Contacts of the helix formed by residues 509 - 523 (chain Y) 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 CYS 509 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476Y ILE* 6.0 4.9 - - + -
507Y SER 4.3 5.6 - - - +
508Y ASP* 1.3 79.6 - - - +
510Y VAL* 1.3 81.1 - - + +
511Y LEU 3.5 0.3 + - - -
512Y HIS* 3.5 15.8 + - - +
513Y ARG* 3.8 3.5 + - - +
535Y ALA* 4.4 6.4 - - - +
538Y LEU* 3.9 11.6 - - - +
539Y ASP* 4.1 26.5 - - - +
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Residues in contact with VAL 510 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476Y ILE* 4.1 16.4 - - + -
480Y VAL* 3.8 25.6 - - + -
509Y CYS* 1.3 88.4 - - + +
511Y LEU* 1.3 62.5 + - - +
513Y ARG* 3.1 22.9 + - - +
514Y ILE* 2.9 31.5 + - + +
542Y ASP* 6.0 0.4 - - - -
544Y LYS* 3.9 24.9 - - - +
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Residues in contact with LEU 511 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474Y ASP 5.8 0.4 - - - +
476Y ILE* 4.3 15.9 - - + +
479Y VAL* 4.4 8.3 - - + -
480Y VAL* 3.5 30.1 - - + -
499Y LEU* 4.1 23.6 - - + +
502Y ALA* 3.4 30.1 - - + -
503Y LEU* 3.6 19.3 - - + +
507Y SER* 3.3 23.8 - - - +
508Y ASP 3.0 14.2 + - - +
510Y VAL* 1.3 81.5 - - - +
512Y HIS* 1.3 55.9 + - - +
514Y ILE* 3.2 5.4 + - + +
515Y LEU* 2.9 29.5 + - - +
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Residues in contact with HIS 512 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F THR 5.1 0.2 + - - -
129F ASP* 3.6 26.0 - - - +
503Y LEU* 3.8 18.3 - - + +
506Y GLN* 4.2 3.7 + - - +
508Y ASP* 3.0 51.6 + - + -
509Y CYS 3.5 7.4 + - - +
510Y VAL 3.3 0.8 - - - -
511Y LEU* 1.3 75.9 - - - +
513Y ARG* 1.3 62.6 + - - +
515Y LEU* 3.3 1.6 + - - -
516Y GLY* 3.0 19.4 + - - -
531Y GLN* 3.4 43.9 + - - +
534Y ILE* 3.3 31.7 - - + +
535Y ALA 4.4 4.7 - - - +
538Y LEU* 3.9 4.7 - - + -
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Residues in contact with ARG 513 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509Y CYS 3.8 1.8 + - - +
510Y VAL* 3.1 22.8 + - - +
512Y HIS* 1.3 78.7 - - - +
514Y ILE* 1.3 83.7 + - - +
516Y GLY* 3.3 3.7 + - - -
517Y ASP* 3.1 43.7 + - - +
531Y GLN 5.3 0.4 - - - -
532Y TYR* 4.6 10.1 - - + +
535Y ALA* 4.2 12.4 - - + +
542Y ASP* 5.2 0.7 - - - +
544Y LYS* 3.3 58.0 + - + +
545Y SER* 4.0 29.6 - - - +
547Y GLU* 5.0 4.9 + - - -
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Residues in contact with ILE 514 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480Y VAL* 4.4 24.2 - - + +
483Y ALA* 4.1 22.0 - - + -
499Y LEU* 3.5 18.6 - - + -
510Y VAL* 2.9 25.8 + - + +
511Y LEU* 3.7 7.9 - - - +
513Y ARG* 1.3 105.1 - - - +
515Y LEU* 1.3 62.0 + - - +
517Y ASP* 3.2 12.0 + - - +
518Y PHE* 3.1 33.2 + - + -
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Residues in contact with LEU 515 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496Y ILE* 4.2 10.1 - - + +
499Y LEU* 3.3 28.0 - - + +
500Y ARG* 3.5 37.0 - - + +
503Y LEU* 3.3 32.3 - - + -
511Y LEU 2.9 15.0 + - - +
512Y HIS 3.8 3.6 - - - +
514Y ILE* 1.3 75.8 - - - +
516Y GLY* 1.3 62.3 + - - +
518Y PHE* 3.2 3.6 + - - -
519Y LEU* 3.0 53.2 + - + +
531Y GLN* 4.1 11.7 - - + +
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Residues in contact with GLY 516 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512Y HIS 3.0 11.9 + - - -
513Y ARG 3.3 4.9 + - - -
515Y LEU* 1.3 75.9 - - - +
517Y ASP* 1.3 60.2 + - - +
519Y LEU* 3.4 1.4 + - - -
520Y VAL* 3.3 26.3 + - - +
528Y ALA* 3.7 8.2 - - - +
531Y GLN* 3.6 22.5 - - - +
532Y TYR* 3.5 19.7 - - - -
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Residues in contact with ASP 517 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513Y ARG* 3.1 47.5 + - - +
514Y ILE* 3.2 15.7 + - + +
516Y GLY* 1.3 73.5 - - - +
518Y PHE* 1.3 71.6 + - + +
520Y VAL* 3.1 26.5 - - - +
521Y ALA* 3.5 4.2 + - - +
532Y TYR* 2.6 26.6 + - - -
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Residues in contact with PHE 518 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483Y ALA* 3.4 30.7 - - + -
486Y LEU* 4.0 9.2 - - + -
487Y SER* 3.8 26.2 - - - -
492Y TYR* 3.4 36.1 - + - +
495Y GLY* 3.5 31.2 - - - -
496Y ILE* 3.6 19.3 - - + +
499Y LEU* 4.9 4.7 - - + -
514Y ILE* 3.1 27.6 + - + +
515Y LEU* 3.2 6.9 + - - +
517Y ASP* 1.3 83.2 - - + +
519Y LEU* 1.3 61.0 + - - +
521Y ALA* 2.9 24.6 + - - +
522Y VAL* 3.0 14.0 + - - +
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Residues in contact with LEU 519 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496Y ILE* 3.4 25.4 - - + -
500Y ARG* 3.9 11.4 - - - +
515Y LEU* 3.0 30.7 + - + +
516Y GLY 3.8 4.3 - - - +
517Y ASP 3.4 0.4 - - - -
518Y PHE* 1.3 75.3 - - - +
520Y VAL* 1.3 58.6 + - - +
522Y VAL* 3.0 6.1 + - + +
523Y ASN 2.9 21.7 + - - -
524Y GLU* 3.3 35.5 + - + +
527Y GLU* 3.3 43.1 - - + +
528Y ALA* 3.4 10.1 - - - +
531Y GLN* 3.6 19.3 - - + -
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Residues in contact with VAL 520 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516Y GLY 3.3 16.0 + - - +
517Y ASP* 3.1 18.8 - - - +
518Y PHE 3.2 0.8 - - - -
519Y LEU* 1.3 76.0 - - - +
521Y ALA* 1.3 58.4 + - + +
523Y ASN* 2.9 22.1 + - - +
525Y TYR* 4.0 25.5 + - + +
528Y ALA* 3.6 15.7 - - + -
532Y TYR* 4.7 10.3 - - + +
551Y LYS* 4.7 20.9 - - + -
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Residues in contact with ALA 521 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492Y TYR* 3.4 49.9 - - + -
493Y GLU* 4.5 6.5 - - - +
517Y ASP 3.5 3.3 + - - +
518Y PHE 2.9 13.3 + - - +
520Y VAL* 1.3 81.4 - - + +
522Y VAL* 1.3 62.1 + - - +
523Y ASN* 3.4 2.9 + - - +
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Residues in contact with VAL 522 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492Y TYR* 5.5 0.9 - - + +
493Y GLU* 3.3 28.0 - - - +
496Y ILE* 3.1 36.8 - - + -
518Y PHE 3.0 4.0 + - - +
519Y LEU* 3.0 10.7 + - + +
521Y ALA* 1.3 73.8 - - - +
523Y ASN* 1.3 67.7 + - - +
524Y GLU* 3.6 23.7 + - + +
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Residues in contact with ASN 523 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656F MET* 5.2 3.1 - - - +
519Y LEU 2.9 4.2 + - - -
520Y VAL 2.9 14.5 + - - +
521Y ALA 4.5 2.2 + - - +
522Y VAL* 1.3 81.5 - - - +
524Y GLU* 1.3 58.6 + - - +
525Y TYR* 3.1 34.7 + - - -
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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