Contacts of the strand formed by residues 196 - 202 (chain A) in PDB entry 3QO0
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 196 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LYS 3.7 1.2 - - - +
155A VAL* 3.2 7.4 - - - +
156A ASP* 2.8 52.7 + - - +
157A ASN* 6.1 2.7 - - - +
195A LYS* 1.3 78.4 - - + +
197A TYR* 1.3 62.0 + - - +
198A ALA* 4.7 7.1 - - + +
213A SER* 4.4 18.4 - - - +
214A PHE 3.7 7.0 - - - +
215A ASN* 3.4 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 3.6 6.5 - - - +
137A VAL* 4.1 20.0 - - + -
153A TRP* 4.9 2.2 - - + -
154A LYS 3.8 2.7 - - - -
155A VAL* 3.7 30.3 - - + -
184A LEU* 4.5 2.9 - - + -
186A LEU* 3.8 13.9 - - + +
190A ASP 3.7 1.0 + - - -
191A TYR* 2.5 54.1 + + - -
194A HIS* 3.4 28.7 - - + +
195A LYS 3.5 15.9 - - - -
196A VAL* 1.3 68.2 - - - +
198A ALA* 1.3 57.7 + - - +
213A SER* 3.1 4.5 - - - -
214A PHE* 3.0 66.5 + + + -
216A ARG* 4.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLN 3.8 0.3 - - - +
153A TRP* 3.3 12.0 - - - -
154A LYS* 2.9 50.3 + - + +
196A VAL* 4.7 8.7 - - + +
197A TYR* 1.3 74.4 - - - +
199A CYS* 1.3 57.9 + - - +
200A GLU* 4.1 0.7 - - + -
211A THR* 4.0 15.7 - - + -
212A LYS 3.6 4.0 - - - -
213A SER* 3.8 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A VAL* 5.4 0.2 - - - +
122A ILE* 4.1 4.0 - - + -
139A CYS* 2.0 54.1 - - + -
151A VAL* 3.8 21.3 - - - -
152A GLN 3.5 2.9 - - - -
153A TRP* 4.0 12.1 - - + -
198A ALA* 1.3 72.7 - - - +
200A GLU* 1.3 57.2 + - - +
201A VAL* 4.1 9.9 - - - +
210A VAL 3.7 1.7 - - - +
211A THR* 3.2 4.5 - - - -
212A LYS* 2.9 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LYS* 3.5 8.5 + - - +
151A VAL* 3.3 5.5 - - - -
152A GLN* 2.7 75.2 + - + +
154A LYS* 6.1 3.8 - - + -
198A ALA* 4.1 0.6 - - + -
199A CYS* 1.3 71.4 - - - +
201A VAL* 1.3 64.3 + - - +
202A THR* 4.1 4.9 + - - -
209A PRO* 4.0 26.8 - - + +
210A VAL 3.4 3.8 - - - +
211A THR* 3.4 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO* 4.0 18.6 - - + -
120A VAL* 3.8 25.4 - - + -
141A LEU* 3.5 49.1 - - + -
150A LYS 3.4 3.1 - - - +
151A VAL* 4.3 2.9 - - + -
199A CYS* 4.1 10.5 - - - +
200A GLU* 1.3 77.1 - - - +
202A THR* 1.3 69.1 + - - +
203A HIS* 4.8 0.2 - - + -
206A LEU* 3.8 10.7 - - + +
209A PRO* 3.1 5.7 - - - +
210A VAL 2.6 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ALA* 3.4 6.9 - - - +
150A LYS* 2.9 61.3 + - + +
200A GLU* 4.4 7.3 + - - -
201A VAL* 1.3 74.2 - - - +
203A HIS* 1.3 65.7 + - - +
209A PRO* 3.6 27.1 - - + +
----------------------------------------------------------
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