Contacts of the helix formed by residues 374 - 391 (chain B) in PDB entry 4R0C
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 PRO 374 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B THR 3.8 4.2 - - - +
373B VAL* 1.3 95.1 - - + +
375B LYS* 1.3 65.6 + - - +
376B VAL* 4.4 6.1 - - + +
377B VAL* 3.2 32.6 + - + +
378B LEU* 3.4 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B VAL 3.6 1.3 + - - +
374B PRO* 1.3 73.1 - - - +
376B VAL* 1.3 63.2 + - - +
378B LEU* 3.1 12.4 + - + +
379B LEU* 3.0 20.9 + - + +
414B LEU 3.4 22.4 - - - +
415B GLY* 3.3 21.2 + - - +
416B ILE* 3.8 35.6 - - + +
484B ILE* 5.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B PRO* 3.3 5.0 - - + +
375B LYS* 1.3 78.7 - - - +
377B VAL* 1.3 60.3 + - + +
379B LEU* 3.2 9.2 + - + +
380B LEU* 2.8 42.0 + - + +
481B GLY* 3.8 32.5 - - - +
484B ILE* 3.5 29.6 - - + -
485B GLY* 3.9 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B VAL* 3.7 22.0 - - + -
374B PRO* 3.2 35.6 + - + +
376B VAL* 1.3 80.5 - - + +
378B LEU* 1.3 58.1 + - - +
380B LEU* 3.9 8.3 - - + +
381B LEU* 3.0 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU* 4.1 26.5 - - + +
373B VAL* 4.3 25.6 - - + +
374B PRO 3.4 9.4 + - - +
375B LYS* 3.1 14.2 + - + +
377B VAL* 1.3 75.4 - - - +
379B LEU* 1.3 61.3 + - - +
381B LEU* 3.0 16.7 + - + +
382B PHE* 2.8 29.0 + - - +
411B LEU* 4.1 10.8 - - + -
414B LEU* 3.6 31.0 - - + -
416B ILE* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LYS 3.0 12.0 + - - +
376B VAL* 3.4 9.6 - - + +
378B LEU* 1.3 79.0 - - - +
380B LEU* 1.3 63.7 + - + +
382B PHE* 3.0 12.3 + - + +
383B VAL* 2.9 25.3 + - - +
411B LEU* 5.3 2.9 - - + -
416B ILE* 3.7 31.0 - - + -
420B ALA* 3.8 25.8 - - + +
421B SER* 4.2 8.3 - - - +
424B ALA* 3.9 14.7 - - + +
480B LEU* 5.2 7.2 - - + -
484B ILE* 3.5 45.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B VAL* 2.8 39.2 + - + +
377B VAL* 4.0 7.2 - - + +
379B LEU* 1.3 74.2 - - + +
381B LEU* 1.3 64.9 + - - +
383B VAL* 2.8 21.7 + - + +
384B VAL* 2.9 19.4 + - + +
477B SER* 3.8 39.9 - - - +
480B LEU* 5.3 4.3 - - + -
481B GLY* 4.7 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B VAL* 5.7 2.7 - - + -
377B VAL* 3.0 41.3 + - + +
378B LEU* 3.4 20.0 - - + +
380B LEU* 1.3 76.5 - - + +
382B PHE* 1.3 52.2 + - - +
384B VAL* 3.3 11.2 + - + +
385B LEU* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU 2.8 13.1 + - - +
379B LEU* 3.0 15.7 + - + +
381B LEU* 1.3 75.4 - - - +
383B VAL* 1.3 56.8 - - - +
385B LEU* 3.7 16.8 - - + +
386B THR* 3.0 40.4 + - - -
400B TRP* 3.9 23.3 - + - -
403B LEU* 4.6 9.6 - - + -
407B PHE* 3.9 43.3 - + + -
408B ILE 5.9 0.2 - - - -
411B LEU* 4.8 11.2 - - + -
421B SER* 3.7 33.7 - - - -
424B ALA* 4.1 10.3 - - + -
425B TYR* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B LEU 2.9 19.6 + - - +
380B LEU* 2.8 18.9 + - + +
382B PHE* 1.3 76.7 - - - +
384B VAL* 1.3 60.1 + - + +
386B THR* 3.4 1.4 + - - -
387B ALA* 3.0 28.8 + - - +
424B ALA* 3.7 30.1 - - + +
427B VAL* 4.0 20.6 - - + -
428B GLY* 3.6 7.2 - - - +
473B LEU* 4.1 12.3 - - + -
477B SER* 3.9 21.3 - - - +
480B LEU* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LEU* 2.9 14.9 + - + +
381B LEU* 3.6 12.6 - - + +
383B VAL* 1.3 80.1 - - + +
385B LEU* 1.3 60.2 + - - +
387B ALA* 4.5 4.9 - - - -
388B LEU* 3.0 40.8 + - + +
473B LEU* 5.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LEU 2.8 19.6 + - - +
382B PHE* 3.7 18.8 - - + +
383B VAL 3.2 0.2 - - - -
384B VAL* 1.3 72.9 - - - +
386B THR* 1.3 68.1 + - - +
388B LEU* 3.7 10.0 - - + +
389B ILE* 3.1 40.9 + - + +
403B LEU* 4.8 4.5 - - + -
407B PHE* 4.1 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PHE* 3.0 23.7 + - - -
383B VAL 3.8 3.6 - - - -
385B LEU* 1.3 74.1 - - - +
387B ALA* 1.3 49.8 - - - +
389B ILE* 2.8 12.7 + - - +
390B ASN* 2.7 33.6 + - - +
399B LYS* 4.0 6.5 - - - -
403B LEU* 4.2 10.4 - - - +
425B TYR* 3.3 47.5 - - + +
428B GLY* 3.3 4.0 - - - -
429B ASP* 3.3 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B VAL 3.0 17.5 + - - +
384B VAL* 4.1 4.7 - - - +
386B THR* 1.3 75.9 - - - +
388B LEU* 1.3 65.6 + - + +
390B ASN* 3.6 2.8 + - - -
391B LEU* 3.5 9.1 - - - +
428B GLY* 3.0 26.2 + - - +
432B THR* 3.3 34.1 + - + +
473B LEU* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 3.0 38.6 + - + +
385B LEU* 3.7 11.2 - - + +
387B ALA* 1.3 79.7 - - - +
389B ILE* 1.3 65.4 + - + +
391B LEU* 3.1 32.8 + - + +
392B MET* 4.3 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LEU* 3.1 33.2 + - + +
386B THR* 2.8 12.5 + - - +
388B LEU* 1.3 75.6 - - + +
390B ASN* 1.3 50.5 + - - +
391B LEU 3.0 0.2 - - - -
392B MET* 2.7 34.5 + - + +
393B ILE* 3.2 21.7 + - + -
399B LYS* 3.5 27.1 - - + -
403B LEU* 4.3 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B THR 2.7 18.4 + - - +
387B ALA 3.7 0.9 - - - +
388B LEU 3.2 0.2 + - - -
389B ILE* 1.3 71.6 - - - +
391B LEU* 1.3 61.5 + - - +
392B MET 3.2 0.4 - - - -
393B ILE 3.2 13.4 - - - +
394B GLY* 3.0 20.8 - - - +
399B LYS* 3.2 13.6 + - - +
428B GLY 3.8 5.6 - - - +
429B ASP* 2.3 35.7 + - - +
432B THR* 3.2 21.1 + - - +
433B ASN* 3.4 12.1 + - - +
436B THR* 4.4 7.3 - - - +
801B NA 2.7 17.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ALA 3.5 5.8 - - - +
388B LEU* 3.2 30.3 - - + +
389B ILE 2.9 1.0 + - - -
390B ASN* 1.3 78.1 - - - +
392B MET* 1.3 60.7 + - + +
432B THR* 3.5 39.9 - - + +
435B ILE* 4.0 20.6 - - + +
436B THR* 3.1 29.9 + - - -
438B LEU* 3.5 12.5 - - - +
----------------------------------------------------------
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