Contacts of the strand formed by residues 200 - 205 (chain B) in PDB entry 3BSQ
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 THR 200 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 3.4 21.7 + - - +
119B LEU 3.8 2.8 + - - -
120B PRO* 3.5 23.1 - - + +
121B SER 4.8 0.3 + - - -
122B ARG 5.5 0.4 - - - +
124B GLU* 4.2 9.0 - - - +
196B VAL* 3.2 10.5 + - - +
197B CYS 3.0 47.8 + - - +
198B ARG 4.0 3.6 - - - +
199B GLY* 1.3 69.3 + - - -
201B LEU* 1.3 58.6 + - - +
202B GLN* 3.1 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.8 29.2 - - + -
52B LEU* 4.2 7.9 - - + -
117B VAL* 4.5 15.0 - - + +
118B ARG 3.1 15.4 + - - +
119B LEU* 4.2 10.3 - - + -
120B PRO* 3.2 26.0 - - + +
194B PRO* 3.7 28.0 - - + -
195B LEU 3.8 4.5 - - - +
196B VAL* 3.8 7.2 - - + +
200B THR* 1.3 71.9 + - - +
202B GLN* 1.3 59.2 + - - +
203B GLY 3.4 20.9 - - - +
204B LEU* 4.5 0.7 - - + -
224B VAL* 3.6 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PRO* 3.3 18.0 - - - +
122B ARG 3.5 8.0 + - - +
123B CYS* 3.8 5.7 - - - +
124B GLU* 3.0 38.0 + - + +
156B LEU* 5.1 1.0 - - + +
175B LEU* 3.6 21.1 - - + +
195B LEU* 3.0 15.0 + - + +
196B VAL 3.4 1.4 - - - +
197B CYS* 3.8 33.0 - - + -
200B THR* 3.1 24.9 - - + +
201B LEU* 1.3 73.5 - - - +
203B GLY* 1.3 58.7 + - - +
223B GLN* 3.4 10.2 + - - +
224B VAL 3.0 20.4 + - - -
225B CYS* 4.1 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 4.5 3.1 - - - -
193B GLY 3.9 0.5 - - - +
195B LEU* 2.6 46.8 + - - +
201B LEU* 3.4 11.7 - - - +
202B GLN* 1.3 75.9 - - - +
204B LEU* 1.3 63.4 + - - -
221B TYR* 4.4 3.4 - - - -
222B THR 3.0 13.7 - - - -
224B VAL* 4.0 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.6 25.8 - - + -
52B LEU* 3.8 22.2 - - + +
53B THR 3.5 26.0 - - - +
54B ALA* 4.5 1.3 - - + +
98B ASP 4.5 3.8 - - - +
99B LEU* 3.9 18.2 - - + -
192B GLY* 3.6 25.8 - - - +
193B GLY 3.2 9.0 - - - +
201B LEU* 4.5 1.3 - - + -
203B GLY* 1.3 79.9 - - - +
205B VAL* 1.3 66.5 + - - +
206B SER* 4.1 0.5 - - - -
221B TYR* 3.1 6.0 - - - -
222B THR* 3.1 32.5 + - + +
224B VAL* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SO4 4.2 15.5 - - - +
54B ALA* 4.0 7.1 - - - +
132B VAL* 4.1 17.3 - - + -
133B SER 5.4 0.2 - - - +
186B ALA* 3.9 22.4 - - + -
190B ASP* 3.2 21.8 - - + +
191B SER* 3.6 21.4 - - - +
192B GLY* 2.8 24.8 + - - +
193B GLY* 3.0 21.3 + - - +
204B LEU* 1.3 71.3 - - - +
206B SER* 1.3 59.1 + - - +
220B VAL 4.1 2.2 - - - +
221B TYR* 3.6 19.8 - - + -
----------------------------------------------------------
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