Contacts of the helix formed by residues 312 - 323 (chain A) in PDB entry 5X1A
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 THR 312 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 3.0 24.1 + - - +
310A ASP* 2.7 19.5 + - - +
311A PRO* 1.3 84.7 - - + +
313A THR* 1.3 63.6 + - - +
314A PRO 3.5 0.9 - - - -
315A ASP* 3.5 12.2 + - - +
316A PHE* 3.3 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLU* 5.1 0.5 + - - -
256A MET 3.5 24.9 - - - +
257A SER* 4.2 0.4 - - - -
258A LYS* 3.9 27.2 + - + +
282A SER* 4.7 2.7 - - - +
285A THR 5.6 0.9 - - - -
286A ASP* 5.8 0.2 - - - -
308A SER* 3.2 19.7 + - - -
310A ASP* 2.6 26.7 + - - +
312A THR* 1.3 75.4 + - - +
314A PRO* 1.4 74.1 - - + +
316A PHE* 3.1 3.5 + - - +
317A LEU* 2.9 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A SER 3.4 14.8 - - - +
283A LEU 3.5 20.6 - - - +
284A GLY 4.4 1.3 - - - +
285A THR* 3.3 35.7 - - - +
286A ASP* 4.8 1.3 - - + +
310A ASP 4.3 1.1 - - - +
311A PRO* 3.5 17.9 - - + +
312A THR 3.7 0.2 - - - -
313A THR* 1.4 93.5 - - - +
315A ASP* 1.3 56.8 + - - +
317A LEU* 3.2 1.0 + - + +
318A ASN* 2.9 36.9 + - - -
368A LYS* 4.3 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A PRO 5.5 2.1 - - - +
312A THR* 3.5 13.9 + - - +
313A THR 3.3 0.6 - - - -
314A PRO* 1.3 80.2 - - - +
316A PHE* 1.3 62.6 - - - +
318A ASN* 3.5 2.1 + - - -
319A SER* 3.1 12.8 + - - -
368A LYS* 3.7 26.9 + - - +
374A LYS* 2.8 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 3.5 65.1 - - + -
261A ALA* 4.2 1.6 - - + -
262A GLU* 4.1 17.7 - - + -
312A THR 3.3 8.2 + - - +
313A THR 3.1 7.9 + - - +
315A ASP* 1.3 74.3 - - - +
317A LEU* 1.3 72.8 + - + +
319A SER* 3.2 8.5 + - - -
320A LEU* 3.0 56.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 3.9 12.1 - - + +
256A MET 4.1 3.1 - - - +
257A SER 3.7 15.3 - - - +
261A ALA* 3.6 29.6 - - + -
278A PRO* 4.9 2.7 - - + -
282A SER* 3.6 44.2 - - - +
283A LEU* 3.9 13.5 - - + -
313A THR* 2.9 30.1 + - + +
314A PRO 3.9 2.9 - - - +
316A PHE* 1.3 81.3 - - + +
318A ASN* 1.3 58.7 + - - +
320A LEU* 3.2 1.7 + - - -
321A LEU* 2.8 29.8 + - - +
326A LEU* 3.8 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 3.1 41.1 + - - +
314A PRO 2.9 28.5 + - - +
315A ASP* 3.9 4.2 + - - +
317A LEU* 1.3 78.7 - - - +
319A SER* 1.3 55.7 + - - +
321A LEU* 3.5 11.5 + - - +
322A SER* 2.8 32.7 + - - -
365A ILE* 4.6 5.7 - - - -
368A LYS* 3.5 33.3 - - - +
369A ALA* 3.6 19.7 - - + +
374A LYS* 4.2 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP 3.1 16.1 + - - -
316A PHE* 3.2 13.2 + - - -
318A ASN* 1.3 77.5 - - - +
320A LEU* 1.3 67.0 + - - +
322A SER* 3.2 14.3 + - - -
323A CYS* 3.2 16.3 + - - +
374A LYS* 3.2 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ALA* 3.7 40.8 - - + +
262A GLU* 4.2 3.4 - - - +
265A ALA* 4.2 12.3 - - + -
316A PHE* 3.0 49.7 + - + +
317A LEU* 3.2 4.0 + - - +
319A SER* 1.3 79.6 - - - +
321A LEU* 1.3 65.0 + - - +
323A CYS* 3.5 6.1 + - - -
324A GLY 3.3 3.3 + - - -
325A ASP* 3.0 43.2 + - + +
326A LEU* 3.1 15.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PRO* 4.2 4.5 - - + -
283A LEU* 4.2 21.5 - - + -
317A LEU 2.8 16.6 + - - +
318A ASN* 3.6 12.3 - - - +
320A LEU* 1.3 77.6 - - - +
322A SER* 1.3 60.5 + - - +
324A GLY* 3.4 9.4 + - - -
326A LEU* 3.5 40.1 - - + +
327A GLN 4.1 4.5 - - - +
329A THR* 3.7 28.5 - - + -
365A ILE* 4.6 5.8 - - + -
375A MET* 3.9 14.3 - - + +
383A VAL* 3.7 39.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASN 2.8 20.8 + - - -
319A SER* 3.2 6.9 + - - -
321A LEU* 1.3 77.5 - - - +
323A CYS* 1.3 59.1 + - - +
324A GLY 3.4 0.4 + - - -
369A ALA* 4.2 1.2 - - - +
374A LYS* 3.2 44.2 - - - +
375A MET* 3.5 21.7 - - - +
379A GLN* 2.9 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ARG* 5.6 0.7 + - - -
319A SER 3.2 14.5 + - - +
320A LEU* 3.6 19.1 - - - -
322A SER* 1.3 78.2 - - - +
324A GLY* 1.3 58.0 + - - +
325A ASP* 3.2 27.4 - - - -
----------------------------------------------------------
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