Contacts of the helix formed by residues 524 - 539 (chain Y) in PDB entry 5G04
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 GLU 524 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656F MET* 4.5 7.0 - - + -
496Y ILE* 5.9 0.3 - - - +
519Y LEU* 3.4 24.3 + - + +
522Y VAL* 3.3 23.1 + - + +
523Y ASN* 1.3 72.9 - - - +
525Y TYR* 1.3 62.8 + - - +
526Y GLN* 3.3 4.2 + - + +
527Y GLU* 2.9 45.2 + - + +
528Y ALA* 3.4 18.9 + - - +
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Residues in contact with TYR 525 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653F LEU* 4.4 25.1 - - + -
656F MET* 3.5 13.0 - - + +
520Y VAL* 4.2 23.7 + - + +
523Y ASN* 3.2 55.1 + - - -
524Y GLU* 1.3 71.7 - - - +
526Y GLN* 1.3 57.0 + - - +
527Y GLU 3.4 0.2 - - - -
528Y ALA* 3.5 6.0 - - + +
529Y MET* 2.7 45.4 + - + +
551Y LYS* 3.4 41.6 + - + -
552Y MET* 4.7 11.9 - - + -
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Residues in contact with GLN 526 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625F ARG* 5.4 0.7 + - - -
638F TRP* 3.4 32.1 - - + -
656F MET* 3.3 53.1 - - + +
657F HIS* 4.6 6.4 - - - +
660F LYS* 3.8 26.7 - - + +
524Y GLU* 3.3 1.3 - - + -
525Y TYR* 1.3 76.1 - - - +
527Y GLU* 1.3 74.5 + - + +
529Y MET* 3.6 6.2 + - - +
530Y ASP* 3.3 20.3 + - - +
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Residues in contact with GLU 527 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500Y ARG* 3.2 28.2 + - - +
519Y LEU* 3.6 13.2 - - + +
524Y GLU* 2.9 44.2 + - + +
525Y TYR 3.4 0.2 - - - -
526Y GLN* 1.3 90.7 - - + +
528Y ALA* 1.3 64.3 + - - +
530Y ASP* 3.3 8.0 + - - +
531Y GLN* 3.1 26.2 + - - +
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Residues in contact with ALA 528 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516Y GLY* 4.0 4.9 - - - +
519Y LEU* 3.6 19.2 - - + +
520Y VAL* 3.8 29.8 - - + +
524Y GLU 3.4 12.3 + - - +
525Y TYR* 3.2 14.1 + - + +
527Y GLU* 1.3 75.9 - - - +
529Y MET* 1.3 63.2 + - - +
531Y GLN* 3.4 2.9 + - - +
532Y TYR* 3.1 32.3 + - + -
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Residues in contact with MET 529 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625F ARG* 3.8 21.5 + - - +
645F TYR* 4.1 18.4 - - + +
653F LEU* 4.3 19.5 - - + -
657F HIS* 4.9 9.2 - - + +
525Y TYR* 2.7 32.2 + - + +
526Y GLN* 3.8 6.3 - - - +
528Y ALA* 1.3 72.0 - - + +
530Y ASP* 1.3 62.8 + - - +
532Y TYR* 3.6 7.7 + - - +
533Y SER* 3.2 23.8 + - - -
548Y GLY 4.8 9.2 - - - +
549Y MET* 4.2 29.2 - - - +
552Y MET* 3.7 36.3 - - + -
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Residues in contact with ASP 530 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625F ARG* 4.8 7.4 + - - +
628F ILE* 4.9 12.2 - - - +
638F TRP* 5.1 12.7 - - + -
526Y GLN* 3.3 17.1 + - - +
527Y GLU* 3.3 13.1 + - - +
529Y MET* 1.3 79.1 - - - +
531Y GLN* 1.3 69.8 + - - +
533Y SER* 3.4 7.5 + - - -
534Y ILE* 3.2 36.8 + - - +
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Residues in contact with GLN 531 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F ASP* 5.3 3.3 - - - +
500Y ARG* 4.6 8.2 + - - +
503Y LEU* 3.7 16.9 - - - +
512Y HIS* 3.2 54.7 + - - +
515Y LEU* 4.0 15.2 - - + +
516Y GLY* 3.8 8.7 - - - +
519Y LEU* 3.7 18.4 - - + -
527Y GLU 3.1 17.0 + - - +
528Y ALA 3.4 7.6 + - - +
530Y ASP* 1.3 83.5 - - - +
532Y TYR* 1.3 64.8 + - - +
534Y ILE* 3.4 8.2 + - - +
535Y ALA* 3.2 20.6 + - - +
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Residues in contact with TYR 532 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512Y HIS 5.4 0.7 - - - -
513Y ARG* 4.5 15.0 - - + -
516Y GLY* 3.8 24.7 - - - -
517Y ASP* 2.7 31.7 + - - -
520Y VAL* 4.5 14.0 - - + +
528Y ALA* 3.1 26.4 + - + +
529Y MET* 3.9 8.7 - - - +
531Y GLN* 1.3 78.2 - - - +
533Y SER* 1.3 52.1 + - - +
535Y ALA* 3.3 7.4 + - - +
536Y LEU* 2.8 42.3 + - + +
544Y LYS 3.8 13.5 - - - -
545Y SER* 3.1 29.0 - - - +
547Y GLU* 5.6 1.0 - - - +
548Y GLY* 3.5 35.1 + - - -
549Y MET* 5.3 6.7 - - + +
551Y LYS* 5.5 1.6 - - + +
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Residues in contact with SER 533 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625F ARG* 3.6 34.0 + - - +
629F ARG* 3.7 25.7 + - - +
529Y MET 3.2 14.4 + - - -
530Y ASP* 3.5 14.1 - - - -
532Y TYR* 1.3 76.1 - - - +
534Y ILE* 1.3 58.2 + - - +
536Y LEU* 3.1 14.2 + - - +
537Y SER* 2.9 25.3 + - - -
549Y MET* 5.3 2.0 - - - +
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Residues in contact with ILE 534 (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 5.6 1.1 - - - +
129F ASP* 4.7 23.3 - - + +
629F ARG* 4.8 19.3 - - + -
508Y ASP* 5.5 0.4 - - - +
512Y HIS* 3.5 36.3 - - + +
530Y ASP* 3.2 29.4 + - - +
531Y GLN* 3.8 9.6 - - - +
532Y TYR 3.4 0.2 - - - -
533Y SER* 1.3 73.2 - - - +
535Y ALA* 1.3 64.0 + - - +
537Y SER* 2.7 24.1 + - - +
538Y LEU* 3.1 17.5 + - + +
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Residues in contact with ALA 535 (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 4.4 7.0 - - - +
512Y HIS* 4.0 17.6 - - + +
513Y ARG* 4.1 12.6 - - + +
531Y GLN 3.2 12.5 + - - +
532Y TYR* 3.4 10.5 - - - +
534Y ILE* 1.3 76.4 - - - +
536Y LEU* 1.3 58.7 + - - +
538Y LEU* 3.4 2.2 + - - -
539Y ASP* 2.9 39.6 + - - +
545Y SER* 3.4 20.6 - - - +
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Residues in contact with LEU 536 (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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629F ARG* 4.3 10.4 + - - +
532Y TYR 2.8 25.5 + - - +
533Y SER* 3.1 11.4 + - - +
535Y ALA* 1.3 78.9 - - - +
537Y SER* 1.3 56.6 + - - +
539Y ASP 4.0 6.7 - - - +
540Y PRO* 3.1 34.7 - - + +
541Y ASN* 4.9 9.2 - - - +
542Y ASP 4.7 5.4 - - - +
545Y SER* 3.7 28.0 - - - +
546Y LEU* 4.1 18.2 - - + +
549Y MET* 4.2 25.6 - - + -
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Residues in contact with SER 537 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629F ARG* 3.5 44.7 - - - +
533Y SER 2.9 6.9 + - - -
534Y ILE* 2.7 27.5 + - - +
536Y LEU* 1.3 76.1 - - - +
538Y LEU* 1.3 66.2 + - - +
540Y PRO* 4.0 7.8 - - - +
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Residues in contact with LEU 538 (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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85F LEU* 6.4 1.6 - - + -
508Y ASP* 3.7 36.8 - - + +
509Y CYS* 3.9 11.7 - - + +
512Y HIS* 3.8 14.8 - - + -
534Y ILE* 3.1 22.9 + - + +
535Y ALA* 3.9 1.6 - - - +
537Y SER* 1.3 85.3 + - - +
539Y ASP* 1.3 67.7 + - - +
540Y PRO* 3.7 5.5 - - - +
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Residues in contact with ASP 539 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509Y CYS* 4.1 27.8 - - - +
535Y ALA* 2.9 20.6 + - - +
536Y LEU* 3.4 7.1 - - - +
538Y LEU* 1.3 86.6 - - - +
540Y PRO* 1.3 69.7 - - - +
542Y ASP* 2.8 43.4 + - + +
545Y SER* 3.7 3.5 + - - -
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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
------------------------------------------------------------
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