Contacts of the helix formed by residues 503 - 516 (chain G) in PDB entry 5O9Z
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 ARG 503 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502G ASN* 1.3 81.0 - - - +
504G GLU* 1.3 54.0 + - - +
505G GLN* 2.7 17.0 + - - -
506G TRP* 2.8 21.2 + - - +
507G ILE* 2.9 14.6 + - + -
529G VAL* 5.3 10.4 - - + +
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Residues in contact with GLU 504 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502G ASN* 4.9 1.6 - - + +
503G ARG* 1.3 75.4 - - - +
505G GLN* 1.3 57.0 + - - +
507G ILE* 3.8 13.0 - - - -
508G GLN* 2.9 34.8 + - + +
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Residues in contact with GLN 505 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468G ILE* 5.0 13.6 - - + +
501G ILE* 4.4 17.7 - - + +
502G ASN* 5.9 0.8 - - - +
503G ARG 2.7 6.0 + - - +
504G GLU* 1.3 74.4 - - - +
506G TRP* 1.3 57.3 + - - +
508G GLN* 3.9 1.7 - - - +
509G ASP* 2.9 27.5 + - - +
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Residues in contact with TRP 506 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468G ILE* 5.6 4.0 - - + -
503G ARG* 2.8 9.6 + - - +
505G GLN* 1.3 73.4 - - - +
507G ILE* 1.3 60.7 + - - +
509G ASP* 3.4 9.4 + - - +
510G ALA* 2.9 26.0 + - - +
525G VAL* 3.9 15.5 - - + +
528G ALA* 5.9 2.7 - - + -
529G VAL* 4.5 19.3 - - + +
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Residues in contact with ILE 507 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503G ARG* 2.9 20.2 + - + +
504G GLU* 3.8 10.8 - - + -
506G TRP* 1.3 75.4 - - - +
508G GLN* 1.3 59.2 + - - +
510G ALA* 3.0 9.9 + - - +
511G GLU* 2.9 25.2 + - - +
526G MET* 6.1 2.2 - - - +
529G VAL* 5.3 6.1 - - + +
550G CYS* 5.7 8.7 - - + -
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Residues in contact with GLN 508 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504G GLU* 2.9 23.1 + - + +
505G GLN* 4.0 2.5 - - - +
507G ILE* 1.3 72.9 - - - +
509G ASP* 1.3 61.1 + - - +
511G GLU* 3.1 9.2 + - - +
512G GLU* 2.9 28.4 + - - +
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Residues in contact with ASP 509 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468G ILE* 4.9 19.3 - - + +
471G ALA* 5.8 5.2 - - + -
472G LYS* 5.7 8.3 - - + +
505G GLN 2.9 18.6 + - - +
506G TRP* 3.5 10.8 - - - +
508G GLN* 1.3 77.4 - - - +
510G ALA* 1.3 55.9 + - - +
512G GLU* 3.9 6.1 - - - +
513G CYS* 2.9 29.3 + - - +
525G VAL* 4.8 6.3 - - + -
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Residues in contact with ALA 510 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506G TRP 2.9 14.4 + - - +
507G ILE* 3.0 13.6 + - - +
509G ASP* 1.3 74.2 - - - +
511G GLU* 1.3 59.2 + - - +
513G CYS* 4.3 1.3 - - - -
514G ASP* 2.9 27.7 + - - +
522G CYS* 3.2 33.6 - - + +
525G VAL* 3.7 12.3 - - + -
526G MET* 4.0 10.8 - - + +
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Residues in contact with GLU 511 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507G ILE 2.9 11.7 + - - +
508G GLN* 3.1 12.3 + - - +
510G ALA* 1.3 75.4 - - - +
512G GLU* 1.3 61.1 + - - +
514G ASP* 3.0 6.9 + - - +
515G ARG* 2.9 31.0 + - - +
554G ASN* 6.3 2.2 - - + -
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Residues in contact with GLU 512 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472G LYS* 6.1 4.7 - - + -
508G GLN 2.9 15.8 + - - +
509G ASP* 4.0 6.7 - - - +
511G GLU* 1.3 76.2 - - - +
513G CYS* 1.3 51.6 + - - +
515G ARG* 4.7 2.4 - - - +
516G ALA* 2.6 43.1 + - + +
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Residues in contact with CYS 513 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475G GLU* 4.0 19.7 - - + +
509G ASP 2.9 19.5 + - - +
510G ALA* 4.0 5.4 - - - +
512G GLU* 1.3 76.1 - - - +
514G ASP* 1.3 61.8 + - - +
516G ALA* 4.0 3.8 - - - -
517G GLY* 3.4 12.5 + - - -
518G SER 3.3 16.7 - - - +
521G THR* 3.9 27.2 - - - +
522G CYS* 4.2 5.2 - - - +
525G VAL* 5.8 1.1 - - + -
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Residues in contact with ASP 514 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510G ALA 2.9 20.0 + - - +
511G GLU* 3.0 10.5 + - - +
513G CYS* 1.3 77.2 - - - +
515G ARG* 1.3 60.0 + - - +
517G GLY 2.8 19.6 - - - +
518G SER 4.6 2.3 - - - +
519G VAL* 5.2 4.2 + - + +
522G CYS* 3.6 16.6 - - + -
554G ASN* 5.5 10.8 - - + -
555G ALA* 6.1 2.2 - - + +
557G GLU* 5.9 2.7 - - + -
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Residues in contact with ARG 515 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511G GLU 2.9 13.6 + - - +
512G GLU* 4.7 2.2 - - - +
514G ASP* 1.3 76.8 - - - +
516G ALA* 1.3 61.0 + - + +
517G GLY 3.3 0.6 + - - -
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Residues in contact with ALA 516 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476G ALA* 6.0 3.1 - - - -
512G GLU* 2.6 23.8 + - + +
513G CYS* 4.2 3.1 - - - -
514G ASP 3.3 0.2 - - - -
515G ARG* 1.3 77.5 - - - +
517G GLY* 1.3 56.8 + - - +
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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