Contacts of the helix formed by residues 483 - 497 (chain B) in PDB entry 5Y7G
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 483 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481B CYS 3.3 5.4 - - - +
482B LEU* 1.3 85.5 - - + +
484B ALA* 1.3 65.0 + - - +
485B ALA* 4.2 4.5 - - + +
486B HIS* 3.1 45.8 + - + +
487B LEU* 3.1 12.7 + - - +
518B TYR* 3.3 23.8 - - + -
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Residues in contact with ALA 484 (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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441B LEU* 3.2 40.5 - - + +
442B GLU* 5.0 7.4 - - - +
443B ASP 5.4 0.2 - - - +
446B TYR* 3.9 18.5 + - + -
447B ARG* 6.0 1.1 - - - +
482B LEU 3.4 3.0 + - - -
483B PRO* 1.3 71.4 - - - +
485B ALA* 1.3 57.6 + - - +
487B LEU* 3.1 5.1 + - - +
488B ARG* 2.9 27.4 + - - +
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Residues in contact with ALA 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B GLU* 5.5 3.8 + - - -
483B PRO* 3.1 4.1 - - + +
484B ALA* 1.3 80.0 - - - +
486B HIS* 1.3 65.5 + - + +
488B ARG* 3.9 7.5 - - - +
489B ALA* 3.1 24.4 + - - +
546B MET* 4.9 0.2 - - - +
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Residues in contact with HIS 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B PRO* 3.1 32.4 + - + +
485B ALA* 1.3 81.3 - - + +
487B LEU* 1.3 61.6 + - - +
489B ALA* 3.3 1.7 + - - +
490B TRP* 2.9 46.4 + - + -
518B TYR* 2.4 34.4 + + - +
544B ARG 4.8 4.0 + - - -
545B GLU 4.6 7.1 + - - -
546B MET* 3.5 39.1 - - + +
547B PRO* 4.1 10.3 - - + -
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Residues in contact with LEU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ILE* 5.9 0.9 - - + -
393B LEU* 4.3 12.3 - - + -
397B LEU* 6.3 0.4 - - + -
441B LEU* 3.5 22.9 - - + -
446B TYR* 3.8 29.4 - - + +
450B ILE* 5.6 4.3 - - + -
479B LEU* 6.5 0.2 - - + -
482B LEU* 3.8 32.5 - - + +
483B PRO 3.1 14.6 + - - +
484B ALA 3.1 7.5 + - - +
486B HIS* 1.3 75.6 - - - +
488B ARG* 1.3 59.2 + - - +
490B TRP* 3.9 17.0 - - + -
491B PHE* 2.9 61.0 + - + -
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Residues in contact with ARG 488 (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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435B GLU* 3.6 22.2 + - - -
438B LEU* 3.0 46.2 + - - +
439B GLY* 4.4 1.2 - - - +
441B LEU* 3.6 16.2 - - + +
442B GLU* 2.4 43.8 + - - +
484B ALA 2.9 15.7 + - - +
485B ALA* 3.9 7.9 - - - +
487B LEU* 1.3 77.2 - - - +
489B ALA* 1.3 62.3 + - - +
491B PHE* 3.9 1.1 - - - +
492B GLU* 2.9 49.2 + - - +
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Residues in contact with ALA 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B ALA 3.1 13.8 + - - +
486B HIS 3.5 1.8 - - - +
487B LEU 3.3 0.4 - - - -
488B ARG* 1.3 76.2 - - - +
490B TRP* 1.3 63.6 + - - +
492B GLU* 3.0 7.9 + - - +
493B ARG 3.0 19.6 + - - -
540B PHE* 3.8 11.3 - - + -
544B ARG* 3.8 22.9 - - + +
546B MET* 3.4 31.2 - - + -
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Residues in contact with TRP 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ILE* 3.8 34.7 - - + +
482B LEU* 4.3 14.8 - - + -
486B HIS* 2.9 27.2 + - + +
487B LEU* 3.9 27.4 - - + +
489B ALA* 1.3 75.9 - - - +
491B PHE* 1.3 62.2 + - + +
493B ARG* 3.4 3.1 + - - +
494B LEU* 2.8 30.1 + - - +
518B TYR* 3.5 30.5 - + - -
520B MET* 3.3 31.2 - - + -
537B TRP* 4.0 18.1 - - + +
540B PHE* 3.7 18.4 - + - -
541B CYS* 4.0 10.3 - - - -
546B MET* 3.4 28.2 - - + -
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Residues in contact with PHE 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ILE* 3.6 22.2 - - + -
393B LEU* 3.8 13.7 - - + -
394B PHE* 3.4 57.4 - + + -
397B LEU* 4.5 17.5 - - + -
438B LEU* 3.9 30.5 - - + -
441B LEU* 4.2 5.4 - - + -
450B ILE* 6.0 0.9 - - + -
487B LEU* 2.9 46.8 + - + +
488B ARG 4.1 1.8 - - - +
490B TRP* 1.3 79.3 - - + +
492B GLU* 1.3 61.8 + - - +
494B LEU* 3.8 6.6 - - + +
495B LEU* 3.0 35.5 + - - +
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Residues in contact with GLU 492 (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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427B ARG* 3.3 28.4 + - - -
438B LEU* 4.3 5.3 - - - +
488B ARG* 2.9 46.5 + - + +
489B ALA* 3.0 6.0 + - - +
491B PHE* 1.3 78.1 - - - +
493B ARG* 1.3 61.6 + - - +
495B LEU* 3.3 6.4 + - - +
496B GLU* 3.1 37.1 + - + +
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Residues in contact with ARG 493 (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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321B ASP* 5.3 6.7 + - - -
489B ALA 3.0 15.6 + - - +
490B TRP* 3.9 3.8 - - - +
492B GLU* 1.3 73.6 - - - +
494B LEU* 1.3 66.5 + - - +
496B GLU* 3.2 21.0 + - - +
501B ASN* 3.1 49.3 + - - +
533B ASN 4.5 0.4 + - - -
536B ARG* 3.7 40.0 + - - +
537B TRP* 3.5 41.3 - - + +
540B PHE* 3.6 49.3 - - + +
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Residues in contact with LEU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ILE* 4.7 7.0 - - + +
391B ASN* 3.8 23.3 - - - +
394B PHE* 3.9 41.3 - - + -
464B PHE* 5.2 4.0 - - + -
490B TRP 2.8 19.6 + - - +
491B PHE* 3.8 7.9 - - + +
493B ARG* 1.3 77.6 - - - +
495B LEU* 1.3 60.8 + - - +
497B ASP 3.2 21.7 - - - +
498B ILE* 3.5 14.1 + - + +
501B ASN* 3.0 34.5 - - - +
502B ARG* 3.6 14.4 - - + +
505B LEU* 6.1 1.8 - - + -
537B TRP* 4.1 8.4 - - + -
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Residues in contact with LEU 495 (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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394B PHE* 3.8 19.7 - - + -
426B PHE* 5.0 1.8 - - + -
427B ARG* 3.6 50.9 - - + +
434B PHE* 3.7 41.5 - - + -
438B LEU* 4.0 17.5 - - + -
491B PHE 3.0 20.0 + - - +
492B GLU* 3.8 7.9 - - - +
493B ARG 3.3 0.2 - - - -
494B LEU* 1.3 77.1 - - - +
496B GLU* 1.3 63.1 + - - +
497B ASP 3.4 0.4 - - - -
498B ILE* 4.5 20.5 - - + +
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Residues in contact with GLU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B GLU* 3.1 28.1 + - + +
493B ARG* 3.2 20.0 + - - +
495B LEU* 1.3 78.9 - - - +
497B ASP* 1.3 60.6 + - + +
498B ILE 4.2 0.2 - - - -
501B ASN* 4.6 4.0 + - - +
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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
----------------------------------------------------------
493B ARG 3.6 2.8 + - - -
494B LEU 3.2 4.0 + - - +
496B GLU* 1.3 79.7 - - + +
498B ILE* 1.3 57.7 + - - +
499B PRO* 3.1 20.3 - - - +
500B GLY* 3.2 21.4 + - - -
501B ASN* 2.9 49.4 + - - +
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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