Contacts of the strand formed by residues 260 - 266 (chain C) in PDB entry 2C10
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 THR 260 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C MET* 3.5 10.0 - - - +
249C VAL* 3.5 4.3 - - - +
250C ASN* 2.8 56.0 + - - +
258C ARG 4.0 8.1 + - - +
259C TRP* 1.3 82.1 - - - +
261C ILE* 1.3 65.1 + - - +
262C GLN* 4.4 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C MET* 3.8 13.1 - - + +
183C ILE* 5.0 1.6 - - + -
187C GLU* 3.3 40.1 + - + +
247C LEU* 4.3 20.0 - - + -
248C LEU 3.4 4.0 - - - +
249C VAL* 3.7 28.0 - - + -
260C THR* 1.3 74.6 - - - +
262C GLN* 1.3 61.4 + - - +
263C LYS 3.5 24.0 - - - +
264C VAL* 3.9 18.6 - - + -
272C ASP 4.6 5.5 - - - +
273C SER* 5.5 6.2 - - - -
274C LEU* 5.1 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ALA* 3.6 21.1 - - - +
248C LEU* 2.9 35.7 + - + +
250C ASN* 3.6 36.4 + - + +
260C THR* 3.7 4.7 + - - +
261C ILE* 1.3 73.9 - - - +
263C LYS* 1.3 70.4 + - - +
272C ASP* 4.3 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C TRP* 3.7 21.5 - - + -
247C LEU* 3.7 1.0 - - - -
248C LEU* 3.0 36.8 + - + -
261C ILE* 3.4 9.4 - - - +
262C GLN* 1.3 84.8 + - - +
264C VAL* 1.3 66.6 + - - +
270C TYR* 4.1 22.7 - - + -
271C TYR 4.1 12.6 - - - +
272C ASP* 3.2 26.5 + - - +
553D TRP* 4.0 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C TRP* 4.7 1.8 - - - -
245C LEU* 3.9 24.2 - - + -
246C GLU 3.6 3.4 - - - -
247C LEU* 3.9 11.7 - - + -
261C ILE* 3.9 13.7 - - + -
263C LYS* 1.3 81.6 - - - +
265C PHE* 1.3 66.8 + - - +
270C TYR* 3.4 9.2 - - - -
271C TYR* 2.9 44.2 + - + +
273C SER* 3.8 29.6 - - - +
274C LEU* 3.8 7.4 - - + +
277C LEU* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C TRP* 4.3 2.5 - - + -
244C GLY 3.3 8.1 - - - +
245C LEU* 3.4 4.2 - - - +
246C GLU* 2.8 47.3 + - + +
264C VAL* 1.3 75.6 - - - +
266C TYR* 1.3 61.7 + - - +
268C GLY* 3.5 33.4 - - - -
269C ARG 3.1 25.6 - - - -
270C TYR* 3.4 42.8 - + + -
375C ASN 4.1 3.4 - - - -
376C SER* 3.6 23.3 - - - -
377C PRO* 3.5 28.7 - - + -
501C PHE* 3.8 16.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU* 3.9 28.1 - - + +
195C LEU* 5.8 0.9 - - + -
198C CYS* 3.3 34.5 - - - +
199C CYS* 5.2 0.7 - - - -
243C VAL 4.1 12.6 - - - -
244C GLY 3.3 6.1 - - - -
245C LEU* 3.9 23.1 - - + -
265C PHE* 1.3 73.7 - - - +
267C GLN* 1.3 106.5 + - + +
268C GLY 3.1 2.6 + - - -
269C ARG* 2.9 25.3 + - - +
271C TYR* 4.0 10.8 + + + -
277C LEU* 3.8 35.7 - - + -
286C VAL* 4.1 14.6 - - + -
287C ASN 5.3 0.2 - - - -
288C VAL* 3.4 9.0 - - + +
----------------------------------------------------------
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