Contacts of the helix formed by residues 480 - 497 (chain B) in PDB entry 5QSY
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 HIS 480 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B PHE* 3.9 4.7 - - + -
477B LEU* 3.3 51.2 + - + +
478B HIS 3.2 2.8 - - - -
479B GLU* 1.3 89.5 - - + +
481B ALA* 1.3 52.6 + - - +
482B ALA 3.2 2.7 - - - -
483B TYR* 2.8 54.4 + + + +
484B LEU* 2.8 19.5 + - + +
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Residues in contact with ALA 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B PHE* 3.5 24.7 - - + -
479B GLU 3.5 4.2 + - - -
480B HIS* 1.3 74.3 - - - +
482B ALA* 1.3 61.9 + - - +
484B LEU* 3.6 2.9 + - - +
485B VAL* 3.2 27.9 + - - +
527B GLU* 3.0 37.0 - - + +
528B LEU* 4.1 7.9 - - + +
531B CYS* 3.7 15.5 - - - -
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Residues in contact with ALA 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B GLU 4.9 1.2 + - - +
480B HIS 3.2 0.4 - - - -
481B ALA* 1.3 77.0 - - - +
483B TYR* 1.3 68.2 + - + +
485B VAL* 3.4 3.5 + - - +
486B ASP* 2.9 28.9 + - - +
531B CYS* 3.7 21.9 - - + -
534B ARG* 5.8 2.2 - - - +
535B GLN* 4.4 1.6 - - - +
542B PRO* 4.0 27.0 - - + +
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Residues in contact with TYR 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B GLU 4.9 4.3 - - - -
480B HIS* 2.8 43.7 + + + +
482B ALA* 1.3 83.3 - - + +
484B LEU* 1.3 57.6 + - - +
486B ASP* 3.1 1.7 + - - -
487B SER* 2.7 34.1 + - - -
542B PRO* 5.1 5.8 - - + -
543B VAL 3.8 21.3 + - - -
544B GLY* 4.1 11.7 + - - -
545B ARG* 3.2 46.0 + - + +
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Residues in contact with LEU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B LEU* 4.2 10.3 - - + -
471B PHE* 3.8 29.4 - - + -
472B PHE* 3.5 45.1 - - + -
480B HIS* 2.8 16.4 + - + +
481B ALA 3.7 9.0 - - - +
483B TYR* 1.3 72.3 - - - +
485B VAL* 1.3 65.0 + - + +
487B SER* 3.2 7.9 + - - +
488B LEU* 3.0 46.8 + - + +
528B LEU* 4.3 7.2 - - + -
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Residues in contact with VAL 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B LEU* 6.2 0.7 - - + -
481B ALA 3.2 17.7 + - - +
482B ALA* 3.7 4.3 - - - +
484B LEU* 1.3 80.8 - - + +
486B ASP* 1.3 57.7 + - - +
488B LEU* 3.4 7.1 + - - +
489B TRP* 3.0 54.2 + - + +
496B LEU* 3.9 11.6 - - + +
528B LEU* 4.1 18.4 - - + +
531B CYS* 4.0 26.0 - - + +
532B THR* 4.1 20.4 - - + -
535B GLN* 4.0 8.5 - - - +
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Residues in contact with ASP 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ALA 2.9 11.4 + - - +
483B TYR 3.1 0.6 + - - +
485B VAL* 1.3 78.4 - - - +
487B SER* 1.3 60.4 + - - +
489B TRP* 3.1 14.7 + - - +
490B GLU 4.5 1.7 + - - -
535B GLN* 2.6 37.3 + - - +
541B PRO* 3.4 24.7 - - - +
542B PRO* 3.6 19.3 - - + -
545B ARG* 2.7 30.7 + - - +
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Residues in contact with SER 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B TYR 2.7 20.6 + - - -
484B LEU* 3.2 13.9 + - - +
486B ASP* 1.3 76.4 - - - +
488B LEU* 1.3 62.7 + - - +
489B TRP 3.4 0.2 - - - -
490B GLU* 4.9 3.3 + - - +
491B SER* 5.2 1.9 + - - -
545B ARG* 3.9 12.7 + - - +
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Residues in contact with LEU 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B LEU* 3.8 22.2 - - + -
471B PHE* 5.7 2.5 - - + -
484B LEU* 3.0 44.5 + - + +
485B VAL* 3.8 0.7 - - - +
487B SER* 1.3 79.7 - - - +
489B TRP* 1.3 59.2 + - - +
490B GLU 3.4 1.6 - - - -
491B SER* 3.3 17.0 + - - +
492B SER* 2.9 36.3 + - - +
496B LEU* 3.7 23.1 - - + -
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Residues in contact with TRP 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B VAL* 3.0 35.6 + - + +
486B ASP* 3.1 12.1 + - - +
488B LEU* 1.3 77.1 - - - +
490B GLU* 1.3 65.3 + - - +
493B GLN* 2.8 56.6 + - + +
496B LEU* 3.9 25.1 - - + -
497B LYS* 4.1 17.7 - - + -
532B THR* 3.7 11.9 - - - -
535B GLN* 3.5 39.6 + - + +
536B ALA* 3.6 37.2 - - + -
539B ALA* 6.3 0.2 - - - +
563B ASP* 5.3 0.9 - - - -
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Residues in contact with GLU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B ASP 4.5 2.4 + - - -
487B SER 4.9 2.8 + - - +
488B LEU 3.4 1.0 - - - -
489B TRP* 1.3 80.8 - - - +
491B SER* 1.3 65.2 - - - +
493B GLN* 4.8 9.2 + - - +
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Residues in contact with SER 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B SER 5.2 0.7 + - - -
488B LEU* 3.3 17.7 + - - +
490B GLU* 1.3 80.9 - - - +
492B SER* 1.3 80.4 + - - +
493B GLN 3.8 0.7 - - - -
494B GLU* 3.3 13.2 - - - +
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Residues in contact with SER 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B LEU* 2.9 22.7 + - - +
491B SER* 1.3 97.8 + - - +
493B GLN* 1.3 59.3 + - - +
494B GLU* 3.3 15.4 + - - -
495B LEU* 3.2 15.5 + - - +
496B LEU* 2.9 39.7 + - - +
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Residues in contact with GLN 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B TRP* 2.8 60.6 + - + +
490B GLU* 5.0 8.2 + - - +
491B SER 3.8 0.8 - - - -
492B SER* 1.3 77.3 - - - +
494B GLU* 1.3 66.1 + - - +
496B LEU* 4.2 7.0 - - - -
497B LYS* 3.0 54.5 + - - +
559B THR* 6.1 0.6 - - - -
563B ASP* 5.0 1.0 - - - +
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Residues in contact with GLU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ASN* 5.2 3.4 + - - +
491B SER 3.3 20.1 - - - +
492B SER* 3.4 13.2 + - - -
493B GLN* 1.3 81.8 + - - +
495B LEU* 1.3 78.1 + - + +
497B LYS* 3.8 5.5 + - - +
498B ASP* 3.7 15.1 + - - +
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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
----------------------------------------------------------
461B ASN* 3.8 34.1 - - + +
464B LEU* 4.0 28.9 - - + +
465B ILE* 3.3 32.4 - - + +
468B LEU* 5.2 6.1 - - + -
492B SER* 3.2 14.9 + - - +
494B GLU* 1.3 93.2 - - + +
496B LEU* 1.3 72.8 + - + +
497B LYS 3.2 0.9 - - - -
498B ASP* 3.2 17.5 + - + +
502B MET* 3.8 6.8 - - - +
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ILE* 5.4 0.9 - - + -
468B LEU* 3.6 31.4 - - + -
485B VAL* 3.9 14.8 - - + +
488B LEU* 3.7 39.3 - - + +
489B TRP* 3.9 33.7 - - + +
492B SER* 2.9 24.5 + - - +
493B GLN* 4.1 2.2 - - - +
495B LEU* 1.3 83.9 - - + +
497B LYS* 1.3 56.8 + - - +
498B ASP 3.5 0.2 - - - -
499B TRP* 3.7 0.3 + - - -
502B MET* 3.0 21.6 - - + +
532B THR* 3.3 28.9 - - + +
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Residues in contact with LYS 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B TRP* 4.1 12.8 - - + -
493B GLN* 3.0 55.7 + - - +
494B GLU* 4.1 6.3 - - - +
495B LEU 3.2 0.4 - - - -
496B LEU* 1.3 77.5 - - - +
498B ASP* 1.3 48.6 + - - -
499B TRP* 2.7 58.6 + - + -
536B ALA* 4.6 2.5 - - + -
559B THR* 5.0 10.3 - - - +
563B ASP* 3.0 43.8 + - - +
566B LYS* 3.8 8.9 + - + -
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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