Contacts of the strand formed by residues 273 - 279 (chain A) in PDB entry 3CRK
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 ILE 273 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 4.8 2.2 - - + -
220A PRO* 3.9 20.0 - - + -
221A ASP 2.8 10.5 + - - +
222A LEU* 3.5 5.7 - - + +
223A GLU* 2.9 25.8 + - - +
253A PHE* 3.9 20.0 - - + -
256A ALA* 4.3 12.6 - - + +
257A MET* 3.5 47.6 - - + +
260A THR* 4.6 2.0 - - - +
272A PRO* 1.3 72.9 - - - +
274A LYS* 1.3 63.1 + - - +
288A MET* 3.5 33.0 - - + -
289A SER 3.5 9.2 - - - +
290A ASP* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLU* 3.5 33.7 - - + +
225A GLN* 6.3 1.1 - - - +
272A PRO* 4.7 1.6 - - - -
273A ILE* 1.3 75.9 - - - +
275A ILE* 1.3 63.0 + - - +
287A LYS 3.4 1.6 - - - +
288A MET* 3.4 3.8 - - - -
289A SER* 2.8 53.0 + - - +
291A ARG* 3.3 39.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A VAL* 3.9 16.6 - - + -
222A LEU* 3.8 22.7 - - + -
223A GLU 2.6 14.3 + - - +
224A ILE* 3.5 14.7 - - + -
225A GLN* 2.9 28.4 + - - +
249A LEU* 4.7 1.6 - - + -
253A PHE* 3.9 12.8 - - + -
274A LYS* 1.3 76.8 - - - +
276A MET* 1.3 63.5 + - - +
277A VAL* 3.8 25.4 - - + -
286A ILE* 4.2 13.2 - - + -
287A LYS 3.2 7.6 - - - +
288A MET* 3.7 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLN* 3.2 44.6 - - + +
227A VAL* 3.7 26.0 - - + -
275A ILE* 1.3 74.5 - - - +
277A VAL* 1.3 68.2 + - - +
278A ALA* 4.8 1.3 - - + +
285A SER 3.6 1.2 - - - +
286A ILE* 3.3 4.5 - - - +
287A LYS* 2.8 45.9 + - + +
349B MET* 3.6 31.9 - - + +
352B PHE* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 3.6 33.0 - - + -
198A SER* 4.4 6.7 - - - +
201A VAL* 4.7 2.7 - - + -
224A ILE* 4.6 0.9 - - + -
225A GLN 2.9 12.7 + - - +
226A GLU* 3.2 17.5 - - + +
227A VAL 2.7 31.7 + - - -
236A ILE* 3.5 21.5 - - + +
275A ILE* 3.8 19.3 - - + -
276A MET* 1.3 78.2 - - - +
278A ALA* 1.3 56.5 + - - +
284A LEU* 3.9 13.7 - - + -
285A SER 3.4 7.9 - - - +
286A ILE* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A VAL* 3.3 10.1 - - + +
236A ILE* 4.1 2.0 - - - -
276A MET* 4.0 2.2 - - + -
277A VAL* 1.3 75.6 - - - +
279A LEU* 1.3 61.1 + - - +
280A GLY 4.2 0.2 - - - -
283A ASP 4.0 0.2 - - - +
284A LEU* 3.4 6.9 - - - +
285A SER* 2.8 37.1 + - - +
349B MET* 4.1 25.1 - - + -
350B GLU 3.9 15.7 - - - +
352B PHE* 4.2 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A VAL 3.0 7.8 + - - +
228A ASN* 3.4 28.7 - - - +
229A ALA* 2.9 32.2 + - - +
230A THR* 3.6 13.0 + - + +
236A ILE* 3.8 27.8 - - + +
237A HIS 4.6 10.3 - - - +
278A ALA* 1.3 74.1 - - - +
280A GLY* 1.3 74.3 + - - +
283A ASP 3.8 2.9 - - - +
284A LEU* 3.8 19.1 - - + -
362A ALA* 3.7 22.9 - - + +
350B GLU 3.9 3.4 - - - +
----------------------------------------------------------
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