Contacts of the helix formed by residues 492 - 503 (chain A) in PDB entry 5EMQ
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 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A LEU 4.9 0.2 - - - -
476A CYS* 3.8 19.7 - - - -
477A ALA 4.7 0.9 - - - -
482A CYS* 3.9 13.2 - - + -
484A ILE* 4.1 5.2 - - + +
488A ARG 3.9 3.8 + - - +
489A ARG 4.0 4.2 + - - -
490A LYS 3.5 0.6 - - - -
491A ASN* 1.3 83.2 - - + +
493A PRO* 1.3 62.3 - - - +
494A ALA 3.2 4.3 - - - -
495A CYS* 3.2 17.8 + - + +
496A ARG* 2.9 27.5 + - - +
602A ZN 2.3 37.0 - - - -
491B ASN* 4.7 5.4 - - + +
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Residues in contact with PRO 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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463A PHE* 3.5 18.7 - - + -
474A TYR* 3.6 36.6 - - + -
475A LEU 5.9 0.9 - - - +
489A ARG 4.6 1.5 - - - +
490A LYS 4.1 3.4 - - - +
491A ASN 3.4 8.7 - - - +
492A CYS* 1.3 86.4 - - - +
494A ALA* 1.3 61.2 + - - +
496A ARG* 4.1 2.2 - - + -
497A TYR* 2.8 34.0 + - - +
491B ASN* 5.0 7.2 - - - +
12D A 5.0 0.7 - - - +
13D T 3.3 22.4 - - - +
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Residues in contact with ALA 494 (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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474A TYR* 3.6 36.3 - - + +
475A LEU 4.2 0.9 - - - -
476A CYS* 3.9 23.3 - - + +
480A ASN* 4.9 4.3 - - - +
492A CYS* 3.2 6.0 - - - -
493A PRO* 1.3 81.2 - - - +
495A CYS* 1.3 58.1 + - - +
497A TYR* 3.9 3.1 - - - +
498A ARG* 3.1 27.5 + - - +
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Residues in contact with CYS 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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476A CYS* 3.9 1.6 - - - -
480A ASN* 3.6 12.6 - - - -
481A ASP* 3.6 11.7 - - - -
482A CYS* 3.3 31.9 - - + +
484A ILE* 4.0 9.3 - - + +
492A CYS* 3.2 8.4 + - - +
494A ALA* 1.3 77.2 - - - +
496A ARG* 1.3 61.0 + - - +
498A ARG* 3.6 12.5 - - - +
499A LYS* 2.9 31.7 + - - +
602A ZN 2.4 35.2 - - - -
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Residues in contact with ARG 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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442A VAL* 4.1 7.4 - - + +
459A SER* 3.3 34.2 + - - -
460A CYS* 3.4 19.2 - - - +
463A PHE* 3.6 44.6 - - + +
484A ILE* 3.8 23.9 - - + +
489A ARG* 3.5 37.4 + - - +
490A LYS 5.0 0.2 - - - +
492A CYS 2.9 16.8 + - - +
493A PRO* 3.7 4.5 - - + +
495A CYS* 1.3 77.1 - - - +
497A TYR* 1.3 57.3 + - - +
499A LYS* 3.2 4.2 + - - +
500A CYS* 2.9 31.9 + - - -
13D T 4.2 9.3 + - - -
14D G 2.7 30.9 + - - -
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Residues in contact with TYR 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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463A PHE* 3.6 14.1 - + + -
464A PHE* 4.0 17.9 - + - -
467A ALA* 3.7 23.6 - - + -
468A VAL* 3.7 38.9 - - + +
474A TYR* 4.4 16.4 - + + -
493A PRO 2.8 18.6 + - - +
494A ALA* 3.9 4.3 - - - +
496A ARG* 1.3 77.2 - - - +
498A ARG* 1.3 62.0 + - - +
500A CYS* 3.1 5.9 + - - +
501A LEU* 3.1 45.0 + - + +
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Residues in contact with ARG 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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480A ASN* 3.8 48.5 + - - +
481A ASP* 5.7 1.1 - - - +
494A ALA 3.1 18.4 + - - +
495A CYS* 3.6 14.5 - - - +
496A ARG 3.3 0.2 - - - -
497A TYR* 1.3 77.6 - - - +
499A LYS* 1.3 64.8 + - + +
501A LEU* 3.2 13.6 + - - +
502A GLN* 3.0 62.7 + - - +
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Residues in contact with LYS 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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441A LEU 4.1 10.3 + - - +
442A VAL* 2.7 42.3 + - + +
443A CYS* 4.7 0.8 - - - +
444A SER* 5.4 3.6 + - - -
482A CYS 5.8 0.7 - - - +
484A ILE* 3.5 33.7 + - + +
495A CYS 2.9 18.1 + - - +
496A ARG* 3.6 4.3 - - - +
498A ARG* 1.3 76.4 - - + +
500A CYS* 1.3 65.9 + - - +
502A GLN* 3.4 11.7 + - + +
503A ALA* 3.0 23.9 + - - +
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Residues in contact with CYS 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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442A VAL* 3.9 17.9 - - - +
460A CYS* 4.8 4.9 - - - -
463A PHE* 4.4 9.6 - - - -
464A PHE* 3.5 31.0 - - + -
496A ARG* 2.9 24.6 + - - -
497A TYR* 3.2 12.1 - - - +
499A LYS* 1.3 78.2 - - - +
501A LEU* 1.3 61.4 + - - +
503A ALA* 3.1 12.0 + - - +
505A MET* 3.1 45.7 + - - +
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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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464A PHE* 3.8 22.4 - - + -
468A VAL* 5.6 0.7 - - + -
497A TYR* 3.1 41.8 + - + +
498A ARG* 3.2 12.1 + - - +
500A CYS* 1.3 75.7 - - - +
502A GLN* 1.3 59.7 + - + +
504A GLY* 2.8 23.2 + - - -
505A MET 4.0 11.3 + - - +
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Residues in contact with GLN 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 ARG* 3.0 56.0 + - - +
499A LYS* 3.7 11.2 - - + +
500A CYS 3.4 0.2 - - - -
501A LEU* 1.3 75.9 - - + +
503A ALA* 1.3 59.8 + - - +
504A GLY 3.3 0.4 + - - -
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Residues in contact with ALA 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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441A LEU* 4.6 15.4 - - + +
442A VAL* 4.2 8.1 - - + -
454A VAL* 3.3 23.0 - - + +
499A LYS* 3.0 13.6 + - + +
500A CYS 3.3 11.7 - - - +
501A LEU 3.0 0.4 - - - -
502A GLN* 1.3 78.2 - - - +
504A GLY* 1.3 57.0 + - - +
505A MET* 3.5 14.4 - - + -
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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