Contacts of the helix formed by residues 268 - 273 (chain C) in PDB entry 2W4V
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 GLU 268 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ARG* 2.4 65.6 + - + +
266C LEU 3.6 1.4 + - - -
267C LEU* 1.3 67.8 - - - +
269C LYS* 1.4 64.4 - - - +
270C SER* 2.9 6.5 - - - +
271C ARG* 2.7 37.0 + - + +
272C VAL* 3.8 9.1 + - - +
431C TYR* 4.5 8.6 - - - -
473C GLU* 3.6 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LEU* 6.1 2.7 - - - -
267C LEU 2.5 18.5 + - - +
268C GLU* 1.4 75.3 - - - +
270C SER* 1.3 51.3 + - - +
272C VAL* 2.7 42.9 - - - +
428C LYS* 3.7 11.4 - - + +
429C SER* 5.8 1.0 - - - +
431C TYR* 5.4 0.7 - - - -
432C ASP* 2.4 60.4 + - - +
473C GLU* 4.2 2.9 + - - +
600C ASP* 4.4 17.9 + - - +
645C ILE* 5.9 5.2 - - - +
649C HIS* 5.7 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C GLU* 2.9 6.5 - - - +
269C LYS* 1.3 78.2 - - - +
271C ARG* 1.3 65.8 + - - -
272C VAL* 3.2 0.8 + - - -
273C THR* 3.7 4.7 + - - -
274C TYR* 3.2 28.6 + - - +
428C LYS* 4.0 17.3 + - - +
473C GLU* 2.9 36.8 + - - +
597C LYS* 5.2 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ALA* 4.0 1.6 - - - -
233C LYS 2.6 25.8 + - - -
234C THR* 2.8 29.8 - - - +
242C ARG* 2.8 40.9 - - - +
268C GLU* 2.5 36.5 - - + +
270C SER* 1.3 74.3 + - - +
272C VAL* 1.3 63.4 + - - +
274C TYR 2.9 11.9 + - - +
275C GLN* 1.5 84.6 + - - +
276C GLN* 3.0 15.4 - - - +
279C GLU* 2.7 19.8 - - - +
280C ARG 2.9 5.6 + - - -
281C ASN* 4.1 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C GLU* 4.0 5.4 - - - +
269C LYS 2.7 26.5 - - - +
270C SER 4.1 0.4 - - - +
271C ARG* 1.3 77.8 - - - +
273C THR* 1.3 75.1 + - + +
281C ASN* 4.8 2.1 - - - +
282C TYR* 5.3 12.6 - - + -
311C PHE* 3.2 35.1 - - + +
355C ILE* 5.9 4.5 - - + -
427C ALA* 5.1 2.9 - - + -
428C LYS* 3.0 34.5 - - + +
431C TYR* 3.6 44.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C SER 3.7 0.4 + - - -
271C ARG 4.2 0.2 - - - -
272C VAL* 1.3 93.7 - - + +
274C TYR* 1.3 63.4 + - - +
311C PHE* 4.4 23.1 - - + +
314C GLN* 5.0 3.8 - - - +
424C GLY* 4.0 13.5 - - - -
427C ALA* 3.9 19.1 - - + -
428C LYS* 3.0 33.8 + - + -
----------------------------------------------------------
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