Contacts of the strand formed by residues 290 - 299 (chain A) in PDB entry 3CBX
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 GLY 290 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLN 4.0 1.0 - - - +
286A SER* 3.4 1.9 - - - -
287A ASN* 2.9 34.4 + - - +
288A GLU 3.3 1.2 + - - -
289A ARG* 1.3 79.4 - - - +
291A ASP* 1.3 64.6 + - - -
292A GLY 4.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLN 3.4 3.8 - - - -
286A SER* 2.6 32.4 + - - -
287A ASN 5.0 0.2 - - - +
290A GLY* 1.3 74.9 - - - -
292A GLY* 1.3 59.8 + - - +
293A GLY 3.4 1.1 + - - -
328A MET 5.2 2.2 - - - +
329A SER* 3.5 17.2 - - - -
330A ASN* 2.8 42.5 + - - +
331A ASP* 4.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLN* 2.9 20.5 + - - -
290A GLY 4.2 0.6 - - - -
291A ASP* 1.3 72.1 - - - +
293A GLY* 1.3 61.1 + - - +
295A TYR* 4.1 7.3 + - - -
316A MET* 3.4 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLY* 3.5 17.3 - - - -
285A GLN 3.9 1.4 + - - -
291A ASP* 3.4 2.6 + - - +
292A GLY* 1.3 80.9 - - - +
294A ILE* 1.3 61.1 + - - -
295A TYR* 3.9 8.5 - - - -
316A MET* 4.6 8.5 - - - -
330A ASN* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE* 3.7 27.4 - - + -
283A VAL 3.5 4.3 - - - +
284A GLY* 4.5 3.1 - - - -
293A GLY* 1.3 77.4 - - - +
295A TYR* 1.3 61.9 + - - +
316A MET* 3.5 8.3 - - - +
317A LEU* 2.8 52.6 + - + +
325A PHE* 4.0 17.5 - - + -
330A ASN* 3.7 35.7 - - + +
333A ALA* 3.8 25.8 - - + +
334A VAL* 4.2 11.0 - - + -
337A LEU* 5.1 2.9 - - + -
361B TYR* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE* 3.3 12.4 - - - +
283A VAL* 2.8 48.5 + - + +
285A GLN 5.8 0.2 - - - -
292A GLY 4.1 6.2 + - - -
293A GLY 3.9 14.1 - - - -
294A ILE* 1.3 77.2 - - - +
296A ILE* 1.3 65.1 + - - +
297A GLY 3.3 0.5 + - - -
314A GLY* 3.3 22.7 - - - +
315A ASP 3.3 8.1 - - - +
316A MET* 3.1 37.5 - - + +
354A SER* 3.7 20.1 - - - -
2001A MPD 6.1 0.4 - - + -
358B TRP* 4.1 24.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.9 31.4 - - + -
281A SER 3.4 4.5 - - - +
282A ILE* 4.1 9.0 - - + -
295A TYR* 1.3 71.3 - - - +
297A GLY* 1.3 61.2 + - - +
298A SER 3.6 21.5 - - - +
299A ILE* 3.9 19.3 - - + -
311A ILE* 3.7 25.4 - - + -
312A GLU 3.7 16.4 - - - +
313A PRO* 4.0 1.8 - - + -
314A GLY* 2.8 29.3 + - - -
315A ASP* 2.8 22.5 + - + +
317A LEU* 4.6 14.6 - - + -
349A LEU* 5.9 0.7 - - + -
351A VAL* 4.8 5.4 - - + -
2001A MPD 3.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A SER* 2.8 24.2 + - - -
283A VAL* 4.1 20.4 - - - +
295A TYR 3.3 3.6 + - - -
296A ILE* 1.3 73.5 - - - +
298A SER* 1.3 52.7 + - - +
313A PRO* 3.9 1.5 - - - +
2001A MPD 2.6 48.2 + - - +
360B TRP* 5.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.6 2.6 - - - -
281A SER* 2.7 40.8 + - - -
296A ILE* 3.5 4.4 - - - +
297A GLY* 1.3 77.0 - - - +
299A ILE* 1.3 71.6 + - - +
313A PRO* 4.0 12.1 - - - -
2001A MPD 4.0 5.8 - - - -
2002A MPD 2.8 39.1 + - - +
360B TRP* 4.8 0.2 - - - -
363B TRP* 3.3 7.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLY 3.3 9.2 - - - +
280A ILE* 4.1 7.6 - - + -
296A ILE* 3.9 11.0 - - + -
298A SER* 1.3 83.7 - - - +
300A MET* 1.3 65.9 + - - +
301A LYS* 4.1 3.3 + - + +
305A VAL* 4.2 10.1 - - + +
306A ALA* 3.8 35.2 - - + +
311A ILE* 3.3 28.9 - - + +
312A GLU* 3.8 3.8 - - - -
313A PRO* 3.7 25.5 - - + +
2002A MPD 5.0 1.4 + - - -
363B TRP* 4.0 6.4 - - - -
----------------------------------------------------------
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