Contacts of the helix formed by residues 490 - 504 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485B SER* 2.9 17.6 + - - +
488B ALA* 4.4 11.9 - - + +
489B ASN* 1.3 71.7 - - - +
491B HIS* 1.3 66.0 + - - +
492B MET 4.1 1.4 + - - -
493B ARG* 3.1 53.4 + - + +
494B VAL* 3.1 23.6 + - - +
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Residues in contact with HIS 491 (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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489B ASN* 2.9 53.7 + - - -
490B ASP* 1.3 72.7 + - - +
492B MET* 1.3 58.6 + - + +
494B VAL* 3.2 7.3 + - - +
495B ILE* 3.0 38.0 + - + +
533B VAL* 3.1 40.0 - - + +
535B LYS* 4.9 8.1 - - + -
536B GLN* 3.1 16.6 + - - -
539B VAL* 3.4 30.5 - - + +
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Residues in contact with MET 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B ASP* 3.5 2.0 + - - +
491B HIS* 1.3 78.0 - - + +
493B ARG* 1.3 93.3 + - - +
495B ILE* 3.4 8.9 + - - +
496B GLN* 2.9 50.9 + - - +
535B LYS* 4.9 16.2 - - + +
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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
----------------------------------------------------------
469B LEU* 5.6 1.1 - - + -
481B PHE* 3.5 27.0 - - + -
485B SER* 3.8 16.2 - - - +
490B ASP* 3.1 43.5 + - - +
492B MET* 1.3 118.0 - - - +
494B VAL* 1.3 54.0 + - - +
496B GLN* 3.7 20.5 + - - +
497B ALA* 2.6 39.9 + - - +
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Residues in contact with VAL 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LEU* 3.7 9.8 - - + +
485B SER* 3.7 5.6 - - - +
486B VAL* 3.5 39.9 - - + +
489B ASN 5.6 0.2 - - - -
490B ASP 3.1 20.9 + - - +
491B HIS* 3.5 9.9 - - - +
493B ARG* 1.3 75.1 - - - +
495B ILE* 1.3 57.3 + - - +
498B SER* 2.7 38.4 + - - +
539B VAL* 4.4 21.1 - - + -
542B TRP* 5.4 0.9 - - + -
543B MET* 3.6 30.5 - - + -
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Residues in contact with ILE 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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491B HIS 3.0 25.9 + - - +
492B MET* 3.7 6.5 - - - +
494B VAL* 1.3 75.2 - - - +
496B GLN* 1.3 64.6 + - + +
498B SER* 3.7 1.7 - - - -
499B GLU* 3.2 24.8 + - + +
535B LYS* 4.0 26.5 - - + +
538B LEU* 3.7 34.1 - - + +
539B VAL* 3.9 29.2 - - + +
542B TRP* 3.7 24.5 + - - +
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Residues in contact with GLN 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B LEU* 3.6 20.5 - - + +
470B GLU* 4.6 9.5 - - - +
492B MET* 2.9 49.0 + - - +
493B ARG* 3.7 21.9 + - - +
495B ILE* 1.3 78.9 - - + +
497B ALA* 1.3 58.6 + - - +
499B GLU* 3.5 11.4 + - - +
500B LYS* 3.0 26.7 + - - +
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Residues in contact with ALA 497 (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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469B LEU* 3.6 13.7 - - + +
478B VAL* 3.6 8.8 - - + +
481B PHE* 3.8 25.8 - - + -
482B LEU* 4.0 22.7 - - + +
493B ARG 2.6 22.6 + - - +
494B VAL 4.1 1.3 - - - +
496B GLN* 1.3 70.5 - - - +
498B SER* 1.3 60.5 + - - +
500B LYS* 3.3 3.2 + - - -
501B LEU* 2.9 29.7 + - - +
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Residues in contact with SER 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LEU* 3.4 15.5 - - - +
494B VAL 2.7 24.9 + - - -
495B ILE 3.7 0.4 - - - -
497B ALA* 1.3 76.3 - - - +
499B GLU* 1.3 61.6 + - - +
501B LEU* 3.1 8.0 + - - +
502B PHE* 3.1 20.3 + - - +
542B TRP* 3.6 35.2 - - - +
543B MET* 3.7 9.7 - - - +
546B LEU* 3.6 23.7 - - - +
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Residues in contact with GLU 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ILE* 3.2 13.7 + - + +
496B GLN* 3.7 10.4 - - - +
498B SER* 1.3 74.4 - - - +
500B LYS* 1.3 68.2 + - - +
502B PHE* 3.2 6.8 + - + +
503B LYS* 3.0 49.8 + - + +
542B TRP* 3.5 33.5 - - + -
569B ILE* 5.7 1.4 - - - +
570B TYR* 4.0 25.2 + - + +
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Residues in contact with LYS 500 (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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469B LEU* 2.9 29.4 + - + +
470B GLU* 3.4 20.2 + - - +
472B LEU 2.8 30.8 + - - +
473B GLN* 4.1 16.2 + - - -
478B VAL* 4.0 13.9 - - + -
496B GLN 3.0 18.4 + - - +
497B ALA* 3.3 6.3 + - - +
499B GLU* 1.3 76.6 - - - +
501B LEU* 1.3 61.6 + - - +
503B LYS* 3.3 11.4 + - + +
504B LEU* 2.9 45.5 + - + +
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Residues in contact with LEU 501 (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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475B TYR* 3.6 25.6 - - + +
478B VAL* 3.9 8.6 - - + +
479B GLY* 3.7 19.7 - - - +
482B LEU* 3.7 28.9 - - + -
497B ALA 2.9 11.5 + - - +
498B SER 3.1 9.8 + - - +
500B LYS* 1.3 74.9 - - - +
502B PHE* 1.3 60.6 + - - +
504B LEU* 3.7 4.8 + - - -
506B THR* 2.6 54.4 + - + +
510B TYR* 4.8 1.1 - - + -
511B LEU* 3.8 25.4 - - + -
514B ILE* 5.0 4.3 - - + -
546B LEU* 4.4 8.5 - - + -
620B ARG* 5.3 0.2 + - - -
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Residues in contact with PHE 502 (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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498B SER 3.1 11.9 + - - +
499B GLU* 3.2 12.3 + - + +
501B LEU* 1.3 73.9 - - - +
503B LYS* 1.3 84.0 + - + +
505B LYS 3.2 5.4 + - - -
542B TRP* 4.1 14.4 - + + -
545B PHE* 3.6 28.7 - + + -
546B LEU* 5.0 3.5 - - + +
562B LEU* 3.3 29.2 - - + -
570B TYR* 3.9 26.2 - + - -
620B ARG* 2.9 56.9 + - - +
636B TYR* 3.7 31.2 - + + -
637B PHE 4.3 7.4 - - - -
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Residues in contact with LYS 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B GLU* 3.0 41.5 + - + +
500B LYS* 3.8 10.3 - - + +
502B PHE* 1.3 90.8 - - + +
504B LEU* 1.3 64.7 + - + +
505B LYS* 3.3 11.6 + - - +
568B LYS 5.4 3.8 + - - -
570B TYR* 3.8 30.4 - - + -
620B ARG* 4.4 4.3 + - - +
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Residues in contact with LEU 504 (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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473B GLN* 3.3 51.4 - - - +
475B TYR* 3.9 20.4 - - + +
478B VAL* 3.8 26.7 - - + -
500B LYS* 2.9 31.4 + - + +
501B LEU* 4.1 5.4 - - - +
502B PHE 3.2 0.6 - - - -
503B LYS* 1.3 77.1 - - + +
505B LYS* 1.3 71.6 + - - +
506B THR* 3.2 6.9 + - - +
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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
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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