Contacts of the strand formed by residues 157 - 162 (chain O) in PDB entry 2V10
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 157 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144O PHE* 3.5 6.2 - - - -
155O GLU* 2.4 36.7 + - + +
156O ASP* 1.4 70.3 - - - +
158O PHE* 1.3 69.9 + - - +
179O GLY 2.8 23.8 + - - -
180O GLY* 3.5 33.0 - - - +
326O GLU* 4.0 25.4 - - + +
327O PHE 3.2 9.6 - - - +
328O ASP* 3.7 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O THR* 4.4 2.2 - - + -
130O MET* 3.4 47.1 - - + -
144O PHE* 3.6 38.8 - + + -
157O VAL* 1.3 81.1 - - - +
159O SER* 1.3 57.2 + - - +
160O PHE* 3.7 14.1 - + - -
176O ILE* 4.7 0.9 - - + -
177O VAL 3.3 13.0 - - - +
178O LEU* 3.9 15.3 - - + -
201O TRP* 3.9 20.0 - + - -
327O PHE* 2.8 69.3 + + + +
329O ARG* 4.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 159 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158O PHE* 1.3 71.6 - - - +
160O PHE* 1.3 66.2 + - - +
175O GLN 4.4 0.2 - - - -
176O ILE* 3.2 12.0 - - - +
177O VAL 2.9 26.8 + - - -
180O GLY 3.4 17.2 + - - -
181O SER* 4.0 1.4 - - - -
324O TYR* 3.6 25.1 - - - -
325O THR 3.0 14.0 + - - -
326O GLU* 3.2 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 160 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O LEU* 4.8 0.9 - - + -
37O PHE* 3.8 18.2 - - + -
39O THR* 4.6 1.1 - - + -
130O MET* 4.6 3.4 - - + -
158O PHE* 3.7 29.6 - + - -
159O SER* 1.3 80.4 - - - +
161O TYR* 1.3 60.3 + - - +
162O TYR* 3.7 24.9 - + - -
175O GLN 3.7 2.5 - - - -
176O ILE* 3.3 33.4 - - + -
227O THR* 3.5 39.7 - - + -
320O ILE* 4.3 15.9 - - + +
324O TYR* 3.6 14.3 - - - -
325O THR* 2.9 31.6 + - - +
327O PHE* 3.7 15.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 161 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160O PHE* 1.3 76.2 - - - +
162O TYR* 1.3 78.5 + - - +
163O ASN* 3.5 24.3 + - + +
172O LEU* 3.1 35.8 - - + +
174O GLY* 2.9 30.1 - - - -
175O GLN* 3.1 22.9 + - + +
185O HIS* 3.2 43.7 + + + -
320O ILE* 5.1 0.4 - - - -
321O ARG 5.9 0.4 - - - -
324O TYR* 3.8 20.2 - + + +
339O ALA* 4.5 12.1 - - + -
340O ARG* 3.5 22.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 162 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O LEU* 3.6 24.2 - - + -
20O TYR* 3.6 33.7 + + + +
37O PHE 4.3 2.3 + - - -
160O PHE* 3.7 20.9 - + - -
161O TYR* 1.3 101.7 - - - +
163O ASN* 1.4 61.9 + - - +
164O ARG* 4.0 0.3 + - - +
173O GLY 3.8 3.6 - - - -
227O THR* 2.3 39.3 + - - -
317O ALA* 3.9 26.0 - - - -
320O ILE* 3.8 33.3 + - + -
321O ARG* 3.4 26.8 - - - +
1341O C61 3.1 19.6 - - - -
----------------------------------------------------------
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