Contacts of the helix formed by residues 499 - 512 (chain B) in PDB entry 4JGV
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 499 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453B TYR* 3.6 0.7 - - - -
497B LEU 3.6 5.0 + - - +
498B VAL* 1.3 73.4 - - - +
500B VAL* 1.3 69.4 + - - +
501B PRO* 3.9 5.9 - - + +
502B ALA* 2.9 21.3 + - - +
503B PHE 2.9 17.2 + - - -
538B HIS* 2.8 29.2 + - - -
542B VAL* 4.0 12.0 - - - +
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Residues in contact with VAL 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B VAL* 4.2 16.6 - - + -
372B HIS* 3.7 26.0 - - + +
373B LEU* 4.2 18.2 - - + -
453B TYR* 3.6 22.2 - - + +
499B ASP* 1.3 72.1 - - - +
501B PRO* 1.3 66.0 - - + +
503B PHE* 3.1 3.8 + - - +
504B ALA* 2.8 27.8 + - + +
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Residues in contact with PRO 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B LEU* 3.8 20.4 - - + +
369B VAL* 3.7 21.5 - - + -
499B ASP* 3.4 12.6 - - + +
500B VAL* 1.3 94.0 - - + +
502B ALA* 1.3 62.3 + - - +
504B ALA* 3.0 3.1 + - - +
505B CYS* 3.0 27.8 + - - -
538B HIS* 3.5 31.0 - - + +
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Residues in contact with ALA 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B VAL* 3.8 14.4 - - + -
499B ASP* 2.9 26.0 + - - +
501B PRO* 1.3 76.5 - - - +
503B PHE* 1.3 59.1 + - - +
505B CYS* 3.4 2.9 + - - +
506B LEU* 3.0 28.6 + - - +
535B LEU* 3.6 26.6 - - + +
538B HIS* 4.0 7.4 - - + -
539B VAL* 5.0 4.3 - - + -
555B LEU* 4.9 9.2 - - + -
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Residues in contact with PHE 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B HIS* 3.4 37.2 - + - +
449B LEU* 3.6 47.1 - - + -
450B ARG* 4.0 14.6 - - + -
453B TYR* 3.6 59.9 - + + -
493B LEU* 4.5 3.4 - - + -
498B VAL* 3.7 10.7 - - + +
499B ASP 2.9 9.4 + - - +
500B VAL 3.5 7.0 - - - +
502B ALA* 1.3 75.7 - - - +
504B ALA* 1.3 60.5 + - - +
506B LEU* 4.3 8.7 - - + +
507B SER* 2.9 38.3 + - - -
601B GOL 5.1 0.2 - - - -
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Residues in contact with ALA 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B LEU* 3.7 40.7 - - + +
369B VAL* 3.8 14.1 - - + +
372B HIS* 4.1 13.5 - - + -
420B TRP* 5.1 2.4 + - - -
500B VAL 2.8 20.2 + - - +
501B PRO 3.0 5.4 + - - +
503B PHE* 1.3 74.1 - - - +
505B CYS* 1.3 59.9 + - - +
507B SER* 3.2 15.9 + - - -
508B ALA* 3.6 12.8 + - - +
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Residues in contact with CYS 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 3.6 23.3 - - - -
368B LEU* 3.8 15.0 - - - -
501B PRO 3.0 16.5 + - - +
502B ALA 3.6 7.4 - - - +
504B ALA* 1.3 76.9 - - - +
506B LEU* 1.3 66.1 + - - +
508B ALA* 3.2 5.4 + - - +
509B LEU* 3.0 26.2 + - - +
531B ILE* 3.8 11.7 - - + +
534B CYS* 4.1 2.5 - - - -
535B LEU* 3.8 43.7 - - + -
538B HIS* 5.7 0.2 - - - -
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Residues in contact with LEU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B LEU* 4.7 11.4 - - + -
493B LEU* 5.2 11.7 - - + -
498B VAL* 4.9 11.4 - - + -
502B ALA 3.0 17.9 + - - +
503B PHE* 3.3 11.9 + - + +
505B CYS* 1.3 76.7 - - - +
507B SER* 1.3 62.3 + - - +
509B LEU* 3.0 18.8 + - + +
510B VAL* 3.1 18.0 + - - +
535B LEU* 4.8 1.5 - - + +
555B LEU* 4.1 35.2 - - + +
556B LEU* 4.0 18.6 - - + -
558B LYS* 5.5 2.2 - - + -
559B LEU* 3.7 39.5 - - + -
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Residues in contact with SER 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B HIS* 4.9 3.3 + - - -
420B TRP* 3.5 24.4 + - - -
446B LEU* 3.4 17.5 - - - +
449B LEU* 4.0 16.1 - - - +
450B ARG* 5.1 5.8 - - - -
503B PHE* 2.9 37.7 + - - -
504B ALA* 3.2 11.1 + - - -
506B LEU* 1.3 74.8 - - - +
508B ALA* 1.3 64.2 + - - +
510B VAL 3.1 10.2 + - - -
511B LEU 3.4 7.6 + - - -
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Residues in contact with ALA 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B LEU* 4.0 14.4 - - + -
420B TRP* 3.8 11.2 - - + -
424B ILE* 4.0 19.5 - - + -
504B ALA 3.6 11.4 + - - +
505B CYS 3.2 9.2 + - - +
506B LEU 3.2 0.4 - - - -
507B SER* 1.3 81.5 + - - +
509B LEU* 1.3 56.7 + - - +
511B LEU* 3.1 4.3 + - - +
512B ILE* 2.9 32.6 + - - +
531B ILE* 4.1 16.4 - - + -
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Residues in contact with LEU 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B CYS 3.0 19.3 + - - +
506B LEU* 3.0 12.1 + - - +
508B ALA* 1.3 75.2 - - - +
510B VAL* 1.3 64.1 + - - +
512B ILE* 3.2 16.1 - - - +
513B THR* 3.8 4.7 - - - -
528B GLN* 3.6 54.4 + - + +
531B ILE* 3.9 17.7 - - + -
532B ALA* 4.4 15.3 - - + +
535B LEU* 4.1 25.4 - - + -
556B LEU* 4.6 12.3 - - + -
559B LEU* 4.8 13.3 - - + +
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Residues in contact with VAL 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B ALA* 3.8 4.0 - - + +
445B GLU* 4.0 33.2 - - + +
446B LEU* 3.8 22.4 - - + -
449B LEU* 3.9 15.9 - - + -
506B LEU 3.1 14.0 + - - +
507B SER 3.1 8.5 + - - +
509B LEU* 1.3 76.3 - - - +
511B LEU* 1.3 62.0 + - - +
513B THR* 3.6 16.2 - - - +
515B ARG* 3.6 9.7 + - - -
559B LEU* 3.8 28.0 - - + -
562B LEU* 4.0 5.6 - - + -
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Residues in contact with LEU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B TRP* 3.8 12.6 - - + -
421B ALA* 3.6 28.0 - - + -
424B ILE* 3.9 14.6 - - + -
427B PHE* 3.8 16.4 - - + -
438B LEU* 3.3 58.8 - - + +
439B LEU* 3.8 20.0 - - + +
442B ALA* 3.8 10.9 - - + +
446B LEU* 4.1 10.5 - - + -
507B SER 3.4 7.5 + - - +
508B ALA 3.1 7.1 + - - +
510B VAL* 1.3 84.0 - - - +
512B ILE* 1.3 62.3 + - + +
513B THR* 3.4 4.0 + - - +
515B ARG* 5.0 0.3 + - - -
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Residues in contact with ILE 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B ILE* 3.9 22.4 - - + -
427B PHE* 4.3 16.4 - - + -
430B LEU* 5.5 0.9 - - + -
438B LEU* 4.6 6.5 - - + -
508B ALA 2.9 14.6 + - - +
509B LEU* 3.2 6.0 - - - +
511B LEU* 1.3 86.2 - - + +
513B THR* 1.3 55.0 + - - +
524B VAL* 3.6 29.6 - - + +
527B LEU* 3.9 20.6 - - + -
528B GLN* 2.7 46.6 + - + +
531B ILE* 3.9 22.0 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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