Contacts of the helix formed by residues 508 - 524 (chain B) in PDB entry 6V3O
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 THR 508 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B PRO 4.3 1.0 + - - +
507B GLN* 1.3 75.9 - - - +
509B GLU* 1.3 60.6 + - - +
510B GLU* 3.6 6.8 + - - +
511B ILE* 3.4 34.2 + - + +
512B ALA* 2.9 28.2 + - - +
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Residues in contact with GLU 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B THR* 1.3 75.2 - - - +
510B GLU* 1.3 66.0 + - + +
512B ALA* 3.5 6.5 + - - +
513B ASP* 3.0 22.7 + - - +
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Residues in contact with GLU 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ARG* 2.8 58.5 + - - +
464B ASP* 4.3 10.7 - - + +
508B THR* 3.3 6.5 + - - +
509B GLU* 1.3 80.8 - - + +
511B ILE* 1.3 65.0 + - + +
513B ASP* 3.1 9.6 + - - -
514B VAL* 3.1 6.8 + - - +
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Residues in contact with ILE 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ARG 5.8 0.2 - - - -
464B ASP* 3.7 31.6 - - + +
465B VAL* 4.1 27.4 - - + +
468B ALA* 3.7 17.0 - - + -
505B LEU* 5.2 5.4 - - + -
506B PRO 5.2 0.9 - - - +
507B GLN* 4.0 15.0 - - + -
508B THR* 3.4 32.0 + - + +
510B GLU* 1.3 77.8 - - + +
512B ALA* 1.3 62.7 + - - +
514B VAL* 3.2 3.5 + - - +
515B ILE* 3.0 41.2 + - + +
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Residues in contact with ALA 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PRO* 5.3 0.2 - - - +
507B GLN* 3.2 26.2 + - + +
508B THR 2.9 18.7 + - - +
509B GLU* 3.7 7.2 - - - +
511B ILE* 1.3 77.1 - - - +
513B ASP* 1.3 53.1 + - - +
515B ILE* 4.0 0.8 - - - +
516B GLY* 2.7 32.7 + - - -
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Residues in contact with ASP 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ARG* 4.3 12.2 + - - +
297B PRO* 4.8 8.8 - - - +
299B VAL 4.1 11.1 - - - +
300B THR* 4.5 9.5 - - - +
301B PRO* 3.9 26.4 - - - +
457B GLN* 5.0 1.6 + - - -
461B ARG* 3.8 12.2 + - - +
509B GLU 3.0 14.8 + - - +
510B GLU* 3.1 10.1 + - - +
512B ALA* 1.3 77.8 - - - +
514B VAL* 1.3 60.1 + - - +
517B ALA* 3.1 23.4 + - - +
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Residues in contact with VAL 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ARG* 6.3 0.2 - - - +
457B GLN* 4.0 18.4 - - + +
461B ARG* 3.7 33.7 - - + +
462B HIS* 4.1 14.1 - - + +
465B VAL* 3.9 20.0 - - + -
510B GLU 3.1 14.3 + - - +
511B ILE 3.2 6.0 + - - +
513B ASP* 1.3 74.6 - - - +
515B ILE* 1.3 66.4 + - + +
517B ALA* 3.4 6.5 + - - +
518B PHE* 3.1 50.3 + - + -
532B TYR* 4.9 2.7 - - - +
549B LEU* 4.9 1.6 - - + -
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Residues in contact with ILE 515 (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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465B VAL* 4.5 15.0 - - + -
501B LEU* 4.5 15.5 - - + -
505B LEU* 4.5 13.0 - - + -
507B GLN* 3.4 37.7 - - + +
511B ILE* 3.0 26.4 + - + +
512B ALA 4.0 2.7 - - - +
514B VAL* 1.3 76.7 - - + +
516B GLY* 1.3 62.3 + - - +
518B PHE* 3.1 11.7 + - + +
519B HIS* 3.0 48.7 + - + +
549B LEU* 6.1 0.2 - - + -
553B CYS* 4.4 13.5 - - - -
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Residues in contact with GLY 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PRO* 3.6 13.6 - - - +
512B ALA 2.7 23.3 + - - -
515B ILE* 1.3 73.7 - - - +
517B ALA* 1.3 61.3 + - - +
519B HIS* 3.2 12.0 + - - +
520B VAL* 3.0 25.8 + - - +
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Residues in contact with ALA 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ARG* 3.7 33.2 - - - +
301B PRO* 3.5 10.8 - - - +
304B THR* 6.6 0.2 - - - -
455B ILE* 5.8 3.6 - - + -
513B ASP 3.1 18.5 + - - +
514B VAL* 3.6 7.9 - - - +
515B ILE 3.2 0.2 - - - -
516B GLY* 1.3 75.5 - - - +
518B PHE* 1.3 63.5 + - + +
520B VAL* 3.0 7.0 + - - +
521B LEU* 2.9 28.8 + - + +
532B TYR* 5.9 5.6 - - + +
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Residues in contact with PHE 518 (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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462B HIS* 4.4 2.9 - + - -
514B VAL* 3.1 41.2 + - + -
515B ILE* 3.1 8.1 + - + +
517B ALA* 1.3 79.3 - - + +
519B HIS* 1.3 58.4 + - - +
521B LEU* 3.2 16.2 + - + +
522B ALA* 3.0 24.4 + - - +
532B TYR* 3.4 39.3 - + - -
546B VAL* 3.8 14.4 - - + -
549B LEU* 3.9 22.7 - - + -
550B GLN* 3.8 32.5 - - + -
553B CYS* 3.7 29.6 - - + -
555B VAL* 3.6 10.5 - - + +
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Residues in contact with HIS 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B LEU* 5.2 4.5 - - + +
515B ILE* 3.0 33.6 + - + +
516B GLY* 3.5 12.2 - - - +
517B ALA 3.2 0.2 - - - -
518B PHE* 1.3 77.3 - - - +
520B VAL* 1.3 62.1 + - + +
522B ALA* 3.3 7.2 + - + +
523B GLU* 3.2 36.8 + - - +
553B CYS* 3.3 38.7 + - + +
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Residues in contact with VAL 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PRO* 3.6 36.3 - - + +
302B GLU* 5.5 0.4 - - - -
304B THR* 4.5 10.8 - - + -
305B ARG* 4.1 17.3 - - + +
516B GLY 3.0 15.1 + - - +
517B ALA* 3.0 10.8 + - - +
519B HIS* 1.3 74.8 - - + +
521B LEU* 1.3 66.2 + - + +
523B GLU* 3.1 24.4 + - - +
524B LEU* 3.4 35.8 + - + +
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Residues in contact with LEU 521 (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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304B THR* 5.0 5.4 - - + -
455B ILE* 4.0 17.3 - - + -
517B ALA* 2.9 19.3 + - + +
518B PHE* 3.4 22.7 - - + +
520B VAL* 1.3 78.0 - - + +
522B ALA* 1.3 60.9 + - - +
523B GLU 3.4 0.5 + - - -
524B LEU 3.6 14.2 + - - +
529B PHE* 3.4 46.5 - - + -
532B TYR* 4.1 27.1 - - + -
550B GLN* 4.9 2.7 - - - +
555B VAL* 4.4 11.9 - - + +
559B LEU* 4.1 24.7 - - + +
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Residues in contact with ALA 522 (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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518B PHE 3.0 13.8 + - - +
519B HIS* 3.6 9.4 - - - +
520B VAL 3.2 0.4 - - - -
521B LEU* 1.3 77.7 - - - +
523B GLU* 1.3 62.0 + - + +
524B LEU 3.6 3.6 + - - +
553B CYS 4.1 6.1 - - - +
554B GLY 3.1 35.5 - - - +
555B VAL* 3.9 10.5 - - + +
556B ARG 5.3 1.3 + - - +
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Residues in contact with GLU 523 (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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305B ARG* 5.6 6.1 - - - -
519B HIS* 3.3 24.3 - - - +
520B VAL* 3.1 18.2 + - + +
522B ALA* 1.3 78.9 - - + +
524B LEU* 1.3 63.0 + - + +
525B PRO* 4.7 1.0 - - - +
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Residues in contact with LEU 524 (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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305B ARG* 4.1 23.3 - - + +
308B CYS* 4.1 24.2 - - + -
309B LEU* 5.0 13.7 - - + -
312B ARG* 6.0 1.6 - - - +
520B VAL* 3.4 33.5 + - + +
521B LEU 3.6 9.6 + - - +
522B ALA 3.4 4.2 - - - +
523B GLU* 1.3 83.4 - - + +
525B PRO* 1.3 81.0 - - + +
526B PRO* 3.5 4.9 - - - +
528B SER* 4.6 1.6 - - - +
529B PHE* 3.6 30.3 - - + -
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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
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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