.1 0.2 - - - -
75A LEU* 3.7 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.4 28.5 + - - +
21A ARG* 3.3 45.1 + - - +
22A PHE 3.2 0.2 - - - -
23A PHE* 1.3 81.7 - - + +
25A GLY* 1.3 57.8 + - - +
26A MET 3.2 8.7 + - - +
75A LEU* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG 3.5 8.4 + - - -
22A PHE* 2.9 12.7 + - - -
24A GLN* 1.3 78.0 - - - +
26A MET* 1.3 60.3 + - - +
27A PRO* 4.1 2.6 - - - +
----------------------------------------------------------
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