Contacts of the helix formed by residues 335 - 346 (chain B) in PDB entry 2CSX
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 SER 335 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL 4.0 1.6 - - - -
292B GLU* 3.5 13.5 - - - -
333B ASP* 3.6 20.8 + - - -
334B PHE* 1.3 76.6 - - - +
336B LYS* 1.3 65.4 + - - +
337B LYS* 3.2 24.7 - - - +
338B ALA* 2.9 40.0 + - - +
339B ILE* 3.0 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 5.7 0.8 - - - +
75A ARG* 3.5 49.9 - - + +
76A ASN* 5.5 2.2 + - - -
79A ARG* 4.6 6.9 - - - +
292B GLU* 3.2 8.6 + - - +
312B GLU* 4.1 6.8 + - - -
313B TYR* 3.4 25.4 - - - +
335B SER* 1.3 70.9 - - - +
337B LYS* 1.3 79.7 + - + +
339B ILE* 3.5 5.0 + - - +
340B LEU* 3.1 52.5 + - + +
497B GLY* 3.9 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 5.5 3.6 - - - +
292B GLU* 2.4 38.5 + - - -
335B SER* 3.2 22.4 - - - +
336B LYS* 1.3 90.2 - - + +
338B ALA* 1.3 58.8 + - - +
340B LEU* 4.0 7.2 - - - +
341B ASN* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE* 3.6 21.5 - - + -
325B GLU* 4.0 13.7 - - - +
333B ASP 4.3 2.7 - - - +
335B SER* 2.9 29.8 + - - +
337B LYS* 1.3 79.4 - - - +
339B ILE* 1.3 64.1 + - - +
341B ASN* 3.0 10.1 + - - +
342B ARG* 3.0 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B TYR* 4.1 32.1 - - + +
317B GLU 5.1 1.1 - - - +
318B VAL* 5.4 3.4 - - + -
321B PHE* 3.5 41.3 - - + -
334B PHE* 3.4 38.8 - - + -
335B SER 3.0 19.2 + - - +
336B LYS* 4.0 2.5 - - - +
338B ALA* 1.3 72.7 - - - +
340B LEU* 1.3 53.8 + - - +
342B ARG* 3.1 2.8 + - - +
343B ILE* 2.7 64.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 6.4 0.2 - - - -
313B TYR* 4.2 17.0 - - + -
336B LYS* 3.1 46.4 + - + +
337B LYS* 4.0 6.1 - - - +
339B ILE* 1.3 78.9 - - - +
341B ASN* 1.3 65.5 + - - +
343B ILE* 4.5 6.3 - - + -
344B ASN* 2.9 47.5 + - - +
495B ARG* 6.3 0.2 - - + -
496B GLU* 3.9 4.0 - - - +
497B GLY* 3.3 35.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LYS 2.9 16.2 + - - +
338B ALA* 3.1 11.2 - - - +
340B LEU* 1.3 75.4 - - - +
342B ARG* 1.3 79.3 + - - +
344B ASN* 5.3 0.2 - - - -
345B GLY* 2.7 38.4 + - - +
346B GLU* 6.2 0.8 - - - +
25D C 3.6 43.9 + - - +
26D G 4.2 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TYR* 4.2 15.2 - - + -
321B PHE* 3.6 25.8 - - + -
324B ARG* 2.7 46.8 - - - +
325B GLU* 2.9 23.6 + - - +
338B ALA 3.0 13.0 + - - +
339B ILE 3.6 4.5 - - - +
341B ASN* 1.3 94.8 + - - +
343B ILE* 1.3 65.6 + - + +
346B GLU* 2.8 44.8 + - - +
347B LEU 3.2 5.7 + - - -
24D G 4.4 12.9 + - - -
25D C 5.1 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B TYR* 3.8 30.7 - - + +
317B GLU* 3.9 34.5 - - + +
320B TYR* 5.3 0.9 - - + -
321B PHE* 5.8 0.4 - - + -
339B ILE* 2.7 48.1 + - + +
340B LEU* 4.0 7.0 - - + +
342B ARG* 1.3 72.7 - - + +
344B ASN* 1.3 64.0 + - - +
347B LEU* 2.9 22.6 + - + +
348B ALA* 2.6 35.0 + - + +
492B PHE* 5.6 2.5 - - + -
493B PRO 4.8 12.6 - - - +
494B LYS* 5.7 0.2 - - - -
495B ARG 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LEU* 2.9 46.8 + - - +
341B ASN* 5.3 0.2 - - - -
343B ILE* 1.3 79.2 - - - +
345B GLY* 1.3 62.4 + - - +
348B ALA* 3.4 6.7 - - - +
349B ASN* 2.8 42.5 + - - +
494B LYS* 3.1 43.2 - - + +
495B ARG 4.7 0.2 + - - -
496B GLU* 4.3 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASN* 2.7 29.2 + - - -
344B ASN* 1.3 79.2 - - - +
346B GLU* 1.3 58.9 + - - -
349B ASN* 3.0 26.4 - - - +
350B GLU* 3.4 12.6 + - - +
39D G 4.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TYR* 2.6 20.8 + - - +
324B ARG* 2.5 40.5 + - - -
341B ASN* 5.8 1.1 + - - +
342B ARG* 2.8 40.2 + - - +
345B GLY* 1.3 73.2 - - - -
347B LEU* 1.3 62.0 + - - +
350B GLU* 3.0 30.5 + - + +
351B ILE* 2.8 31.7 + - - +
406B LEU* 2.6 26.1 - - + +
25D C 6.4 1.6 - - - -
----------------------------------------------------------
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