Contacts of the strand formed by residues 188 - 192 (chain A) in PDB entry 4WGK
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 VAL 188 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A VAL* 3.4 21.1 - - + -
156A VAL* 5.1 0.4 - - + -
168A ARG* 2.9 24.4 + - - -
172A LEU* 4.3 9.6 - - + -
175A LEU* 4.4 18.2 - - + -
183A TYR* 3.8 28.5 - - + -
184A ARG 3.2 19.8 + - - +
185A ARG 3.9 0.7 - - - +
186A ASP 3.5 2.0 + - - -
187A ASN* 1.3 85.4 - - - +
189A ILE* 1.3 64.5 + - - +
190A LEU* 3.9 27.8 - - + -
231A ILE* 5.2 0.4 - - + -
525A GLN* 3.3 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A VAL 2.8 14.3 + - - +
155A PHE* 3.7 22.8 - - + -
156A VAL* 2.8 32.1 + - - +
188A VAL* 1.3 71.4 - - - +
190A LEU* 1.3 65.5 + - - +
525A GLN* 3.4 26.7 - - + +
527A ILE* 3.6 29.8 - - + -
534A ILE* 3.8 31.4 - - + +
536A ALA* 4.1 12.3 - - + -
570A SER* 4.2 0.9 - - - +
573A CYS* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A VAL* 3.7 30.7 - - + -
158A ILE* 4.1 9.2 - - + -
163A VAL* 3.4 19.8 - - + +
167A LEU* 5.0 0.9 - - + -
168A ARG* 3.9 39.3 - - + +
171A VAL* 4.0 25.1 - - + -
172A LEU* 5.7 1.1 - - + -
188A VAL* 3.9 17.2 + - + -
189A ILE* 1.3 76.8 - - - +
191A SER* 1.3 60.4 + - - +
227A ILE* 4.3 15.7 - - + -
231A ILE* 5.0 1.1 - - + -
573A CYS* 3.2 3.3 - - - -
574A ASN* 3.0 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PHE* 4.1 16.1 - - - -
156A VAL 2.8 16.1 + - - +
157A SER* 3.4 3.5 + - - -
158A ILE* 2.7 34.6 + - - +
163A VAL* 3.8 3.6 - - - -
189A ILE* 3.9 0.6 + - - -
190A LEU* 1.3 74.7 - - - +
192A GLY* 1.3 54.6 + - - +
347A SER* 3.5 12.8 + - - -
570A SER* 3.4 22.4 + - - -
571A GLY 2.8 20.4 + - - -
572A LEU 3.6 3.1 - - - -
573A CYS* 3.6 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A SER* 5.4 0.4 - - - -
158A ILE 3.5 6.5 - - - -
160A ILE* 3.8 19.1 - - - -
162A MET 5.0 0.2 - - - -
163A VAL* 3.5 4.1 - - - +
191A SER* 1.3 73.2 + - - +
193A THR* 1.3 61.0 + - - -
194A HIS 3.1 3.4 + - - -
347A SER* 2.7 28.9 + - - -
571A GLY 3.6 2.6 - - - +
572A LEU* 2.9 25.3 + - - +
----------------------------------------------------------
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