Contacts of the strand formed by residues 271 - 274 (chain B) in PDB entry 4YVF
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 ILE 271 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 4.1 20.2 - - + -
209B VAL* 4.7 6.1 - - + -
211B ILE* 4.0 29.4 - - + -
214B LYS* 3.9 30.3 - - + -
215B VAL 3.1 6.2 + - - +
216B ALA* 3.4 11.6 - - + -
217B VAL* 2.8 27.1 + - - +
232B LEU* 5.1 6.3 - - + -
270B ASN* 1.3 85.0 - - + +
272B PHE* 1.3 70.4 + - - +
273B VAL* 4.0 21.1 - - + -
295B ILE* 3.2 22.4 - - + +
297B CYS* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B VAL* 3.4 26.0 - - + +
262B MET* 3.8 20.4 - - + -
266B CYS* 3.5 42.0 - - - -
269B GLY* 3.1 34.3 - - - -
271B ILE* 1.3 77.0 - - - +
273B VAL* 1.3 66.8 + - - +
282B ILE* 3.6 17.7 - - + -
290B MET* 3.8 32.5 - - + -
294B ALA* 4.1 5.8 - - + -
295B ILE 2.6 18.1 + - - +
296B VAL* 3.6 6.0 - - + -
297B CYS* 2.8 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU* 4.0 27.4 - - + -
203B ILE* 4.5 1.3 - - + -
216B ALA* 5.8 0.2 - - + -
217B VAL 2.8 12.7 + - - +
218B VAL* 3.3 10.1 - - + +
219B ALA* 2.8 26.6 + - - -
228B CYS* 4.2 6.7 - - + -
232B LEU* 4.7 7.2 - - + -
271B ILE* 4.0 15.5 - - + -
272B PHE* 1.3 80.7 - - - +
274B THR* 1.3 63.6 + - - +
275B THR* 3.9 6.7 - - + -
297B CYS* 3.2 20.4 - - - +
299B ILE* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ALA* 4.0 5.2 - - + -
262B MET* 5.1 0.2 - - + -
273B VAL* 1.3 72.0 - - - +
275B THR* 1.3 62.7 + - - +
281B ILE* 3.5 29.2 - - + -
282B ILE* 3.6 27.1 - - + -
297B CYS 3.0 4.8 + - - +
298B ASN* 2.5 39.0 + - - +
299B ILE 2.9 22.2 + - - -
300B GLY 3.1 0.2 + - - -
305B GLU* 3.2 20.3 - - - +
306B ILE* 3.9 9.5 - - + +
----------------------------------------------------------
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