Contacts of the helix formed by residues 490 - 504 (chain A) in PDB entry 5ULM
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 490 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485A SER* 2.9 17.8 + - - +
488A ALA* 3.2 11.6 - - + +
489A ASN* 1.3 71.3 - - - +
491A HIS* 1.3 66.3 + - - +
492A MET 4.1 1.4 + - - -
493A ARG* 3.1 52.5 + - + +
494A VAL* 3.1 23.9 + - - +
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Residues in contact with HIS 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A ASN* 2.9 53.0 + - - -
490A ASP* 1.3 72.2 + - - +
492A MET* 1.3 60.8 + - + +
494A VAL* 3.2 6.5 + - - +
495A ILE* 3.0 37.0 + - + +
533A VAL* 3.7 35.1 - - + +
535A LYS* 4.8 8.3 - - + -
536A GLN* 3.1 29.3 + - - -
539A VAL* 3.5 31.0 - - + +
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Residues in contact with MET 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A ASP* 3.5 1.6 + - - +
491A HIS* 1.3 76.2 - - + +
493A ARG* 1.3 84.7 + - - +
495A ILE* 3.4 14.9 + - + +
496A GLN* 2.9 48.2 + - + +
535A LYS* 3.8 43.3 - - + +
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Residues in contact with ARG 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A LEU* 5.6 1.6 - - + -
481A PHE* 3.5 27.4 - - + -
485A SER* 3.8 15.7 - - - +
490A ASP* 3.1 45.0 + - - +
492A MET* 1.3 99.5 - - - +
494A VAL* 1.3 55.3 + - - +
496A GLN* 3.7 25.0 + - - +
497A ALA* 2.6 39.9 + - - +
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Residues in contact with VAL 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 3.7 9.7 - - + +
485A SER* 3.7 6.7 - - - +
486A VAL* 3.5 39.5 - - + +
489A ASN* 6.0 0.2 - - - -
490A ASP 3.1 21.3 + - - +
491A HIS* 3.2 11.0 + - - +
493A ARG* 1.3 74.3 - - - +
495A ILE* 1.3 57.6 + - - +
498A SER* 2.7 38.9 + - - +
539A VAL* 4.4 20.6 - - + -
542A TRP* 5.4 0.7 - - + -
543A MET* 3.6 30.7 - - + -
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Residues in contact with ILE 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A HIS 3.0 25.3 + - - +
492A MET* 3.7 13.7 - - + +
494A VAL* 1.3 76.4 - - - +
496A GLN* 1.3 63.8 + - + +
498A SER* 3.7 1.7 - - - -
499A GLU* 3.2 25.4 + - + +
535A LYS* 4.0 25.8 - - + +
538A LEU* 3.8 33.4 - - + +
539A VAL* 3.9 30.1 - - + +
542A TRP* 3.7 25.6 + - + +
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Residues in contact with GLN 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A LEU* 3.6 21.6 - - + +
470A GLU* 4.7 9.7 - - - +
492A MET* 2.9 38.8 + - + +
493A ARG* 3.7 32.0 + - - +
495A ILE* 1.3 78.4 - - + +
497A ALA* 1.3 57.2 + - - +
499A GLU* 3.5 12.0 + - - +
500A LYS* 3.0 27.4 + - - +
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Residues in contact with ALA 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A LEU* 3.6 12.7 - - + +
478A VAL* 3.6 8.7 - - + +
481A PHE* 3.8 25.4 - - + -
482A LEU* 4.0 24.2 - - + +
493A ARG 2.6 22.0 + - - +
494A VAL 4.1 0.9 - - - +
496A GLN* 1.3 71.1 - - - +
498A SER* 1.3 67.3 + - - +
500A LYS* 3.3 3.0 + - - -
501A LEU* 2.9 23.4 + - - +
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Residues in contact with SER 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A LEU* 3.4 15.5 - - - +
494A VAL 2.7 22.4 + - - -
495A ILE 3.7 0.2 - - - -
497A ALA* 1.3 77.2 - - - +
499A GLU* 1.3 61.7 + - - +
501A LEU* 3.1 7.7 + - - +
502A PHE* 3.1 21.0 + - - +
542A TRP* 3.6 35.8 - - - +
543A MET* 3.7 10.2 - - - +
546A LEU* 3.6 24.0 - - - +
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Residues in contact with GLU 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A ILE* 3.2 13.5 + - + +
496A GLN* 3.7 11.0 - - - +
498A SER* 1.3 74.9 - - - +
500A LYS* 1.3 67.6 + - - +
502A PHE* 3.2 6.8 + - + +
503A LYS* 2.9 50.1 + - + +
542A TRP* 3.6 33.3 - - + +
569A ILE* 5.6 1.2 - - - +
570A TYR* 4.0 26.6 + - + +
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Residues in contact with LYS 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A LEU* 2.9 30.8 + - + +
470A GLU* 3.4 19.6 + - - +
472A LEU 2.8 29.5 + - - +
473A GLN* 4.1 16.0 + - - -
478A VAL* 4.0 14.6 - - + -
496A GLN 3.0 17.6 + - - +
497A ALA* 3.7 6.3 - - - +
499A GLU* 1.3 77.6 - - - +
501A LEU* 1.3 56.1 + - - +
503A LYS* 3.3 11.6 + - + +
504A LEU* 3.0 50.1 + - + +
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Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A TYR* 3.6 25.6 - - + +
478A VAL* 3.9 8.2 - - + +
479A GLY* 3.8 19.3 - - - +
482A LEU* 3.7 28.9 - - + -
497A ALA 2.9 11.0 + - - +
498A SER* 3.1 9.6 + - - +
500A LYS* 1.3 76.0 - - - +
502A PHE* 1.3 62.1 + - - +
504A LEU* 3.7 1.3 + - - -
505A LYS* 3.7 5.4 + - - -
506A THR* 2.6 50.8 + - + +
510A TYR* 4.7 0.9 - - + -
511A LEU* 3.8 25.8 - - + -
514A ILE* 5.0 4.7 - - + -
546A LEU* 4.4 7.9 - - + -
620A ARG* 5.3 0.2 + - - -
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Residues in contact with PHE 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A SER 3.1 12.3 + - - +
499A GLU* 3.4 11.7 - - + +
501A LEU* 1.3 73.0 - - - +
503A LYS* 1.3 82.0 + - + +
505A LYS 3.2 5.7 + - - -
542A TRP* 4.1 13.5 - + + -
545A PHE* 3.6 29.4 - + + -
546A LEU* 5.0 3.0 - - + +
562A LEU* 3.3 29.4 - - + -
570A TYR* 3.8 28.0 - + - -
620A ARG* 2.9 57.5 + - - +
636A TYR* 3.7 30.5 - + + -
637A PHE 4.2 6.5 - - - -
638A CYS* 5.7 0.2 - - - -
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Residues in contact with LYS 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A GLU* 2.9 43.9 + - + +
500A LYS* 3.8 10.3 - - + +
502A PHE* 1.3 88.8 - - + +
504A LEU* 1.3 64.3 + - + +
505A LYS* 3.3 11.4 + - - +
568A LYS 5.4 4.2 + - - -
570A TYR* 3.8 31.4 - - + -
620A ARG* 4.4 4.4 + - - +
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Residues in contact with LEU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A GLN* 3.3 50.7 - - - +
475A TYR* 3.9 20.2 - - + +
478A VAL* 3.8 27.4 - - + -
500A LYS* 3.0 30.7 + - + +
501A LEU* 4.1 6.3 - - - +
502A PHE 3.2 0.6 - - - -
503A LYS* 1.3 77.7 - - + +
505A LYS* 1.3 70.4 + - - +
506A THR* 3.2 6.5 + - - +
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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