Contacts of the strand formed by residues 178 - 183 (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 PHE 178 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K TYR* 4.6 6.1 - + - -
5K ILE* 6.0 1.6 - - + -
16K ALA* 5.1 4.3 - - + -
17K SER* 3.6 4.7 - - - +
18K ASP* 3.8 31.6 - - + -
19K ARG* 3.2 13.5 + - - -
164K LEU* 3.4 52.5 - - + -
167K LEU* 3.4 35.2 - - + -
168K GLN* 5.4 3.6 - - + -
175K LEU* 3.3 34.8 - - + -
176K PRO 4.1 7.4 - - - -
177K THR* 1.3 76.7 - - - +
179K SER* 1.4 59.6 + - - +
180K VAL* 3.2 20.5 + - + +
191K LEU 5.7 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K ALA* 3.4 0.5 - - - -
17K SER* 2.9 33.3 + - - -
19K ARG* 3.3 33.5 + - - +
33K ASP* 5.4 4.1 + - - -
35K MET* 4.9 4.2 - - - +
178K PHE* 1.4 66.3 - - - +
180K VAL* 1.3 60.9 + - - +
181K ARG* 3.1 32.8 + - - -
190K ASP* 3.8 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K LEU* 3.7 15.0 - - + -
16K ALA* 3.7 10.5 - - + -
157K VAL* 5.9 4.7 - - + -
160K LEU* 3.4 35.0 - - + -
164K LEU* 5.4 5.2 - - + -
178K PHE* 3.2 20.4 + - + +
179K SER* 1.3 73.0 - - - +
181K ARG* 1.3 65.4 + - - +
190K ASP* 3.6 6.6 - - - +
191K LEU* 3.0 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 181 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K LEU* 3.2 6.4 - - - +
15K VAL* 2.8 39.6 + - + +
16K ALA* 3.6 6.7 - - - +
17K SER* 3.1 29.8 + - - -
33K ASP* 6.2 0.4 - - - +
34K LYS 5.3 0.4 - - - +
35K MET* 3.3 43.2 - - + +
43K LEU* 3.7 26.2 - - + -
45K LEU* 3.3 23.9 - - - +
179K SER* 3.1 41.5 + - - -
180K VAL* 1.3 75.5 - - - +
182K ILE* 1.3 63.9 + - - +
188K ILE* 4.8 3.4 - - + -
189K HIS 3.2 17.3 - - - +
190K ASP* 4.4 4.5 - - - +
191K LEU* 4.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K TYR* 4.7 9.9 - - + -
13K VAL 3.7 9.9 - - - +
14K LEU* 3.6 21.8 - - + -
153K ARG* 4.5 27.4 - - + +
156K ALA* 6.2 1.1 - - + -
181K ARG* 1.3 77.9 - - - +
183K ILE* 1.3 67.9 + - - +
184K ASP* 4.8 13.2 - - + +
187K GLY 4.8 0.2 - - - -
188K ILE* 3.2 10.6 - - - +
189K HIS* 2.9 46.9 + - + +
191K LEU* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 183 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K TYR* 3.3 5.2 - - - +
13K VAL* 2.9 56.7 + - + +
15K VAL* 3.9 20.4 - - + -
41K LYS* 4.1 21.5 - - + -
43K LEU* 3.8 18.2 - - + -
105K ALA* 3.8 27.8 - - + -
106K GLY* 4.5 2.9 - - - +
107K TYR* 3.7 28.9 - - + +
182K ILE* 1.3 78.5 - - - +
184K ASP* 1.3 64.6 + - - +
187K GLY 4.2 3.6 - - - -
188K ILE* 3.9 13.2 - - + +
----------------------------------------------------------
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