Contacts of the strand formed by residues 192 - 197 (chain B) in PDB entry 2XWA
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 192 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ARG* 3.5 33.9 - - - +
109B PRO* 3.6 9.9 - - + +
110B TRP 3.8 3.1 - - - +
111B GLN* 3.7 38.4 - - - +
188B VAL* 3.4 4.1 - - - +
189B CYS* 2.7 39.2 + - - +
190B GLY 3.8 8.5 - - - +
191B GLY* 1.3 84.1 - - - +
193B LEU* 1.3 74.2 + - - +
194B GLU* 3.4 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.8 25.8 - - + -
31B VAL* 4.1 11.7 - - + -
37B LEU* 4.4 3.8 - - + -
108B LEU* 3.6 19.8 - - + +
109B PRO 3.0 15.0 + - - +
110B TRP* 3.7 19.5 - - + -
111B GLN* 3.2 25.8 + - - +
186B PRO* 3.6 27.8 - - + -
187B LEU 3.8 6.1 - - - +
188B VAL* 4.3 1.3 - - - +
192B VAL* 1.3 70.3 - - - +
194B GLU* 1.3 59.5 + - - +
195B GLY 3.4 24.7 - - - +
196B VAL* 4.9 0.4 - - + -
216B VAL* 3.6 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLN* 2.9 36.8 + - - +
115B ARG* 2.8 30.1 + - - +
117B VAL* 3.5 31.8 - - + +
169B MET* 4.6 7.1 - - - +
187B LEU* 3.0 5.2 + - + -
189B CYS* 3.7 31.3 - - + +
192B VAL* 3.4 5.8 + - - +
193B LEU* 1.3 75.7 - - - +
195B GLY* 1.3 60.9 + - - +
215B ARG* 3.7 8.5 + - - +
216B VAL* 3.1 31.6 + - - +
217B ALA* 5.0 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B MET* 4.7 2.5 - - - -
186B PRO* 3.5 0.5 - - - +
187B LEU* 2.6 50.1 + - - +
193B LEU* 3.4 12.7 - - - +
194B GLU* 1.3 79.8 - - - +
196B VAL* 1.3 61.3 + - - -
213B TYR* 4.2 9.0 - - - -
214B THR 3.4 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 5.1 2.7 - - + -
37B LEU* 3.8 29.8 - - + -
38B SER* 4.0 17.3 - - - +
39B ALA* 4.9 1.3 - - + -
89B ASP 5.1 0.7 - - - +
90B LEU* 3.8 17.0 - - + -
184B GLY* 3.6 32.1 - - - +
185B GLY 3.3 3.4 - - - +
193B LEU* 4.9 5.2 - - + -
195B GLY* 1.3 79.0 - - - +
197B VAL* 1.3 73.5 + - - +
213B TYR* 3.3 3.7 - - - -
214B THR* 2.8 36.8 + - - +
216B VAL* 3.8 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 4.0 6.1 - - - +
89B ASP 5.3 0.3 - - - +
125B VAL* 4.0 15.5 - - + -
178B SER* 3.6 21.3 - - - +
179B CYS 5.4 0.2 - - - +
182B ASP* 3.6 22.4 - - + +
183B SER* 3.8 18.9 - - - +
184B GLY* 3.1 17.3 + - - -
185B GLY* 2.9 21.5 + - - +
186B PRO 4.9 0.7 - - - -
196B VAL* 1.3 76.0 - - - +
198B THR* 1.3 69.0 + - - +
200B GLY* 4.9 5.2 - - - +
212B ILE 4.8 0.9 - - - +
213B TYR* 3.5 28.4 - - + -
214B THR* 5.4 0.2 + - - -
----------------------------------------------------------
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