Contacts of the strand formed by residues 297 - 302 (chain B) in PDB entry 4EVI
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 LYS 297 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ASP 4.9 0.8 + - - -
197B ALA* 2.6 32.4 + - - +
199B GLU 5.4 2.2 + - - -
201B LEU* 4.3 14.2 - - + +
262B ASP 3.0 14.0 + - - +
263B ALA* 3.2 7.7 - - + +
264B VAL 3.0 23.9 + - - -
289B LEU* 3.5 11.2 - - - +
296B GLY* 1.3 76.4 - - - +
298B LEU* 1.3 60.4 + - - +
299B MET* 3.9 24.2 - - + -
365B GLU* 2.7 31.7 + - + +
366B VAL 3.7 11.9 - - - +
367B TYR* 4.4 22.4 - - + -
368B PRO* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B VAL* 3.6 11.2 - - + +
266B PHE* 3.7 36.1 - - + -
282B LEU* 3.7 24.2 - - + -
285B CYS* 4.9 5.6 - - + -
289B LEU* 3.6 5.6 - - + +
297B LYS* 1.3 74.2 - - - +
299B MET* 1.3 68.2 + - - +
300B ILE* 4.1 19.7 - - + -
344B PHE* 4.9 3.1 - - + -
349B PHE* 3.7 29.8 - - + -
364B ILE 3.6 0.4 - - - +
365B GLU* 3.4 4.9 - - - -
366B VAL* 2.8 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ALA* 3.9 14.8 - - + +
198B PHE* 3.9 27.1 - - + -
201B LEU* 4.2 4.5 - - - -
204B LEU* 4.2 14.1 - - - -
263B ALA* 3.8 22.2 - - + -
264B VAL 2.7 15.5 + - - +
265B LEU* 3.2 17.6 - - + +
266B PHE* 2.8 27.4 + - - +
297B LYS* 3.9 23.6 - - + -
298B LEU* 1.3 79.6 - - - +
300B ILE* 1.3 63.4 + - - +
301B ALA 4.1 0.2 - - - -
363B LEU* 3.9 30.3 - - + -
364B ILE 3.4 3.8 - - - -
365B GLU* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PHE* 3.6 8.7 - - + +
270B LEU* 3.6 29.4 - - + -
282B LEU* 4.9 0.9 - - + -
298B LEU* 4.1 24.5 - - + -
299B MET* 1.3 75.9 - - - +
301B ALA* 1.3 60.7 + - - +
302B ASP* 3.7 22.7 + - + +
340B TRP* 4.1 16.4 - - + -
344B PHE* 3.7 33.9 - - + -
362B VAL 3.6 1.6 - - - +
363B LEU* 3.4 4.1 - - - +
364B ILE* 2.7 54.9 + - + +
366B VAL* 4.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PHE* 3.6 33.1 - - + -
190B LEU* 4.8 4.9 - - + -
265B LEU* 4.4 11.9 - - + -
266B PHE 2.9 8.7 + - - +
267B LYS* 3.4 17.1 - - + +
268B TRP* 2.9 27.0 + - - +
299B MET 4.1 1.0 - - - -
300B ILE* 1.3 69.6 - - - +
302B ASP* 1.3 60.5 + - - +
361B ARG* 5.2 1.5 - - - -
362B VAL 3.4 7.4 - - - +
363B LEU* 4.5 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PHE 4.9 0.7 - - - +
268B TRP* 3.6 11.9 + - - -
269B VAL 3.7 2.6 + - - -
270B LEU* 3.9 5.0 + - - +
271B CYS* 3.4 48.0 + - - +
300B ILE* 3.7 20.8 + - + +
301B ALA* 1.3 75.9 - - - +
303B HIS* 1.3 87.0 + - - +
304B VAL* 5.5 0.2 - - - -
340B TRP* 4.3 12.0 - - + -
361B ARG* 3.4 14.8 - - - +
362B VAL* 2.9 37.0 + - - +
364B ILE* 5.9 1.3 - - + +
----------------------------------------------------------
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