Contacts of the strand formed by residues 193 - 197 (chain B) in PDB entry 1WLP
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 TRP 193 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 4.6 2.0 - - + -
9A PRO* 3.5 28.5 - - + +
11A ASN 2.7 31.3 + - - -
12A PRO* 3.3 10.3 - - - +
13A PRO* 3.3 33.0 - - + -
167B TYR* 3.1 31.4 - + - -
170B THR* 4.3 6.5 - - + -
174B GLU* 3.8 7.0 - - + -
189B SER* 3.9 13.5 + - - -
191B SER* 3.2 8.0 + - - +
192B GLY* 1.3 78.3 + - - +
194B TRP* 1.3 66.5 + - - +
204B TRP* 3.1 39.8 - - + -
205B ILE 3.6 39.0 - - - -
206B PRO* 3.6 3.4 - - + -
278B MET* 3.4 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B TYR* 3.4 40.2 - + - -
185B VAL* 4.3 12.3 - - + -
187B GLU 4.3 0.9 - - - +
188B LYS* 3.7 41.0 - - + +
189B SER 3.7 3.4 + - - -
192B GLY 3.9 0.4 + - - -
193B TRP* 1.3 81.5 - - - +
195B PHE* 1.3 60.3 + - - +
196B CYS* 4.0 9.0 - - - -
203B GLY 3.5 0.3 - - - +
204B TRP* 3.1 10.4 - - - -
205B ILE* 2.9 41.7 + - + +
207B ALA* 3.9 20.6 - - + +
210B LEU* 4.1 17.9 - - + -
219B THR* 3.4 42.0 - - + -
220B GLU* 6.2 0.4 - - + -
260B LEU* 3.0 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LYS* 3.6 41.5 - - + -
185B VAL* 3.1 4.2 - - - +
186B VAL* 2.8 48.8 + - + -
187B GLU* 2.8 35.4 + - + +
194B TRP* 1.3 70.1 - - - +
196B CYS* 1.3 61.9 + - - +
202B ARG* 3.5 38.6 - - + -
203B GLY* 3.0 31.0 - - - -
204B TRP* 3.4 38.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B MET* 3.2 9.7 - - - +
183B VAL* 3.6 13.9 - - + -
185B VAL* 3.5 39.7 - - - +
186B VAL* 3.5 7.4 - - - -
194B TRP* 3.9 10.7 + - - -
195B PHE* 1.3 81.8 - - - +
197B GLN* 1.3 60.6 + - - +
202B ARG* 3.0 20.1 - - - +
203B GLY 3.1 10.5 + - - -
205B ILE* 3.4 32.5 - - + -
210B LEU* 4.6 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B VAL* 4.3 0.2 - - - -
184B GLU* 3.3 42.8 + - - +
186B VAL* 3.4 10.7 - - + +
196B CYS* 1.3 73.1 - - - +
198B MET* 1.3 74.4 + - - +
200B ALA 5.4 2.6 - - - +
201B LYS* 4.8 0.7 - - - -
202B ARG* 2.8 48.9 + - + +
----------------------------------------------------------
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