Contacts of the strand formed by residues 152 - 157 (chain B) in PDB entry 2VES
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 PHE 152 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PHE* 3.8 2.9 - - - -
151B GLY* 1.3 74.6 - - - +
153B LYS* 1.3 61.0 + - - +
154B VAL* 3.5 27.8 - - + -
175B ASP* 3.9 3.4 + - - +
176B PHE* 3.0 60.5 + + + +
177B SER 5.7 1.6 - - - +
243B ILE* 4.1 21.3 - - + -
246B LEU* 4.5 14.8 - - + -
253B LEU* 3.7 46.9 - - + +
255B GLY 3.4 12.8 - - - -
257B PHE* 5.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PHE* 3.9 34.4 - - + -
152B PHE* 1.3 77.1 - - - +
154B VAL* 1.3 68.6 + - - +
155B SER* 3.9 1.1 - - - +
173B SER* 3.1 28.4 + - - +
174B VAL 3.2 14.6 - - - +
175B ASP* 4.2 11.4 - - + +
255B GLY 3.2 6.3 + - - +
256B GLU* 3.2 35.8 + - + +
257B PHE* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PHE* 3.5 33.7 - - + -
153B LYS* 1.3 77.4 - - - +
155B SER* 1.3 66.0 + - - +
156B PHE* 5.3 0.4 - - + -
172B ALA 4.0 0.9 - - - +
173B SER* 3.4 1.1 - - - -
174B VAL* 2.8 46.2 + - + +
176B PHE* 3.9 4.7 - - + -
239B ILE* 3.9 23.1 - - + +
242B ALA* 4.1 13.7 - - + -
243B ILE* 3.9 12.3 - - + -
246B LEU* 5.3 1.8 - - + -
257B PHE* 3.5 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS* 3.9 2.1 - - - -
154B VAL* 1.3 74.2 - - - +
156B PHE* 1.3 63.0 + - - +
171B GLN* 4.6 6.5 - - - -
172B ALA 3.4 6.7 - - - -
173B SER* 2.6 24.7 + - - -
256B GLU* 3.5 15.9 + - - -
257B PHE* 2.8 16.5 + - - +
258B ARG* 3.3 15.5 - - - -
259B GLY 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 4.3 0.6 - - + -
155B SER* 1.3 73.5 - - - +
157B GLU* 1.3 91.3 + - - +
158B ILE* 3.8 10.1 - - + -
171B GLN* 3.2 5.9 + - - +
172B ALA 2.9 33.2 + - - +
235B VAL* 3.5 7.8 - - + +
238B LYS* 3.5 51.6 - - + -
239B ILE* 3.7 20.6 - - + -
242B ALA* 4.7 4.3 - - + -
257B PHE* 4.1 21.3 - + - -
259B GLY* 3.4 9.6 - - - -
261B LYS* 4.0 5.6 - - - -
262B SER* 3.2 47.1 - - - -
267B ASN* 5.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PHE* 1.3 81.9 - - - +
158B ILE* 1.3 72.5 + - - +
170B GLN* 3.2 9.7 - - - +
171B GLN* 3.9 21.4 - - + +
259B GLY 3.0 9.8 + - - +
260B PHE* 3.4 15.6 - - + -
261B LYS 2.9 26.5 + - - -
195C ARG* 2.8 53.5 + - - +
218C ASP* 6.1 0.3 - - - +
219C GLU* 4.7 9.2 + - - +
----------------------------------------------------------
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