Contacts of the helix formed by residues 334 - 343 (chain Y) in PDB entry 4CCG
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 HIS 334 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307Y CYS* 3.2 12.2 - - + +
310Y CYS* 3.4 6.7 - - - -
312Y ALA 3.2 25.4 - - - -
313Y TYR 2.9 23.1 + - - -
315Y LEU* 3.7 17.6 + - + +
318Y THR* 3.4 26.7 + - - +
319Y ILE 3.3 26.2 - - - -
320Y PRO* 3.5 4.3 - - + +
322Y GLN* 4.1 0.8 - - - +
333Y PHE* 1.3 76.9 - - - +
335Y GLN* 1.3 65.9 + - - +
336Y ILE* 4.1 3.1 - - + +
337Y CYS* 3.7 11.4 - - - +
338Y LEU* 3.2 22.3 + - - +
1372Y ZN 2.0 36.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 335 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318Y THR* 5.4 6.1 + - + -
319Y ILE 5.1 0.6 + - - -
321Y ASP* 4.0 13.2 + - - +
322Y GLN* 3.3 38.9 - - + +
334Y HIS* 1.3 72.4 - - - +
336Y ILE* 1.3 65.6 + - + +
339Y TYR* 3.0 27.9 + - - +
368Y LEU* 3.6 12.3 - - + +
369Y LYS 3.8 13.6 + - - +
370Y MET* 4.0 14.6 - - + +
371Y SER* 3.6 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 336 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLN* 3.5 20.2 - - - +
315Y LEU* 4.5 19.7 - - + +
316Y ASP* 4.2 23.8 - - + -
318Y THR* 4.7 11.7 - - + +
334Y HIS* 3.3 2.1 - - + +
335Y GLN* 1.3 79.1 - - + +
337Y CYS* 1.3 57.2 + - - +
339Y TYR* 3.8 7.6 - - + +
340Y GLU* 2.9 29.8 + - + +
370Y MET* 5.1 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 337 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLN* 3.3 25.4 - - - +
63B PHE* 3.3 12.3 - - - -
307Y CYS* 4.0 3.4 - - - -
309Y ILE* 3.5 25.5 - - + +
310Y CYS* 3.6 9.6 - - - -
315Y LEU* 3.5 11.4 - - - -
334Y HIS* 3.5 4.9 + - - +
335Y GLN 3.3 0.4 - - - -
336Y ILE* 1.3 79.2 - - - +
338Y LEU* 1.3 64.4 + - - +
340Y GLU 3.2 1.4 + - - -
341Y TRP 3.1 17.8 + - - -
1372Y ZN 2.3 37.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309Y ILE* 3.6 9.4 - - + +
322Y GLN* 4.4 8.5 - - + -
333Y PHE* 4.1 19.1 - - + -
334Y HIS 3.2 15.5 + - - +
337Y CYS* 1.3 78.6 - - - +
339Y TYR* 1.3 58.2 + - - +
341Y TRP* 3.3 2.8 + - + +
342Y LEU* 2.9 53.6 + - + +
360Y PRO* 4.1 25.8 - - + -
366Y ILE* 3.4 32.5 - - + -
367Y THR 5.2 0.7 - - - +
368Y LEU* 3.8 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 339 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335Y GLN 3.0 18.6 + - - +
336Y ILE* 3.8 6.3 - - + +
338Y LEU* 1.3 77.8 - - - +
340Y GLU* 1.3 70.5 + - + +
342Y LEU* 4.7 2.2 - - - -
343Y ARG* 3.0 55.4 + - + +
355Y ILE* 4.3 19.3 - - + -
368Y LEU* 3.3 13.4 - - + +
370Y MET* 4.0 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 340 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLN* 5.1 3.1 - - - +
60B ARG* 2.8 34.8 + - - +
63B PHE* 3.3 41.6 - - + +
336Y ILE* 2.9 21.9 + - + +
339Y TYR* 1.3 84.0 - - + +
341Y TRP* 1.3 59.3 + - - +
343Y ARG* 3.5 27.8 - - - +
344Y GLY* 4.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 341 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B PHE* 3.7 38.8 - + + -
92B LEU* 4.6 3.8 - - + -
93B PRO* 4.5 9.6 - - + -
98B TRP* 3.4 26.2 - + - -
99B ARG* 3.8 11.2 - - + -
100B PRO* 3.6 33.2 - - + -
309Y ILE* 4.3 8.1 - - + -
337Y CYS 3.1 15.5 + - - +
338Y LEU* 3.7 3.8 - - + +
340Y GLU* 1.3 76.9 - - - +
342Y LEU* 1.3 76.9 + - + +
343Y ARG 3.5 0.3 + - - -
344Y GLY* 3.6 6.9 + - - -
345Y LEU* 3.2 52.8 + - + +
358Y GLU 4.5 1.6 + - - -
360Y PRO* 3.9 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338Y LEU* 2.9 42.1 + - + +
339Y TYR* 4.2 0.9 - - - +
341Y TRP* 1.3 87.3 - - + +
343Y ARG* 1.3 64.8 + - - +
345Y LEU* 2.9 18.7 + - + -
348Y SER* 2.6 27.5 + - - +
355Y ILE* 4.0 29.2 - - + -
356Y PHE 4.6 0.4 - - - -
357Y GLY* 4.0 13.9 - - - +
358Y GLU 3.4 35.4 - - - +
366Y ILE* 4.1 15.3 - - + +
368Y LEU* 4.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 343 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 6.1 0.2 - - - +
339Y TYR* 3.0 50.7 + - + +
340Y GLU* 3.5 29.8 - - - +
342Y LEU* 1.3 77.8 - - - +
344Y GLY* 1.3 63.3 + - - +
345Y LEU 3.6 3.5 + - - +
348Y SER* 5.1 1.6 - - - -
355Y ILE* 4.5 7.6 - - + +
----------------------------------------------------------
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