Contacts of the strand formed by residues 268 - 272 (chain L) in PDB entry 1VYH
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 CYS 268 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259L ARG* 3.6 35.0 - - - -
260L VAL 3.3 15.7 - - - +
261L TRP* 3.8 22.7 - - + -
267L GLU* 1.3 83.3 - - - +
269L LYS* 1.3 65.9 + - - +
270L ALA* 3.2 10.1 + - - +
271L GLU* 5.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 269 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248L LEU* 4.4 13.5 - - + -
260L VAL* 3.0 17.3 + - + +
262L VAL* 3.8 22.0 - - + -
267L GLU* 3.4 25.8 + - - +
268L CYS* 1.3 70.8 - - - +
270L ALA* 1.3 62.9 + - + +
325L VAL* 5.3 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 270 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258L VAL 4.4 0.2 - - - -
259L ARG* 3.5 5.7 - - - +
260L VAL* 3.1 29.0 + - + +
268L CYS* 3.2 8.8 - - - +
269L LYS* 1.3 83.1 - - - +
271L GLU* 1.3 60.5 + - - +
272L LEU* 3.9 23.8 - - + -
325L VAL* 4.0 30.1 - - + +
328L GLY* 5.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 271 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257L THR* 3.6 25.5 + - + +
258L VAL 3.5 3.6 - - - -
259L ARG* 3.9 32.5 + - + +
268L CYS* 5.8 2.5 - - - -
270L ALA* 1.3 73.7 - - - +
272L LEU* 1.3 64.8 + - - +
273L ARG* 3.3 38.4 + - + +
328L GLY* 6.0 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 272 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256L GLN 4.2 1.0 - - - +
257L THR* 3.6 5.2 + - - -
258L VAL* 2.7 60.2 + - + +
260L VAL* 4.8 2.2 - - + -
270L ALA* 3.9 22.9 - - + -
271L GLU* 1.3 75.4 - - - +
273L ARG* 1.3 61.2 + - - +
275L HIS* 5.6 0.7 - - - +
311L LEU* 3.9 13.9 - - + -
323L TRP* 3.2 59.0 - - + -
325L VAL* 4.8 11.9 - - + -
328L GLY* 4.1 22.9 - - - +
----------------------------------------------------------
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