Contacts of the helix formed by residues 298 - 318 (chain A) in PDB entry 1VJY
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 298 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 1.3 75.6 - - - +
299A VAL* 1.3 65.9 + - - +
300A GLU* 3.7 15.0 + - - +
301A GLY* 3.0 17.8 + - - +
302A MET* 2.8 21.3 + - - +
415A CYS* 4.0 2.7 - - - -
416A SER* 4.6 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 1.3 74.9 - - - +
300A GLU* 1.3 77.8 + - - +
302A MET* 3.3 2.9 + - + +
303A ILE* 3.1 38.0 + - + +
415A CYS* 4.0 10.2 - - - -
417A ILE* 3.4 31.8 - - + +
461A CYS* 4.2 10.5 - - - -
463A ALA* 3.4 30.1 - - + -
499A GLU* 4.1 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 3.8 13.7 + - - +
299A VAL* 1.3 84.8 + - - +
301A GLY* 1.3 58.8 + - - +
303A ILE* 3.4 6.4 + - - +
304A LYS* 3.0 35.7 + - + +
499A GLU* 3.5 29.1 - - + +
500A GLY 4.3 6.5 - - - +
501A ILE* 3.6 46.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 4.3 8.5 - - - -
298A THR* 3.0 19.1 + - - -
300A GLU* 1.3 77.5 - - - +
302A MET* 1.3 63.8 + - - +
304A LYS* 3.3 12.1 + - - +
305A LEU* 3.1 28.4 + - - +
345A GLY 4.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 3.9 19.1 - - + +
298A THR 2.8 16.3 + - - +
299A VAL* 3.7 8.1 - - - +
301A GLY* 1.3 71.2 - - - +
303A ILE* 1.3 62.5 + - + +
305A LEU* 3.2 4.6 + - - +
306A ALA* 2.9 27.2 + - - +
411A ILE* 3.7 21.0 - - + +
412A ALA* 3.8 15.5 - - - -
415A CYS* 3.8 15.0 - - - -
463A ALA* 3.9 25.8 - - + -
464A LEU* 3.5 34.1 - - + -
467A MET* 4.0 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 3.1 35.3 + - + +
300A GLU* 3.7 8.5 - - - +
302A MET* 1.3 86.0 - - + +
304A LYS* 1.3 57.8 + - + +
306A ALA* 4.0 4.2 - - - +
307A LEU* 2.8 33.9 + - + +
463A ALA* 4.5 0.9 - - + -
467A MET* 5.9 2.2 - - + -
492A LEU* 4.2 13.9 - - + +
495A LEU* 3.9 40.8 - - + +
496A SER* 3.9 30.7 - - - +
499A GLU* 4.3 9.9 - - + +
501A ILE* 5.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLU* 3.0 30.2 + - + +
301A GLY* 3.6 9.2 - - - +
302A MET 3.3 0.2 - - - -
303A ILE* 1.3 75.3 - - + +
305A LEU* 1.3 54.6 + - - +
307A LEU* 4.2 3.8 - - - +
308A SER* 2.7 38.2 + - - -
344A ASN 2.8 29.3 + - - -
345A GLY* 3.8 17.3 - - - +
346A THR* 4.6 4.8 - - + +
501A ILE* 4.0 19.1 - - + -
502A LYS* 3.0 55.3 - - - +
503A MET* 4.4 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 4.1 14.4 - - + -
291A TYR* 4.1 11.7 - - + -
292A LEU* 4.4 3.4 - - + -
297A VAL* 3.9 24.9 - - + -
301A GLY 3.1 18.6 + - - +
302A MET 3.6 5.4 - - - +
304A LYS* 1.3 78.0 - - - +
306A ALA* 1.3 54.5 + - - +
308A SER* 2.9 13.0 + - - -
309A THR* 2.8 27.1 + - - -
341A VAL* 4.1 17.3 - - + -
345A GLY* 3.5 17.7 - - - +
347A CYS* 3.4 23.9 - - - -
411A ILE* 4.0 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A MET 2.9 16.1 + - - +
303A ILE* 4.0 3.6 - - - +
305A LEU* 1.3 73.8 - - - +
307A LEU* 1.3 61.9 + - - +
309A THR* 3.3 1.4 + - - -
310A ALA* 2.9 24.9 + - - +
408A PHE* 3.5 24.7 - - + -
411A ILE* 4.1 5.8 - - + +
467A MET* 3.8 29.6 - - + -
492A LEU* 3.6 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ILE* 2.8 23.7 + - + +
304A LYS* 4.2 3.1 - - - +
306A ALA* 1.3 72.6 - - - +
308A SER* 1.3 58.6 + - - +
310A ALA* 3.1 1.8 + - - -
311A SER* 2.8 44.7 + - - +
489A LYS* 3.5 32.1 - - + +
492A LEU* 3.6 23.7 - - + +
493A SER* 3.6 12.1 - - - +
496A SER* 4.3 5.4 - - - +
503A MET* 3.7 51.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ASN* 3.1 32.1 - - - +
304A LYS 2.7 23.7 + - - -
305A LEU* 2.9 12.5 + - - -
307A LEU* 1.3 78.5 - - - +
309A THR* 1.3 55.5 + - - +
311A SER* 3.3 1.5 + - - -
312A GLY 2.9 23.7 + - - -
346A THR* 3.9 9.6 - - - -
347A CYS* 2.8 33.0 + - - +
503A MET* 5.4 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 5.0 3.3 - - - +
305A LEU 2.8 20.9 + - - -
306A ALA 3.6 4.5 - - - -
307A LEU 3.2 0.2 - - - -
308A SER* 1.3 79.5 + - - +
310A ALA* 1.3 57.8 + - - +
312A GLY* 3.1 2.3 + - - -
313A LEU* 2.9 27.7 + - - +
334A LEU* 5.1 3.6 - - + -
339A ILE* 3.8 27.5 - - + +
347A CYS* 3.5 20.7 - - - +
349A ILE* 3.8 14.2 - - + +
404A MET* 4.0 22.2 - - + -
407A VAL* 5.1 4.0 - - + -
408A PHE* 4.4 6.1 - - + -
411A ILE* 5.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ALA 2.9 17.9 + - - +
307A LEU 3.6 3.6 - - - +
309A THR* 1.3 77.5 - - - +
311A SER* 1.3 58.7 + - - +
313A LEU* 3.8 1.4 - - - +
314A ALA* 2.8 31.1 + - - +
404A MET* 3.8 18.6 - - + -
408A PHE* 4.2 0.9 - - + -
485A ALA* 4.1 4.5 - - - +
488A ILE* 3.9 27.8 - - + -
489A LYS* 4.2 16.6 - - - +
492A LEU* 4.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A HIS* 4.0 8.0 + - - -
257A GLU* 5.6 0.7 - - - -
258A ASN* 3.1 22.0 - - - -
307A LEU* 2.8 30.8 + - - +
308A SER* 4.2 1.0 - - - -
310A ALA* 1.3 70.7 - - - +
312A GLY* 1.3 64.9 + - - +
314A ALA* 3.4 2.2 + - - +
315A HIS* 3.1 23.4 + - - +
489A LYS* 3.5 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A HIS* 4.6 2.9 - - - -
258A ASN* 3.3 33.6 - - - +
259A ILE* 4.3 2.8 - - - +
308A SER 2.9 10.7 + - - -
309A THR 3.1 3.5 + - - -
311A SER* 1.3 78.4 - - - +
313A LEU* 1.3 59.5 + - - +
315A HIS* 3.3 6.3 + - - +
316A LEU* 3.2 24.1 + - - +
349A ILE* 3.6 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A THR 2.9 15.4 + - - +
310A ALA 3.8 3.4 - - - +
312A GLY* 1.3 74.1 - - - +
314A ALA* 1.3 61.5 + - - +
316A LEU* 3.3 16.2 + - + +
317A HIS* 2.9 65.5 + - + +
331A HIS* 4.9 4.5 - - + -
334A LEU* 4.1 20.4 - - + -
349A ILE* 3.4 9.5 - - + +
400A ASP* 4.1 14.8 - - + +
401A ILE* 3.9 17.5 - - + -
404A MET* 3.6 28.0 - - + -
485A ALA* 4.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ALA 2.8 18.8 + - - +
311A SER* 3.7 8.1 - - - +
313A LEU* 1.3 72.7 - - - +
315A HIS* 1.3 60.3 + - - +
317A HIS* 4.1 2.5 - - - +
318A MET* 2.9 35.2 + - - +
485A ALA* 3.6 19.9 - - + +
486A LEU* 4.1 21.8 - - + +
489A LYS* 4.5 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A MET 3.6 12.3 + - - -
254A LEU 2.8 32.5 - - - -
255A ARG 3.6 5.1 + - - -
256A HIS* 3.3 34.7 - + + +
259A ILE* 3.1 20.8 - - + +
311A SER 3.1 14.1 + - - +
312A GLY 3.5 9.0 - - - +
314A ALA* 1.3 77.6 - - - +
316A LEU* 1.3 62.9 + - - +
318A MET* 3.3 35.2 + - + +
320A ILE* 4.1 5.6 - - + +
326A LYS* 3.0 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU* 3.9 26.9 - - + -
259A ILE* 4.0 11.2 - - + -
312A GLY 3.2 14.8 + - - +
313A LEU* 3.5 15.5 - - + +
315A HIS* 1.3 79.8 - - - +
317A HIS* 1.3 56.6 + - + +
326A LYS* 3.0 16.1 + - - +
329A ILE* 2.7 58.0 + - + +
331A HIS* 4.5 26.7 - - + +
349A ILE* 4.5 17.7 - - + -
352A LEU* 4.5 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU* 2.9 42.3 + - + +
314A ALA* 4.1 5.2 - - - +
316A LEU* 1.3 77.5 - - + +
318A MET* 1.3 57.9 + - - +
319A GLU 3.6 0.9 + - - -
328A ALA* 3.2 20.9 - - - +
329A ILE 3.1 22.2 - - - +
330A ALA* 4.2 0.2 - - - -
397A LYS* 3.3 68.5 + - + +
400A ASP* 2.7 30.8 + - + -
401A ILE* 4.4 4.9 - - + +
485A ALA* 4.3 10.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ALA 2.9 20.1 + - - +
315A HIS* 3.3 34.2 - - + +
316A LEU 3.2 0.4 - - - -
317A HIS* 1.3 76.5 - - - +
319A GLU* 1.3 70.9 + - - +
320A ILE* 3.7 22.0 + - + +
326A LYS* 2.7 31.4 + - - +
328A ALA* 4.3 0.7 - - - -
486A LEU* 6.1 6.3 - - - -
----------------------------------------------------------
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