Contacts of the helix formed by residues 468 - 480 (chain P) in PDB entry 5A31
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 MET 468 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437P VAL* 5.7 5.2 - - + -
464P ASP* 4.9 0.4 - - - -
466P GLU* 4.2 24.1 - - + +
467P LYS* 1.3 78.8 - - - +
469P ALA* 1.3 64.8 + - - +
470P LEU 3.3 1.3 + - - -
471P VAL* 3.5 24.4 + - + +
472P LYS* 3.3 27.1 + - + +
493P TYR* 4.9 9.0 - - + +
511P THR* 6.0 4.3 - - + +
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Residues in contact with ALA 469 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437P VAL* 4.1 13.6 - - + +
456P TYR* 4.1 15.6 - - + +
459P ALA* 3.9 16.8 - - + -
460P TYR* 4.4 0.7 - - + +
464P ASP* 2.7 36.2 + - - +
467P LYS 3.4 1.6 - - - -
468P MET* 1.3 75.2 - - - +
470P LEU* 1.3 65.9 + - - +
472P LYS* 3.3 7.2 + - - +
473P LEU* 2.9 24.7 + - - +
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Residues in contact with LEU 470 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457P TRP* 4.3 6.3 - - + -
460P TYR* 3.2 59.2 - - + +
464P ASP* 4.1 1.5 + - - +
467P LYS 4.2 3.7 + - - +
468P MET 3.3 0.6 - - - -
469P ALA* 1.3 79.2 - - - +
471P VAL* 1.3 51.1 + - - +
473P LEU* 3.2 22.1 + - + +
474P ALA* 2.7 35.9 + - - +
489P CYS* 4.6 12.4 - - + +
492P LYS* 4.1 11.9 - - + +
493P TYR* 3.9 43.5 - - + +
496P ASP* 5.1 4.9 - - + -
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Residues in contact with VAL 471 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467P LYS 4.6 0.7 - - - +
468P MET* 3.5 24.0 + - + +
470P LEU* 1.3 77.6 - - - +
472P LYS* 1.3 58.0 + - - +
474P ALA* 3.3 7.6 + - - +
475P LYS* 2.9 28.7 + - + +
490P TYR* 4.9 1.7 - - + -
493P TYR* 3.2 51.8 - - + +
515P TYR* 3.5 42.8 - - + +
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Residues in contact with LYS 472 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437P VAL* 4.6 8.1 - - + -
441P GLU* 3.2 43.4 - - - +
444P GLU* 3.0 16.8 + - - +
456P TYR* 2.8 46.4 + - + +
468P MET* 3.3 14.9 + - + +
469P ALA 3.5 7.6 - - - +
471P VAL* 1.3 80.2 - - - +
473P LEU* 1.3 61.9 + - - +
475P LYS* 3.2 8.9 + - + +
476P LEU* 3.1 29.8 + - - +
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Residues in contact with LEU 473 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453P LYS* 4.2 31.4 - - + +
456P TYR* 4.0 18.3 - - + +
457P TRP* 3.4 45.1 - - + +
469P ALA 2.9 12.9 + - - +
470P LEU* 3.3 17.7 - - + +
472P LYS* 1.3 73.0 - - - +
474P ALA* 1.3 65.1 + - - +
476P LEU* 3.2 6.4 + - + +
477P HIS* 3.1 54.3 + - + +
489P CYS* 4.0 12.6 - - - -
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Residues in contact with ALA 474 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470P LEU 2.7 16.8 + - - +
471P VAL* 3.3 10.3 - - - +
473P LEU* 1.3 72.8 - - - +
475P LYS* 1.3 62.6 + - - +
477P HIS* 3.0 8.3 + - - +
478P GLU* 2.9 20.1 + - - +
486P ALA* 4.3 0.6 - - - +
489P CYS* 3.9 21.5 - - + +
490P TYR* 3.3 45.2 + - + +
493P TYR* 6.1 0.2 - - + -
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Residues in contact with LYS 475 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444P GLU* 5.1 8.5 - - - +
471P VAL* 2.9 15.6 + - + +
472P LYS* 3.5 12.3 - - + +
474P ALA* 1.3 76.2 - - - +
476P LEU* 1.3 55.1 + - + +
478P GLU* 3.2 20.2 + - - +
479P GLN* 2.3 74.5 + - - +
490P TYR* 3.9 8.7 + - - +
515P TYR* 6.0 5.6 - - + +
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Residues in contact with LEU 476 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444P GLU* 3.6 28.5 - - + +
449P LEU* 3.9 31.6 - - + +
452P ALA* 3.5 28.3 - - + -
453P LYS* 4.4 14.8 - - + +
456P TYR* 3.4 25.1 - - + -
472P LYS 3.1 27.6 + - - +
473P LEU* 3.6 8.1 - - + +
474P ALA 3.2 0.4 - - - -
475P LYS* 1.3 73.2 - - + +
477P HIS* 1.3 62.5 + - - +
479P GLN* 3.2 9.1 + - + +
480P LEU* 2.9 38.4 + - + +
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Residues in contact with HIS 477 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453P LYS* 3.8 29.8 + - + +
473P LEU* 3.1 30.9 + - + -
474P ALA 3.0 9.0 + - - +
476P LEU* 1.3 80.3 - - - +
478P GLU* 1.3 50.8 + - - +
480P LEU* 2.5 35.3 + - + +
482P GLU* 3.3 30.7 + - - +
485P GLN* 3.7 20.2 + - + +
486P ALA* 3.6 21.5 - - + +
489P CYS* 3.2 33.4 - - - -
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Residues in contact with GLU 478 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474P ALA 2.9 5.9 + - - -
475P LYS* 3.5 24.5 + - - +
477P HIS* 1.3 75.4 - - - +
479P GLN* 1.3 67.1 + - - +
480P LEU 3.1 7.4 - - - +
481P THR* 5.2 0.2 - - - -
486P ALA* 4.2 0.9 - - + -
490P TYR* 2.4 47.5 + - + +
518P GLN* 2.5 30.3 + - - +
522P LYS* 3.7 30.9 + - - +
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Residues in contact with GLN 479 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444P GLU* 5.5 6.0 + - - +
449P LEU* 5.9 4.9 - - + -
475P LYS* 2.3 83.1 + - - +
476P LEU* 3.2 14.1 + - + +
478P GLU* 1.3 79.5 - - - +
480P LEU* 1.3 63.9 + - + +
481P THR* 3.8 5.0 + - - +
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Residues in contact with LEU 480 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449P LEU* 4.1 31.0 - - + -
453P LYS* 3.5 36.8 - - - +
476P LEU* 2.9 33.6 + - + +
477P HIS* 2.5 27.7 + - - +
478P GLU* 3.1 10.2 - - - +
479P GLN* 1.3 78.9 - - + +
481P THR* 1.3 60.2 + - - +
482P GLU* 2.9 16.5 + - + +
522P LYS* 5.5 0.7 + - - -
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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