Contacts of the strand formed by residues 11 - 16 (chain O) in PDB entry 3Q2K
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 ILE 11 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O ILE* 3.0 57.2 - - + +
9O ARG 5.2 0.4 - - - +
10O LYS* 1.3 72.7 - - - +
12O ARG* 1.3 61.9 + - - +
13O PHE* 3.7 31.9 + - + -
35O ARG 2.8 15.0 + - - +
36O ALA* 3.3 6.9 - - + +
37O GLU* 2.9 30.7 + - - +
74O ASP* 4.2 6.7 - - + +
309O ILE* 4.8 13.5 - - + +
312O LEU* 4.1 26.9 - - + +
313O ARG* 4.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O ARG* 3.3 38.9 - - - +
10O LYS 4.4 1.1 - - - +
11O ILE* 1.3 70.9 - - - +
13O PHE* 1.3 61.8 + - - +
37O GLU* 3.8 22.2 - - - +
39O VAL* 4.0 11.7 - - + -
72O ASN* 2.6 57.4 + - - +
73O ALA* 3.2 7.4 - - - +
74O ASP* 2.4 53.7 + - - +
75O ALA 3.4 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 13 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O ILE* 3.7 24.4 + - + -
12O ARG* 1.3 73.8 - - - +
14O GLY* 1.3 58.0 + - - +
29O ILE* 3.8 31.6 - - + -
36O ALA* 4.1 21.1 - - + -
37O GLU 2.9 14.3 + - - +
38O LEU* 3.7 4.5 - - + +
39O VAL* 2.9 27.4 + - - +
40O GLU 3.5 3.8 + - - -
73O ALA* 3.7 2.5 - - - -
75O ALA* 3.5 34.1 - - + -
77O VAL* 4.1 10.8 - - + -
100O VAL* 4.1 16.2 - - + -
305O TYR* 3.9 20.0 - + - -
308O VAL* 3.7 24.5 - - + -
309O ILE* 4.2 7.4 - - + -
312O LEU* 4.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 14 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O PHE* 1.3 73.0 - - - +
15O LEU* 1.3 54.8 + - - -
16O VAL 4.1 0.2 - - - -
38O LEU* 4.4 2.0 - - - -
40O GLU* 3.8 13.7 - - - -
73O ALA* 3.5 14.5 - - - +
75O ALA 3.0 9.0 + - - +
76O LEU* 3.2 14.2 - - - -
77O VAL* 2.7 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O GLY* 1.3 71.0 - - - -
16O VAL* 1.3 62.8 + - - +
17O GLY 3.8 12.4 + - - +
18O CYS* 4.2 16.4 - - - -
22O SER* 3.5 29.6 - - - +
25O HIS* 3.6 34.8 - - + -
26O ILE* 4.5 17.9 - - + +
29O ILE* 5.4 1.8 - - + -
38O LEU* 4.0 17.5 - - + +
40O GLU 3.4 5.7 + - - -
41O ILE* 3.6 13.6 - - + +
42O CYS* 3.0 27.4 + - - +
52O ALA* 5.8 0.9 - - + -
67O MET* 4.4 1.4 - - - +
76O LEU* 4.9 0.4 - - - +
77O VAL* 3.7 14.4 - - + -
79O ALA* 4.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 16 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15O LEU* 1.3 73.8 - - - +
17O GLY* 1.3 60.6 + - - +
42O CYS* 3.9 10.8 - - + -
64O LEU* 4.1 10.8 - - + -
67O MET* 3.6 21.5 - - + -
76O LEU* 4.0 15.9 - - + -
77O VAL 2.6 17.7 + - - +
78O LEU* 3.9 19.1 - - + -
79O ALA* 2.8 29.8 + - - +
80O THR* 3.5 7.1 + - + -
88O GLN* 3.8 26.9 - - - +
500O NAI 3.9 15.0 - - + -
----------------------------------------------------------
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