Contacts of the helix formed by residues 363 - 376 (chain B) in PDB entry 3R29
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 ASP 363 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B HIS* 3.7 6.5 - - - -
361B GLN 3.8 1.3 + - - +
362B MET* 1.3 74.1 - - - +
364B LYS* 1.3 52.7 + - - +
365B THR* 2.9 7.5 + - - -
366B GLU* 2.5 34.5 + - - +
367B LEU* 2.8 31.0 + - - +
403B TYR* 2.5 33.8 + - - -
407B LYS* 3.7 6.7 + - - +
408B TYR* 3.3 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 3.6 26.0 - - + +
239B GLU* 3.9 15.4 - - + +
240B LEU* 5.2 6.4 - - + +
243B GLU* 3.5 32.6 + - - +
315B HIS* 4.8 18.2 - - + +
318B ILE* 6.1 2.5 - - - -
363B ASP* 1.3 72.3 - - - +
365B THR* 1.3 65.6 + - - +
367B LEU* 3.9 12.8 - - + -
368B GLY* 3.1 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B VAL* 3.3 44.0 - - + +
233B GLU* 5.0 1.7 - - - +
235B ILE* 4.6 0.8 - - - +
236B LEU* 3.5 27.4 - - + +
363B ASP* 2.9 7.0 + - - -
364B LYS* 1.3 78.1 - - - +
366B GLU* 1.3 59.1 + - - +
368B GLY* 3.8 0.5 - - - -
369B CYS* 2.5 38.2 + - - -
403B TYR* 3.6 36.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B MET* 3.1 13.4 - - + -
363B ASP* 2.5 50.5 + - - +
365B THR* 1.3 74.8 - - - +
367B LEU* 1.3 69.8 + - - +
369B CYS* 2.8 14.9 + - - +
370B LEU* 3.0 17.3 + - - +
400B LEU* 4.4 5.7 - - + +
403B TYR* 4.2 11.7 - - + -
404B CYS* 4.5 3.0 - - - -
408B TYR* 3.7 7.1 - - - -
414B ARG* 2.4 44.4 + - - +
418B LEU* 3.9 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B GLU* 3.8 16.8 - - - +
311B ALA* 4.1 10.8 - - + +
312B SER* 4.7 9.9 - - - +
315B HIS* 3.3 52.7 - - + -
357B MET* 4.1 16.8 - - + -
362B MET* 4.5 7.7 - - - +
363B ASP 2.8 12.9 + - - +
364B LYS* 4.0 12.6 - - + +
366B GLU* 1.3 75.0 - - - +
368B GLY* 1.3 66.3 + - - +
369B CYS 2.8 0.2 + - - -
370B LEU* 2.9 16.1 + - + +
371B ARG* 3.0 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE* 3.6 15.0 - - - +
239B GLU* 3.5 31.9 - - - +
282B TRP* 4.1 2.0 - - - -
364B LYS 3.1 11.7 + - - -
367B LEU* 1.3 78.8 - - - +
369B CYS* 1.3 56.4 + - - +
371B ARG* 3.4 3.1 + - - +
372B ALA* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B VAL* 4.0 13.2 - - - -
235B ILE* 4.3 13.9 - - - -
365B THR* 2.5 46.4 + - - +
366B GLU 2.8 6.6 + - - +
368B GLY* 1.3 75.3 - - - +
370B LEU* 1.3 56.2 + - - +
372B ALA* 3.5 7.2 + - - +
373B ILE* 2.7 37.6 + - - +
396B VAL* 3.8 7.6 - - + +
400B LEU* 3.6 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B MET* 5.7 2.5 - - + -
362B MET* 4.1 31.4 - - + -
366B GLU 3.0 12.4 + - - +
367B LEU* 2.9 11.6 + - + +
369B CYS* 1.3 73.1 - - - +
371B ARG* 1.3 66.3 + - - +
373B ILE* 2.8 24.4 - - + +
374B VAL* 3.0 11.4 + - + +
400B LEU* 4.7 6.3 - - + -
418B LEU* 3.8 41.1 - - + +
419B LEU* 4.4 12.6 - - + -
421B ARG* 5.2 4.3 - - + -
422B LEU* 3.8 28.4 - - + +
425B LEU* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B GLU* 3.0 13.7 + - - -
242B VAL* 5.5 2.0 - - - +
278B THR* 5.2 11.3 - - - +
279B LEU* 5.0 9.1 - - - +
282B TRP* 2.9 71.2 - - + +
308B LEU* 3.1 38.3 + - + +
309B LEU* 4.9 2.4 - - - +
311B ALA* 4.2 17.9 - - + -
312B SER* 2.3 36.0 + - - +
367B LEU* 3.0 28.3 + - + +
368B GLY 3.5 4.5 - - - +
370B LEU* 1.3 72.4 - - - +
372B ALA* 1.3 70.2 + - - +
374B VAL* 2.5 20.3 + - + +
375B LEU 2.8 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE* 4.9 4.7 - - + -
282B TRP* 3.6 14.0 - - + -
286B ILE* 4.7 12.8 - - + -
368B GLY 2.8 21.3 + - - +
369B CYS* 3.6 7.0 - - - +
370B LEU 3.4 0.2 - - - -
371B ARG* 1.3 72.8 - - - +
373B ILE* 1.3 62.2 + - - +
375B LEU* 3.3 3.7 + - - +
376B PHE* 3.0 36.8 + - + -
396B VAL* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LEU* 4.1 8.1 - - + -
369B CYS 2.7 26.3 + - - +
370B LEU* 2.8 24.7 + - + +
371B ARG 2.7 3.0 + - - -
372B ALA* 1.3 74.2 - - - +
374B VAL* 1.3 55.0 + - - +
376B PHE* 3.2 11.3 + - - +
393B ARG* 2.7 58.1 + - + +
396B VAL* 4.3 6.3 - - + -
397B TYR* 3.7 42.4 - - + +
400B LEU* 4.9 3.6 - - + -
419B LEU* 4.8 8.1 - - + -
422B LEU* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLY* 4.6 11.2 - - - -
307B GLU* 3.3 37.0 - - + +
308B LEU* 3.9 17.3 - - + +
370B LEU* 3.4 14.6 - - + +
371B ARG* 2.5 16.6 + - + +
373B ILE* 1.3 74.1 - - + +
375B LEU* 1.3 62.7 + - - +
377B ASN* 3.5 19.7 + - - +
393B ARG* 4.1 5.2 - - - +
422B LEU* 4.2 18.8 - - + -
425B LEU* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B TRP* 4.0 25.1 - - + -
283B ALA* 4.6 4.9 - - + -
286B ILE* 4.6 3.8 - - + -
289B PHE* 4.2 18.6 - - + -
300B LEU* 3.3 37.7 - - + +
301B LEU* 3.9 29.6 - - + -
304B GLY* 5.5 0.2 - - - -
308B LEU* 4.0 19.8 - - + +
371B ARG 2.8 12.2 + - - +
372B ALA 3.5 5.6 - - - +
374B VAL* 1.3 74.6 - - - +
376B PHE* 1.3 90.2 + - + +
377B ASN* 2.8 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B MET* 4.6 0.9 - - + -
286B ILE* 3.1 36.3 - - + -
289B PHE* 4.3 4.5 - + + -
292B LEU* 4.1 13.5 - - + -
300B LEU* 4.3 10.5 - - + -
372B ALA* 3.0 28.8 + - + +
373B ILE 3.2 3.7 + - - +
375B LEU* 1.3 92.1 - - + +
377B ASN* 1.3 57.4 + - - +
378B PRO* 3.2 6.6 - - - +
389B VAL* 3.8 23.4 - - + +
392B LEU* 3.1 48.9 - - + -
393B ARG* 3.1 29.7 + - + +
396B VAL* 4.0 16.6 - - + -
----------------------------------------------------------
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