Contacts of the strand formed by residues 207 - 210 (chain B) in PDB entry 2WA2
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 GLY 207 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLN* 4.0 5.4 - - - -
205B GLY 4.0 0.2 + - - -
206B GLY* 1.3 74.3 - - - -
208B LEU* 1.3 61.0 + - - -
209B ILE* 4.8 0.7 - - - -
222B TYR 3.6 0.3 - - - +
223B PHE* 3.3 12.2 - - - -
224B VAL* 2.9 34.9 + - - +
227B ILE 3.0 10.2 + - - -
229B ASN* 3.2 15.5 - - - -
231B ILE* 4.3 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B VAL* 3.6 32.3 - - + -
188B PRO* 4.0 7.9 - - + -
197B LEU* 3.9 17.3 - - + -
207B GLY* 1.3 72.8 - - - -
209B ILE* 1.3 55.9 + - - +
221B MET* 3.7 22.0 - - + -
222B TYR 3.3 2.5 - - - -
223B PHE* 3.7 17.3 - - + +
229B ASN* 2.9 18.2 + - - +
231B ILE* 3.9 20.8 - - + +
234B ASN* 2.6 28.5 + - - +
235B VAL* 3.2 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TRP* 4.1 22.2 - - + -
66B ILE* 4.1 31.6 - - + -
69B ARG* 6.1 0.2 - - + -
208B LEU* 1.3 80.3 - - - +
210B ARG* 1.3 63.0 + - - +
211B VAL* 4.1 1.4 + - + -
221B MET* 3.3 9.8 - - - +
222B TYR* 2.8 46.9 + - + +
224B VAL* 4.1 13.5 - - + -
227B ILE* 4.1 40.4 - - + -
229B ASN* 4.1 11.7 - - - +
234B ASN* 3.6 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TRP* 3.7 13.2 - - - -
209B ILE* 1.3 74.2 - - - +
211B VAL* 1.3 73.6 + - - +
212B PRO* 3.6 10.8 - - + +
214B SER* 3.7 21.2 + - - -
215B ARG 2.9 26.9 + - - -
216B ASN* 4.2 0.8 + - - +
218B THR 2.9 19.4 + - - -
219B HIS* 3.3 9.1 - - - +
220B GLU 2.8 35.6 + - - +
221B MET* 4.2 1.8 - - + -
234B ASN* 3.9 5.8 - - - +
238B VAL* 3.6 39.1 - - + +
241B GLN* 4.6 12.7 + - - +
242B LEU* 3.7 21.6 - - - +
245B ARG* 5.9 0.4 - - - +
----------------------------------------------------------
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