Contacts of the helix formed by residues 457 - 469 (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 457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A CYS* 3.3 8.8 - - + +
443A CYS* 3.7 4.7 - - - -
445A ASP* 4.4 7.6 - - + +
446A GLU 3.6 18.8 - - - +
447A ALA* 4.0 6.3 - - - +
448A SER* 4.0 3.1 - - - +
451A HIS* 4.6 0.2 - - - -
456A THR* 1.3 82.4 + - - +
458A GLY* 1.3 65.5 + - - +
459A SER* 3.2 26.5 - - - +
460A CYS 3.2 7.1 + - - -
461A LYS* 3.0 18.9 + - - +
489A ARG* 4.0 2.9 - - - -
601A ZN 2.4 35.9 - - - -
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Residues in contact with GLY 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A GLU 5.3 0.2 + - - -
448A SER* 3.7 16.4 + - - -
457A CYS* 1.3 71.7 - - - +
459A SER* 1.3 65.5 + - - +
461A LYS* 3.0 23.1 + - - +
462A VAL* 3.2 18.2 + - - +
15D T 4.0 13.2 + - - -
16D T 6.2 3.4 - - - -
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Residues in contact with SER 459 (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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457A CYS* 3.2 9.1 - - - +
458A GLY* 1.3 75.5 - - - +
460A CYS* 1.3 60.1 + - - +
462A VAL* 3.5 5.0 - - - +
463A PHE* 3.0 29.5 + - - +
489A ARG* 3.1 28.4 - - - -
496A ARG* 3.3 4.9 + - - -
13D T 6.0 0.2 - - - +
14D G 3.6 41.6 + - - -
15D T 4.0 17.8 + - - -
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Residues in contact with CYS 460 (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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440A CYS* 3.8 5.6 - - - -
442A VAL* 3.8 25.6 - - + -
443A CYS* 3.9 6.1 - - - -
456A THR* 4.2 8.5 - - + -
457A CYS* 3.2 7.2 - - - +
459A SER* 1.3 80.9 + - - +
461A LYS* 1.3 65.3 + - - +
463A PHE* 3.8 3.4 - - - +
464A PHE* 3.1 25.3 + - - +
496A ARG* 3.5 27.4 - - - +
500A CYS* 4.8 3.4 - - - -
505A MET* 4.5 2.8 - - - +
601A ZN 2.4 34.8 - - - -
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Residues in contact with LYS 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A HIS* 3.6 38.1 - - + +
452A TYR* 3.5 31.3 - - + -
456A THR* 4.2 3.8 + - - -
457A CYS 3.0 13.0 + - - +
458A GLY* 3.0 14.6 + - - +
460A CYS* 1.3 79.8 - - - +
462A VAL* 1.3 79.4 + - + +
464A PHE* 3.4 0.9 + - - +
465A LYS* 3.2 15.4 + - - +
505A MET* 5.6 1.3 - - - -
3C A 4.0 19.1 + - - +
4C G 3.2 48.4 + - - -
5C A 4.3 1.6 - - - +
16D T 4.3 4.4 + - - +
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Residues in contact with VAL 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLY 3.2 11.6 + - - +
459A SER 3.5 9.4 - - - +
461A LYS* 1.3 98.0 - - - +
463A PHE* 1.3 69.6 + - - +
465A LYS* 4.0 6.2 - - - +
466A ARG* 3.1 60.0 + - + +
4C G 5.4 1.1 - - + +
5C A 4.1 9.4 - - - +
6C A 5.4 0.9 - - - +
13D T 6.0 0.7 - - + -
14D G 4.1 4.9 - - + +
15D T 3.8 31.4 - - + +
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Residues in contact with PHE 463 (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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459A SER 3.0 19.6 + - - +
460A CYS 3.8 3.1 - - - +
461A LYS 3.3 0.2 - - - -
462A VAL* 1.3 79.7 - - - +
464A PHE* 1.3 63.2 + - - +
466A ARG* 3.1 9.0 + - + +
467A ALA* 2.8 30.7 + - + +
474A TYR* 4.2 13.0 - + - -
493A PRO* 3.5 39.0 - - + -
496A ARG* 3.6 44.2 - - + +
497A TYR* 3.6 33.0 - - + -
500A CYS* 4.4 6.5 - - - -
13D T 4.0 28.0 - - + -
14D G 5.1 0.2 - - - +
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Residues in contact with PHE 464 (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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452A TYR* 4.0 13.9 - + + -
460A CYS 3.1 15.8 + - - +
461A LYS 3.8 2.7 - - - +
463A PHE* 1.3 85.6 - - - +
465A LYS* 1.3 63.9 + - - +
467A ALA* 3.5 2.7 + - - +
468A VAL* 3.1 41.9 + - + +
497A TYR* 4.0 8.1 - + - -
500A CYS* 3.5 23.8 - - + -
501A LEU* 3.8 22.2 - - + -
505A MET* 3.4 52.5 - - + -
506A ASN* 3.8 10.3 - - - -
507A LEU* 3.5 26.9 - - + -
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Residues in contact with LYS 465 (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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452A TYR* 3.6 19.1 - - + +
461A LYS 3.2 13.8 + - - +
462A VAL* 4.0 7.9 - - - +
463A PHE 3.2 0.2 - - - -
464A PHE* 1.3 81.5 - - - +
466A ARG* 1.3 61.5 + - + +
468A VAL* 4.1 2.9 - - + +
469A GLU* 3.1 42.2 + - + +
507A LEU* 4.2 18.4 - - + +
4C G 3.6 45.7 + - + +
5C A 4.8 12.3 - - - +
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Residues in contact with ARG 466 (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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462A VAL* 3.1 34.2 + - + +
463A PHE* 3.1 7.4 + - + +
465A LYS* 1.3 79.4 - - + +
467A ALA* 1.3 68.8 + - - +
469A GLU* 3.7 2.4 - - - -
470A GLY* 3.1 15.4 + - - -
472A HIS* 3.2 21.3 - - + -
474A TYR* 5.8 0.7 - - - +
6C A 3.9 12.7 - - - +
7C C 5.2 1.0 - - - +
13D T 3.5 34.7 + - - +
14D G 2.7 47.7 + - - -
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Residues in contact with ALA 467 (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* 2.8 23.2 + - + +
464A PHE 3.7 3.1 - - - +
466A ARG* 1.3 80.2 - - - +
468A VAL* 1.3 64.5 + - - +
470A GLY 3.2 14.6 + - - +
471A GLN 4.8 0.3 - - - +
472A HIS* 3.7 14.5 + - - +
474A TYR* 4.0 18.3 + - + +
497A TYR* 3.7 36.6 + - + -
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Residues in contact with VAL 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A PHE* 3.1 49.1 + - + +
465A LYS* 4.1 2.9 - - + +
467A ALA* 1.3 74.5 - - - +
469A GLU* 1.3 59.0 + - + +
470A GLY 3.3 6.8 + - - +
497A TYR* 3.7 21.5 - - + +
501A LEU* 5.6 0.7 - - + -
507A LEU* 4.0 22.4 - - + -
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Residues in contact with GLU 469 (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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465A LYS* 3.1 35.6 + - - +
466A ARG* 3.7 4.9 - - - -
468A VAL* 1.3 78.7 - - + +
470A GLY* 1.3 55.5 + - - +
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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