Contacts of the strand formed by residues 203 - 207 (chain B) in PDB entry 2FQ6
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 203 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B SER* 4.5 0.7 - - - +
97B PHE* 4.5 2.9 - - + -
181B ILE* 4.3 11.9 - - + -
182B ILE 3.1 3.6 + - - -
183B MET* 3.3 13.9 - - + +
184B ILE 3.0 26.3 + - - +
197B LEU* 4.3 0.4 - - - -
201B ILE* 3.4 6.6 - - - +
202B ASP* 1.3 93.5 - - + +
204B SER* 1.3 59.7 + - - +
205B ILE* 3.9 14.8 + - + -
223B ALA* 3.9 17.5 - - + -
224B VAL 3.5 6.1 - - - +
225B CYS* 4.2 4.3 - - - -
229B CYS* 4.1 14.6 - - + -
233B LEU* 3.6 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLU* 2.6 32.2 + - - +
184B ILE* 3.7 5.2 - - - -
186B ASN* 3.3 24.1 + - - +
196B ALA* 3.9 11.2 - - - -
197B LEU* 3.8 18.8 - - - +
203B VAL* 1.3 71.9 - - - +
205B ILE* 1.3 60.6 + - - +
206B GLN 4.2 0.2 + - - -
222B THR* 4.0 0.9 + - - +
223B ALA* 3.5 0.5 - - - -
224B VAL* 2.9 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLY 4.8 0.4 - - - +
89B ALA* 3.8 22.0 - - + +
90B VAL* 4.1 19.3 - - + -
93B SER* 3.7 28.0 - - - +
152B PHE* 3.9 28.5 - - + -
183B MET* 4.2 12.8 - - + -
184B ILE 2.8 16.0 + - - +
185B ASP* 3.6 6.7 - - - -
186B ASN* 2.8 26.3 + - - -
203B VAL* 3.9 15.0 - - + +
204B SER* 1.3 75.7 - - - +
206B GLN* 1.3 69.5 + - - +
222B THR 3.3 10.8 - - - +
223B ALA* 4.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B MET* 3.9 2.8 - - - +
75B GLU* 2.9 27.0 + - - +
86B GLY* 4.1 2.5 - - - -
186B ASN* 3.8 14.8 - - + +
187B THR* 3.4 9.8 - - - +
190B ALA* 3.1 46.2 + - - -
191B GLY* 3.2 4.2 - - - +
204B SER 4.2 0.2 + - - -
205B ILE* 1.3 84.7 - - - +
207B ALA* 1.3 68.2 + - - +
208B ALA* 3.2 2.7 + - - +
211B TYR 6.0 0.2 + - - -
212B LEU* 3.6 26.6 + - - +
221B GLY* 3.3 4.5 - - - -
222B THR* 2.9 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLY* 3.6 14.5 - - - -
185B ASP* 4.7 0.2 + - - -
187B THR* 2.9 25.0 + - + +
206B GLN* 1.3 73.0 - - - +
208B ALA* 1.3 60.6 + - - +
209B THR* 3.0 5.2 + - - -
210B LYS* 3.1 26.3 + - + +
211B TYR 4.8 0.2 + - - -
212B LEU 5.4 0.2 + - - -
220B ILE 3.9 0.7 - - - -
700B P3F 3.2 45.0 - - + +
----------------------------------------------------------
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