Contacts of the strand formed by residues 261 - 267 (chain C) in PDB entry 2V90
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 261 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C LEU* 4.2 0.7 - - + -
259C PHE* 3.7 19.1 - + + -
260C GLY* 1.3 77.4 - - - +
262C LEU* 1.3 59.5 + - - +
263C LEU* 4.2 16.6 - - + -
277C LEU* 3.2 31.0 - - + -
279C GLU 3.3 13.2 - - - +
280C VAL* 4.4 4.3 - - + -
281C ASP* 3.4 7.5 + - - -
286C ALA* 3.9 7.6 - - + -
291C MET* 3.3 29.6 - - + -
297C LEU* 5.5 0.4 - - + -
317C ILE* 4.2 19.7 - - + -
326C LEU* 3.9 23.1 - - + -
338E SER* 3.5 4.2 + - - -
339E VAL* 2.9 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C PHE* 1.3 72.9 - - - +
263C LEU* 1.3 61.6 + - - +
264C ARG* 5.3 2.9 - - + +
277C LEU* 3.4 4.5 - - - -
278C TRP* 2.8 47.9 + - + -
279C GLU* 3.0 52.0 + - + +
281C ASP* 4.9 1.5 + - - +
336E GLU* 4.4 24.0 - - + +
337E THR 3.6 24.9 - - - +
338E SER* 4.0 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C PHE* 4.0 9.6 + - + -
262C LEU* 1.3 73.4 - - - +
264C ARG* 1.3 60.0 + - - +
275C GLN* 3.8 24.5 - - + +
276C PHE 3.3 17.7 - - - +
277C LEU* 3.5 23.8 - - + -
297C LEU* 4.3 7.4 - - + -
310C HIS* 3.3 17.1 - - + -
313C THR* 3.9 28.7 - - + -
314C VAL* 4.5 7.6 - - + -
317C ILE* 4.3 16.2 - - + -
336E GLU* 3.1 4.3 - - - +
337E THR* 2.8 39.8 + - - +
339E VAL* 5.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C LEU* 4.0 4.6 + - + +
263C LEU* 1.3 76.2 - - - +
265C GLU* 1.3 72.2 + - - +
266C GLU* 3.7 13.0 - - - -
275C GLN* 4.0 2.7 - - - -
276C PHE* 2.8 37.0 + - - +
278C TRP* 3.5 54.4 - - + +
310C HIS* 4.3 0.2 - - - -
293E ALA* 3.9 23.3 + - - +
294E GLY* 4.1 1.3 - - - -
331E PRO* 3.8 27.9 - - - +
332E GLU 4.7 6.3 + - - -
333E ALA* 5.4 2.4 + - - +
335E ARG 3.5 8.2 + - - +
336E GLU* 2.7 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C ARG* 1.3 80.2 + - - +
266C GLU* 1.3 78.6 + - - +
267C LYS* 3.8 14.1 - - - +
273C PRO* 3.6 20.6 - - + +
274C GLY 3.4 5.6 - - - -
275C GLN* 3.0 32.1 + - - +
309C GLY* 3.9 2.4 - - - -
310C HIS* 3.2 19.1 + - - +
331E PRO* 5.6 2.6 - - - +
332E GLU* 4.4 3.5 - - - +
335E ARG* 2.8 63.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C ARG* 3.7 5.8 + - - -
265C GLU* 1.3 81.3 - - - +
267C LYS* 1.3 65.9 + - - +
268C GLY 3.8 0.3 + - - -
274C GLY 3.0 28.7 + - - +
276C PHE* 3.7 17.8 - - + -
278C TRP* 3.5 26.9 - - + -
266E GLU* 6.6 0.2 - - + -
276E PHE* 3.4 37.2 - - + -
294E GLY* 2.6 39.7 - - - +
296E ARG* 5.0 6.2 + - - +
331E PRO* 4.8 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C GLU* 3.8 22.1 - - + +
266C GLU* 1.3 80.2 + - - +
268C GLY* 1.3 66.1 + - - +
271C GLY* 3.4 26.2 + - - +
272C ARG 3.3 6.5 - - - +
273C PRO* 4.1 12.3 - - + -
276E PHE* 4.6 9.0 - - - -
296E ARG* 4.5 18.2 + - - +
332E GLU* 4.6 12.7 + - - +
335E ARG* 3.8 15.8 - - - +
----------------------------------------------------------
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