Contacts of the strand formed by residues 273 - 277 (chain B) in PDB entry 2C1H
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 VAL 273 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ILE* 4.4 0.9 - - - -
250B VAL* 3.5 6.5 - - + +
252B VAL* 4.7 5.4 - - + -
262B VAL* 4.1 27.4 - - + +
265B THR* 3.8 31.4 - - + +
266B LYS* 4.0 26.9 - - + -
271B VAL 3.3 15.0 - - - +
272B PRO* 1.3 73.6 - - - +
274B ALA* 1.3 70.6 + - - +
311B GLY 4.0 10.3 - - - +
312B ALA* 3.7 2.1 - - - -
313B ASP* 2.8 37.2 + - - +
314B ILE* 3.3 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LEU* 4.0 8.7 - - + -
249B ILE* 3.7 20.3 - - + +
250B VAL 2.7 11.6 + - - +
251B MET* 3.0 23.1 - - + -
252B VAL* 2.9 23.2 + - - +
273B VAL* 1.3 80.4 - - - +
275B ILE* 1.3 63.3 + - - +
312B ALA* 5.1 0.2 - - - -
314B ILE* 3.3 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B MET* 3.7 5.9 - - - +
252B VAL 3.5 14.1 - - - +
254B PRO 4.5 0.2 - - - +
255B GLY* 3.6 22.2 - - - -
259B LEU* 3.5 32.1 - - + -
262B VAL* 3.7 17.0 - - + -
274B ALA* 1.3 77.0 - - - +
276B TYR* 1.3 63.8 + - - +
307B MET* 3.8 16.2 - - + -
312B ALA* 3.9 11.4 - - + -
314B ILE 3.0 16.1 + - - +
315B ILE* 3.6 25.1 - - + -
316B PHE* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PRO* 3.6 12.3 - - + +
82B ASP* 4.2 1.8 - - - -
84B PHE* 3.6 23.0 - + - -
197B TYR* 3.3 31.4 - + - -
251B MET* 3.8 12.5 - - - -
252B VAL 3.3 5.1 + - - -
253B LYS* 3.7 25.1 - - + -
254B PRO 3.7 0.7 - - - -
255B GLY* 3.1 29.0 + - - -
275B ILE* 1.3 77.8 - - - +
277B HIS* 1.3 69.4 + - - +
278B VAL* 3.2 4.5 + - + +
307B MET* 4.8 0.9 - - - -
316B PHE* 3.7 26.0 - + + -
318B TYR* 2.8 42.1 + + - -
1330B DSB 3.6 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LEU* 4.4 7.4 - - + -
275B ILE 4.0 0.8 + - - -
276B TYR* 1.3 71.5 - - - +
278B VAL* 1.3 66.3 + - - +
281B GLU* 3.0 37.4 + - + -
282B TYR* 4.9 9.5 + + + +
285B VAL* 5.5 2.5 - - + -
300B MET* 4.3 20.1 + - - -
303B SER* 4.4 17.5 + - - -
304B LEU* 4.1 10.1 - - + +
307B MET* 3.5 23.1 - - + +
315B ILE* 4.5 4.4 - - + +
316B PHE 2.7 18.8 + - - +
317B THR* 3.1 30.2 - - - -
318B TYR* 3.5 21.3 - - - -
319B TYR* 5.0 5.2 - - + -
----------------------------------------------------------
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