Contacts of the strand formed by residues 211 - 217 (chain B) in PDB entry 2WLM
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 SER 211 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ARG* 4.5 8.0 + - - -
163B LEU 3.2 11.3 + - - -
164B ALA* 4.6 5.6 - - - -
208B PHE* 3.8 4.3 - - - -
210B LEU* 1.3 83.0 + - - +
212B TRP* 1.3 67.5 + - - +
213B THR* 4.8 2.1 + - - -
274B VAL* 4.8 13.1 - - - +
275B PHE* 4.7 18.5 - - - -
285B LEU* 5.1 3.4 - - - -
290B PHE* 3.9 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ARG* 3.1 3.4 - - - -
163B LEU* 2.8 57.3 + - + +
174B ALA* 4.1 13.5 - - + -
175B ASP* 4.1 9.0 - - - -
176B VAL* 4.0 16.4 - - + -
202B ARG* 3.2 46.2 + - + +
203B SER 3.5 20.9 - - - -
204B ARG 4.2 2.5 - - - -
205B SER* 3.6 35.7 - - - -
208B PHE* 3.6 24.4 - + + -
211B SER* 1.3 76.0 + - - +
213B THR* 1.3 80.6 + - - +
214B VAL* 3.7 10.3 + - + +
243B PHE* 4.7 2.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B MET* 4.2 15.3 - - + -
161B MET 3.6 12.3 - - - +
162B ARG* 3.6 23.9 + - + +
211B SER* 4.8 2.3 + - - -
212B TRP* 1.3 82.6 + - - +
214B VAL* 1.3 66.7 + - - +
215B MET* 3.7 30.3 + - + +
271B PHE* 4.8 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B MET* 2.9 28.6 - - - +
161B MET* 2.8 33.6 + - + +
163B LEU* 4.2 13.7 - - + -
176B VAL* 3.5 22.0 - - + -
178B LEU* 5.4 5.3 - - + +
200B LEU* 3.2 39.0 - - + -
202B ARG 4.1 9.2 - - - +
212B TRP* 4.2 18.4 - - - +
213B THR* 1.3 73.0 - - - +
215B MET* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PHE* 4.1 42.0 - - + -
158B THR* 3.4 12.8 - - + -
159B LEU 3.4 3.6 - - - -
160B MET* 3.7 22.4 - - + +
200B LEU* 3.0 12.3 - - - +
201B THR* 2.9 46.1 + - + +
202B ARG 5.4 1.2 + - - +
213B THR* 3.7 28.9 + - + +
214B VAL* 1.3 83.6 - - - +
216B HIS* 1.3 59.7 + - - +
217B PRO* 3.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B THR* 3.3 2.2 - - - -
159B LEU* 2.7 36.7 + - + +
178B LEU* 4.6 6.3 - - + +
198B LEU* 3.3 33.9 - - + +
199B THR* 2.8 31.1 + - - +
200B LEU* 3.9 11.4 - - + +
215B MET* 1.3 74.3 - - - +
217B PRO* 1.3 76.7 + - - +
218B ILE* 3.4 3.2 + - + +
222B SER* 2.4 41.6 + - - -
223B PRO* 4.5 0.9 - - + -
224B ILE* 3.8 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LYS* 5.1 8.7 - - + -
157B PRO 3.8 0.4 - - - +
158B THR* 3.4 17.9 - - + +
199B THR* 3.8 13.5 - - + +
200B LEU 5.2 0.4 - - - -
201B THR* 3.1 36.3 - - + +
215B MET 3.5 1.6 - - - +
216B HIS* 1.3 102.5 + - - +
218B ILE* 1.3 60.8 + - - +
219B ASP* 3.9 10.9 + - + +
222B SER* 4.0 0.7 - - - -
----------------------------------------------------------
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