Contacts of the helix formed by residues 491 - 512 (chain B) in PDB entry 5I4V
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 LEU 491 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ILE* 4.8 2.2 - - + -
396A GLN* 3.7 31.9 - - - +
400A VAL* 4.1 22.2 - - + -
422A LEU* 4.4 20.0 - - + +
425A LEU* 4.2 24.9 - - + -
487B ALA* 2.9 25.7 + - + +
488B LYS* 4.0 10.1 - - + +
489B LEU 3.2 0.6 - - - -
490B LEU* 1.3 72.9 - - - +
492B ARG* 1.3 80.8 + - - +
493B LEU 3.3 0.7 - - - -
494B PRO* 3.5 16.3 - - + +
495B ALA* 4.5 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 492 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA* 6.3 0.4 - - - +
382A ASP* 6.2 0.6 - - - +
393A GLU* 4.5 11.1 + - - +
423B GLU* 2.7 60.6 + - - +
424B LEU* 4.6 10.6 - - + +
427B LYS* 3.6 32.7 - - - +
428B MET* 6.1 1.1 - - + -
431B MET* 4.0 12.1 - - + +
433B MET* 4.8 11.0 - - + -
441B LEU* 5.1 3.8 - - + -
488B LYS 3.7 12.0 + - - +
489B LEU* 3.1 16.7 + - - +
491B LEU* 1.3 94.2 + - - +
493B LEU* 1.3 64.4 + - + +
494B PRO 3.5 0.2 - - - -
495B ALA* 3.2 17.5 + - - +
496B LEU* 2.8 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A MET* 3.7 27.1 - - + -
426A VAL* 3.7 17.8 - - + +
378B GLU* 5.5 0.2 - - - +
441B LEU* 3.8 39.5 - - + -
444B ILE* 3.7 23.3 - - + -
445B ILE* 4.6 21.5 - - + -
489B LEU 4.1 3.1 - - - +
490B LEU* 3.0 17.5 + - + +
492B ARG* 1.3 78.9 - - + +
494B PRO* 1.3 70.0 - - + +
496B LEU* 3.1 9.1 + - + +
497B ARG* 2.8 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU 5.1 1.6 - - - +
425A LEU* 4.0 34.1 - - + +
426A VAL* 3.7 14.1 - - + -
429A ARG* 3.3 40.6 + - + +
490B LEU 3.4 11.9 - - - +
491B LEU* 3.5 19.3 - - + +
493B LEU* 1.3 91.6 - - + +
495B ALA* 1.3 61.6 + - - +
497B ARG* 3.2 3.9 + - + +
498B SER* 3.2 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ASP* 3.5 32.5 + - + +
429A ARG* 4.5 0.4 - - - +
419B ARG* 4.9 0.2 + - - -
423B GLU* 4.4 11.7 - - + +
424B LEU* 5.1 1.8 - - + -
491B LEU 4.5 2.4 + - - +
492B ARG* 3.2 35.3 + - - +
494B PRO* 1.3 80.3 - - - +
496B LEU* 1.3 62.3 + - - +
498B SER* 3.4 2.6 + - - -
499B ILE* 3.1 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLU* 4.0 23.5 - - + +
381B ILE* 3.7 35.7 - - + -
382B ALA* 4.3 10.5 - - + +
424B LEU* 4.0 19.9 - - + +
445B ILE* 3.4 33.2 - - + -
492B ARG* 2.8 17.4 + - + +
493B LEU* 3.1 14.3 + - + +
495B ALA* 1.3 76.2 - - - +
497B ARG* 1.3 59.4 + - - +
499B ILE* 3.7 4.7 - - + -
500B GLY* 2.8 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 497 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A VAL* 3.6 35.2 + - + +
427A SER* 4.8 2.4 - - - +
429A ARG* 3.6 22.7 - - + -
430A THR* 2.6 38.1 + - - +
378B GLU* 2.7 39.1 + - - +
445B ILE* 5.9 3.8 + - - +
448B ASN* 4.1 22.3 - - - +
464B ARG* 5.1 7.1 - - - +
493B LEU 2.8 16.0 + - - +
494B PRO 3.2 4.7 + - - +
496B LEU* 1.3 76.0 - - - +
498B SER* 1.3 63.0 + - - +
500B GLY* 3.2 2.3 + - - -
501B LEU* 3.0 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ASP* 4.6 0.4 - - - -
429A ARG* 2.7 46.5 + - - +
419B ARG* 3.7 18.8 + - - -
494B PRO 3.2 3.7 + - - -
495B ALA 3.9 2.5 - - - -
497B ARG* 1.3 74.1 - - - +
499B ILE* 1.3 66.4 + - - +
501B LEU* 3.3 12.4 + - - +
502B LYS* 3.2 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ILE* 4.4 14.4 - - + -
416B ILE* 3.9 10.3 - - + +
419B ARG* 3.7 52.7 - - + +
420B VAL* 3.9 21.3 - - + +
423B GLU* 4.1 16.8 - - + -
424B LEU* 4.1 16.2 - - + -
495B ALA* 3.1 22.2 + - + +
496B LEU* 3.7 5.4 - - - +
498B SER* 1.3 75.2 - - - +
500B GLY* 1.3 63.1 + - - +
502B LYS* 3.3 2.9 + - - +
503B CYS* 3.0 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ASN* 2.6 33.4 + - - -
378B GLU* 4.6 7.2 - - - -
381B ILE* 4.0 10.5 - - - -
496B LEU 2.8 17.1 + - - -
497B ARG 3.2 4.7 + - - -
499B ILE* 1.3 78.0 - - - +
501B LEU* 1.3 61.8 + - - +
503B CYS 3.4 0.2 + - - -
504B LEU* 3.1 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG 4.1 12.1 - - - +
430A THR* 4.7 5.2 - - + +
433A SER* 3.9 34.3 - - - +
497B ARG* 3.0 37.6 + - + +
498B SER* 3.3 12.1 + - - +
500B GLY* 1.3 76.2 - - - +
502B LYS* 1.3 62.4 + - - +
504B LEU* 3.5 15.3 + - + +
505B GLU* 3.1 24.6 + - - +
226E LEU* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ILE* 3.7 32.8 - - + -
419B ARG* 4.0 13.9 - - - +
498B SER 3.2 12.6 + - - +
499B ILE 3.3 2.0 + - - +
501B LEU* 1.3 78.4 - - - +
503B CYS* 1.3 60.7 + - - +
505B GLU* 3.0 53.2 + - - +
506B HIS* 3.3 27.8 + - + -
509B PHE* 6.2 0.2 - - - -
230E GLN* 3.5 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ASN* 4.4 4.7 - - - +
381B ILE* 4.0 25.4 - - + -
384B PHE* 6.0 2.0 - - - -
416B ILE* 3.7 21.5 - - - -
420B VAL* 5.0 5.6 - - - -
499B ILE* 3.0 27.6 + - - +
500B GLY 3.9 4.3 - - - +
502B LYS* 1.3 72.9 - - - +
504B LEU* 1.3 66.9 + - - +
506B HIS* 3.1 11.8 + - - +
507B LEU* 3.0 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B TRP* 4.3 27.8 - - + +
377B ASN* 4.1 12.7 - - + +
500B GLY 3.1 18.1 + - - +
501B LEU* 3.7 15.7 - - + +
503B CYS* 1.3 76.7 - - - +
505B GLU* 1.3 63.8 + - - +
507B LEU* 3.0 13.4 + - + +
508B PHE* 2.9 55.0 + - + -
526B LEU* 4.8 5.8 - - + -
226E LEU* 5.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B LEU 3.1 11.6 + - - +
502B LYS* 3.0 52.2 + - - +
504B LEU* 1.3 76.6 - - - +
506B HIS* 1.3 60.1 + - + +
508B PHE* 3.1 14.6 + - - +
509B PHE* 3.2 41.4 + - + -
226E LEU* 4.2 41.0 - - + +
229E GLN* 5.6 1.7 - - - +
230E GLN* 3.7 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B GLY 3.9 11.9 - - - -
413B VAL* 3.4 26.4 - - + +
416B ILE* 3.9 27.7 - - + +
502B LYS* 3.3 40.0 + - + -
503B CYS* 3.1 11.2 + - - +
505B GLU* 1.3 78.0 - - + +
507B LEU* 1.3 63.0 + - + +
509B PHE* 3.0 33.7 + + - +
510B PHE* 3.0 35.4 + - + -
230E GLN* 6.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ILE* 5.5 8.1 - - + -
340B CYS* 4.0 27.4 - - - -
343B ALA* 5.6 3.4 - - + -
376B TRP* 3.9 29.4 - - + -
377B ASN* 4.1 14.6 - - - +
503B CYS* 3.0 20.9 + - + +
504B LEU* 3.0 12.7 + - + +
506B HIS* 1.3 74.5 - - + +
508B PHE* 1.3 60.9 + - - +
510B PHE* 3.5 11.4 + - + +
511B LYS 3.1 16.6 + - - -
518B ILE* 5.8 0.2 - - - +
522B LEU* 4.7 13.2 - - + -
526B LEU* 3.5 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B LEU* 2.9 50.4 + - + -
505B GLU* 3.1 7.4 + - - +
507B LEU* 1.3 75.5 - - - +
509B PHE* 1.3 66.1 + - + +
511B LYS* 3.4 12.0 + - + +
512B LEU* 3.2 25.6 + - - +
526B LEU* 3.7 44.2 - - + -
221E THR* 6.5 0.2 - - + -
222E ALA* 4.8 13.9 - - + -
223E ALA* 4.0 28.6 - - + +
226E LEU* 3.5 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B LYS* 6.2 0.2 - - - -
505B GLU* 3.4 39.5 - - + -
506B HIS* 3.0 30.3 + + - +
508B PHE* 1.3 77.4 - - + +
510B PHE* 1.3 71.8 + - + +
512B LEU* 3.1 14.1 + - + -
513B ILE* 3.2 22.6 + - + +
223E ALA 4.6 2.0 - - - -
226E LEU* 3.8 7.6 - - + -
227E MET* 3.6 39.0 - - + -
230E GLN* 3.8 31.4 - - + -
290E PRO* 3.9 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B VAL* 3.3 50.9 - - + -
339B ILE* 5.2 8.1 - - + -
340B CYS* 3.6 23.3 - - - -
411B ALA 5.9 1.1 - - - -
413B VAL* 4.4 18.4 - - + -
506B HIS* 3.0 30.7 + - + -
507B LEU* 3.7 14.6 - - + +
508B PHE 3.3 0.2 - - - -
509B PHE* 1.3 80.2 - - + +
511B LYS* 1.3 63.2 + - - +
513B ILE* 2.8 28.2 + - - +
517B PRO* 5.3 0.5 - - - +
518B ILE* 4.0 23.1 - - + +
294E GLN* 5.2 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU 3.1 14.8 + - - +
508B PHE* 3.4 20.0 - - + +
510B PHE* 1.3 77.0 - - - +
512B LEU* 1.3 62.5 + - + +
513B ILE 3.3 1.7 + - - -
518B ILE* 4.4 12.7 - - + +
523B MET* 4.1 29.5 - - + +
526B LEU* 3.8 41.1 + - + -
527B GLU* 4.5 11.3 - - - +
221E THR* 5.8 6.3 - - - +
223E ALA* 5.3 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B PHE 3.2 10.8 + - - +
509B PHE* 3.1 10.1 + - + +
511B LYS* 1.3 81.1 - - + +
513B ILE* 1.3 62.0 + - - +
221E THR* 6.2 0.2 - - + -
223E ALA* 3.9 37.0 - - + +
224E GLN* 4.4 15.3 - - + +
227E MET* 3.4 37.5 - - + -
398E PRO* 3.6 29.2 - - + +
----------------------------------------------------------
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