Contacts of the helix formed by residues 495 - 511 (chain B) in PDB entry 2BVA
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 GLU 495 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B HIS* 5.2 0.4 - - - -
485B GLU* 4.7 1.5 - - - +
493B GLY* 2.6 22.5 + - - +
494B PRO* 1.3 86.5 - - - +
496B VAL* 1.3 61.8 + - - +
497B ASP 3.4 0.4 - - - -
498B ILE* 3.5 16.3 + - - +
499B TRP 3.8 0.2 + - - -
557B PRO* 3.5 28.0 - - + +
560B ARG* 3.0 44.4 + - + +
561B ALA 4.9 9.6 - - - +
562B THR* 5.0 14.7 - - + +
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Residues in contact with VAL 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ILE* 3.7 21.8 - - + -
439B ARG* 4.6 7.6 - - + -
483B ALA* 4.3 12.6 - - + +
485B GLU* 3.2 28.7 - - + +
486B LEU* 4.9 9.2 - - + -
492B TYR* 3.9 29.8 - - + -
493B GLY 3.3 17.7 - - - +
495B GLU* 1.3 76.8 - - - +
497B ASP* 1.3 78.7 + - - +
499B TRP* 2.9 17.5 + - - +
500B SER* 3.3 13.7 + - - +
560B ARG* 4.2 0.9 - - - +
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Residues in contact with ASP 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B LEU* 3.6 20.9 - - + +
432B HIS* 4.0 12.4 + - - +
436B VAL 5.2 0.2 - - - +
437B ILE* 3.7 14.1 - - - +
438B HIS* 3.3 26.9 + - - +
439B ARG* 3.0 27.3 + - - -
440B ASP 4.3 0.3 + - - -
441B ILE* 4.0 14.9 - - - +
494B PRO 3.5 9.1 + - - +
495B GLU 3.4 1.0 - - - -
496B VAL* 1.3 82.4 - - - +
498B ILE* 1.3 57.5 + - - +
500B SER* 3.5 7.5 + - - -
501B LEU* 3.0 29.7 + - - +
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Residues in contact with ILE 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B LEU* 4.2 8.1 - - + -
428B LEU* 4.7 2.5 - - + -
432B HIS* 4.0 18.2 - - + -
494B PRO 4.5 0.7 - - - +
495B GLU* 3.6 12.6 - - - +
496B VAL 3.0 0.4 + - - -
497B ASP* 1.3 76.0 - - - +
499B TRP* 1.3 65.4 + - - +
501B LEU* 3.5 10.9 - - + +
502B GLY 3.0 16.3 + - - -
551B ARG 4.7 0.7 - - - +
552B LEU* 3.6 33.8 - - + +
560B ARG* 4.2 8.3 - - + -
561B ALA 3.7 15.7 - - - +
562B THR 4.1 0.7 - - - -
563B ALA* 3.7 23.3 - - + +
566B LEU* 3.4 33.4 - - + -
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Residues in contact with TRP 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B TYR 5.9 0.2 + - - -
481B TRP 3.9 4.0 - - - -
482B MET 3.1 19.7 + - - -
483B ALA* 3.3 28.7 - - + -
484B PRO* 3.4 25.3 - - + +
495B GLU 3.8 1.2 + - - -
496B VAL 2.9 10.5 + - - +
498B ILE* 1.3 79.8 - - - +
500B SER* 1.3 58.6 + - - +
502B GLY* 2.9 16.6 + - - -
503B ILE* 3.2 22.4 + - + +
527B ILE* 4.5 12.4 - - + +
532B PRO* 3.9 8.3 - - + -
533B PRO* 3.3 38.1 - - + -
552B LEU 3.8 10.9 + - - +
553B LEU* 3.3 46.5 - - + +
554B VAL 3.6 20.2 - - - -
555B ARG* 4.6 3.1 - - + -
560B ARG* 4.4 10.7 - - - +
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Residues in contact with SER 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ARG* 5.9 1.9 - - - -
440B ASP 5.9 0.8 + - - -
441B ILE* 4.0 29.9 - - - +
481B TRP* 3.0 33.3 + - - -
482B MET* 4.9 0.2 - - - -
483B ALA* 4.7 3.5 + - - +
496B VAL* 3.3 14.1 + - - +
497B ASP* 3.9 8.5 + - - -
499B TRP* 1.3 76.2 - - - +
501B LEU* 1.3 64.1 + - - +
503B ILE* 3.0 16.6 + - - +
504B MET 3.2 9.0 + - - -
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Residues in contact with LEU 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B CYS* 4.9 14.4 - - - -
424B VAL* 3.7 22.0 - - + -
425B LEU* 4.0 20.6 - - + -
428B LEU* 3.7 26.9 - - + -
441B ILE* 3.7 17.6 - - + +
497B ASP 3.0 16.7 + - - +
498B ILE* 3.5 17.3 - - + +
500B SER* 1.3 74.8 - - - +
502B GLY* 1.3 63.3 + - - +
504B MET* 3.2 21.7 + - + +
505B VAL* 3.3 19.8 + - + +
552B LEU* 4.1 13.7 - - + -
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Residues in contact with GLY 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B ILE 3.0 7.8 + - - -
499B TRP 2.9 11.4 + - - -
501B LEU* 1.3 76.5 - - - +
503B ILE* 1.3 62.0 + - - +
505B VAL* 3.4 7.7 + - - -
506B ILE* 3.6 10.6 + - - +
549B LEU* 3.6 15.6 - - - +
552B LEU* 3.8 17.3 - - - -
553B LEU* 3.6 20.1 - - - +
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Residues in contact with ILE 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B TYR 4.1 8.3 - - - +
481B TRP* 3.4 41.5 - - + +
499B TRP* 3.2 28.4 + - + +
500B SER* 3.0 10.0 + - - +
502B GLY* 1.3 77.0 - - - +
504B MET* 1.3 63.0 + - - +
506B ILE* 2.9 21.3 + - + +
507B GLU* 3.0 9.4 + - + +
513B PRO* 4.1 20.8 - - + +
514B PRO* 4.2 14.1 - - + -
527B ILE* 5.4 3.4 - - + -
533B PRO* 4.0 26.7 - - + -
553B LEU* 4.6 6.1 - - + -
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Residues in contact with MET 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B LEU* 3.5 25.6 - - + -
420B VAL* 4.3 13.0 - - + -
424B VAL* 5.3 4.7 - - + -
441B ILE* 3.7 19.5 - - + -
442B LYS* 3.3 26.7 - - - +
443B SER* 3.3 23.8 - - - +
446B ILE* 3.7 19.1 - - + -
481B TRP* 4.3 1.1 - - - +
500B SER 3.2 7.5 + - - +
501B LEU* 3.2 18.7 + - + +
503B ILE* 1.3 79.8 - - - +
505B VAL* 1.3 57.3 + - + +
507B GLU* 2.8 37.1 + - - +
508B MET* 2.8 16.2 + - + +
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Residues in contact with VAL 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B ILE* 4.7 10.3 - - + -
421B CYS* 4.4 19.7 - - - -
501B LEU* 3.5 18.2 - - + +
502B GLY* 3.7 2.0 - - - +
503B ILE 3.1 0.8 + - - -
504B MET* 1.3 76.4 - - + +
506B ILE* 1.3 62.4 + - - +
508B MET* 3.0 31.5 + - + +
509B VAL* 3.2 18.8 + - + +
545B LEU* 4.2 19.1 - - + -
548B PHE* 4.5 6.7 - - + -
549B LEU* 3.5 29.2 - - + -
552B LEU* 4.8 3.8 - - + -
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Residues in contact with ILE 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B GLY 3.6 11.4 + - - +
503B ILE* 2.9 13.1 + - + +
505B VAL* 1.3 72.3 - - - +
507B GLU* 1.3 58.4 - - - +
509B VAL* 2.9 7.2 + - - -
510B ASP* 2.5 55.4 + - - +
512B GLU 3.9 12.6 - - - +
514B PRO* 4.6 17.9 - - + -
533B PRO* 4.6 6.7 - - + +
534B ARG 3.3 32.3 - - - +
535B LEU* 3.9 18.4 - - + +
549B LEU* 4.2 19.7 - - + -
553B LEU* 4.8 3.8 - - + -
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Residues in contact with GLU 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B THR* 4.8 4.0 - - - +
407B VAL* 2.9 23.2 - - + +
408B THR* 6.2 0.2 - - - +
443B SER* 2.3 48.5 + - - -
444B ASP* 4.7 0.9 - - - +
481B TRP* 3.3 28.8 + - - +
503B ILE 3.0 6.6 + - - +
504B MET* 2.8 20.9 + - + +
506B ILE* 1.3 77.9 - - - +
508B MET* 1.3 54.2 + - + +
509B VAL 3.1 0.5 + - - -
511B GLY* 2.9 27.3 + - - +
512B GLU* 4.0 11.4 + - - +
513B PRO* 4.1 25.6 - - + +
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Residues in contact with MET 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B LEU* 4.0 27.1 - - + -
407B VAL* 3.3 14.5 - - + +
410B THR 5.3 1.7 - - - +
411B ARG* 5.2 2.8 - - - +
412B MET* 3.3 47.2 + - - +
417B ILE* 3.6 53.4 - - + +
420B VAL* 4.0 15.5 - - + -
421B CYS* 4.9 6.1 - - - -
504B MET* 2.8 19.3 + - + +
505B VAL* 3.0 23.1 + - + +
507B GLU* 1.3 74.3 - - - +
509B VAL* 1.3 59.9 + - - +
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Residues in contact with VAL 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ARG* 5.9 4.3 - - - +
417B ILE* 4.4 16.8 - - + -
505B VAL* 3.5 19.3 - - + +
506B ILE 2.9 5.8 + - - +
508B MET* 1.3 84.1 - - - +
510B ASP* 1.3 59.1 + - - +
511B GLY 3.4 2.4 + - - -
535B LEU* 3.5 30.5 - - + -
537B ASN* 3.5 25.9 - - + +
541B VAL* 5.0 11.9 - - + -
545B LEU* 5.6 6.3 - - + -
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Residues in contact with ASP 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B ILE* 2.5 33.8 + - + +
509B VAL* 1.3 77.6 - - - +
511B GLY* 1.3 54.7 + - - +
512B GLU* 2.9 25.7 + - - +
534B ARG 4.5 0.7 - - - +
535B LEU* 3.9 1.9 - - - +
536B LYS* 2.9 42.7 + - + +
537B ASN* 2.3 33.6 + - - +
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Residues in contact with GLY 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B VAL* 3.9 19.9 - - - +
408B THR* 4.3 20.4 - - - +
507B GLU* 2.9 22.8 + - - +
508B MET 4.8 0.2 - - - -
509B VAL 3.4 2.4 + - - -
510B ASP* 1.3 76.0 - - - +
512B GLU* 1.3 66.3 + - - +
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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) + - + + + + + -
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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