Contacts of the strand formed by residues 12 - 18 (chain K) in PDB entry 5A0Q
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 TYR 12 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K ILE* 4.2 8.5 - - + +
9K GLY* 2.9 40.8 + - - +
10K PRO* 3.4 21.3 - - + -
11K ASP* 1.4 92.1 - - - +
13K VAL* 1.3 80.6 + - - +
14K LEU* 3.7 23.1 - - + -
107K TYR* 4.0 4.8 - - - -
113K PRO* 3.6 4.6 - - - +
151K ILE* 3.1 31.2 - - - +
152K SER 3.7 0.7 - - - -
153K ARG* 3.6 40.2 - - + +
156K ALA* 3.2 19.3 - - + +
182K ILE* 4.7 9.0 - - + -
183K ILE 3.3 14.6 - - - +
184K ASP* 4.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 13 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K ILE 3.5 14.8 - - - +
8K GLN* 5.0 2.7 - - - +
12K TYR* 1.3 71.7 - - - +
14K LEU* 1.3 61.3 + - - +
15K VAL* 4.3 4.0 - - + -
105K ALA* 4.1 16.4 - - + -
106K GLY 3.4 19.1 - - - +
107K TYR* 4.6 4.0 - - + -
113K PRO* 3.2 30.5 - - + -
114K ALA* 3.8 5.8 - - - +
115K LEU* 3.9 26.7 - - + -
182K ILE* 3.7 1.6 - - - -
183K ILE* 2.9 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K GLY* 3.4 0.9 - - - -
7K ILE* 3.0 53.6 + - + -
12K TYR* 3.7 18.3 - - + -
13K VAL* 1.3 71.1 - - - +
15K VAL* 1.4 68.9 + - - +
156K ALA* 3.5 41.3 - - + +
157K VAL* 5.3 2.5 - - + -
160K LEU* 4.0 13.5 - - + -
180K VAL* 3.7 22.2 - - + -
181K ARG 3.2 20.0 - - - +
182K ILE* 3.6 14.4 - - + -
191K LEU* 4.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ILE 3.4 4.7 - - - +
6K GLY* 4.1 1.6 - - - -
13K VAL* 4.3 6.7 - - + -
14K LEU* 1.4 81.9 - - - +
16K ALA* 1.4 62.0 + - - +
43K LEU* 4.1 6.5 - - + -
45K LEU* 3.5 16.2 - - + -
103K LEU* 3.6 25.6 - - + -
105K ALA* 3.6 20.6 - - + -
115K LEU* 5.1 0.2 - - + -
181K ARG* 2.8 63.9 + - + +
183K ILE* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K LEU* 3.7 1.7 - - - -
5K ILE* 3.0 46.6 + - + +
15K VAL* 1.4 76.3 - - - +
17K SER* 1.4 66.0 + - - +
45K LEU* 4.2 1.4 - - - +
160K LEU* 3.7 28.5 - - + -
164K LEU* 5.9 0.4 - - + -
178K PHE* 5.1 5.8 - - + -
179K SER 3.4 5.6 - - - +
180K VAL* 3.7 16.4 - - + +
181K ARG* 3.6 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K TYR* 4.0 5.2 - - - -
4K LEU* 3.5 21.5 - - - +
16K ALA* 1.4 76.6 + - - +
18K ASP* 1.4 68.2 + - - +
34K LYS* 4.0 10.8 - - - +
45K LEU* 3.6 8.7 - - - +
178K PHE* 3.6 6.6 - - - -
179K SER* 2.9 33.1 + - - -
181K ARG* 3.1 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 18 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K TYR* 2.9 40.0 + - + +
17K SER* 1.4 73.5 - - - +
19K ARG* 1.4 59.2 + - - +
20K VAL* 4.5 10.4 - - + +
32K HIS 4.2 0.3 - - - +
34K LYS* 2.9 39.8 + - - +
175K LEU* 3.6 45.2 - - + +
177K THR 3.8 7.4 - - - +
178K PHE* 3.8 14.1 - - + -
----------------------------------------------------------
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