Contacts of the helix formed by residues 506 - 516 (chain A) in PDB entry 3C5R
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 HIS 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469A CYS 3.3 23.3 - - - -
470A ASN 3.4 11.7 + - - -
471A HIS 3.9 2.6 - - - -
472A GLY* 3.4 27.0 + - - -
501A ALA* 3.0 12.4 + - - +
504A ASN* 3.4 33.2 + - + +
505A GLY* 1.3 75.3 + - - +
507A VAL* 1.3 64.9 + - - +
508A ASP* 3.4 14.5 + - - +
509A ILE* 3.2 14.7 + - + +
510A VAL* 3.1 23.6 + - - +
539A MET* 3.6 2.6 - - - +
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Residues in contact with VAL 507 (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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505A GLY 3.3 7.2 + - - +
506A HIS* 1.3 68.9 - - - +
508A ASP* 1.3 71.6 + - + +
510A VAL* 3.1 6.1 + - - +
511A LYS* 3.0 33.6 + - - +
536A ASP* 4.0 17.5 - - - +
538A SER* 4.4 11.7 - - - +
539A MET* 3.7 31.6 - - + +
542A LEU* 3.9 8.1 - - + +
470B ASN* 5.6 5.4 - - - +
471B HIS* 5.8 7.0 - - + +
504B ASN* 6.3 1.3 - - - +
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Residues in contact with ASP 508 (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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472A GLY 5.5 1.6 - - - +
474A LEU* 3.9 36.6 - - + +
506A HIS* 3.7 13.9 + - - +
507A VAL* 1.3 80.9 - - + +
509A ILE* 1.3 71.7 + - - +
511A LYS* 3.4 12.5 + - - +
512A LEU* 3.1 25.5 + - - +
504B ASN* 4.4 15.1 - - - +
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Residues in contact with ILE 509 (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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468A ALA 4.1 6.7 - - - +
469A CYS* 3.7 25.4 - - - +
472A GLY* 3.5 40.2 - - - +
473A HIS 3.8 3.8 - - - +
474A LEU* 3.6 31.0 - - + +
477A VAL* 3.9 11.9 - - + -
501A ALA* 3.6 17.9 - - + -
506A HIS* 3.2 15.0 + - + +
507A VAL 3.2 0.8 - - - -
508A ASP* 1.3 83.1 + - - +
510A VAL* 1.3 66.7 + - - +
512A LEU* 3.3 1.7 + - - +
513A LEU* 2.9 27.2 + - + +
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Residues in contact with VAL 510 (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 LEU* 4.0 19.5 - - + -
501A ALA* 3.9 4.7 - - + -
502A ALA* 3.8 20.6 - - + +
506A HIS 3.1 15.6 + - - +
507A VAL 3.1 7.4 + - - +
509A ILE* 1.3 76.4 - - - +
511A LYS* 1.3 62.9 + - - +
513A LEU* 3.3 1.3 + - - +
514A LEU* 3.0 42.9 + - + +
539A MET* 3.4 30.7 - - + -
542A LEU* 3.9 15.5 - - + -
543A LEU* 4.1 11.7 - - + -
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Residues in contact with LYS 511 (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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507A VAL* 3.0 19.7 + - - +
508A ASP* 3.6 12.6 - - - +
510A VAL* 1.3 78.5 - - - +
512A LEU* 1.3 56.2 + - - +
514A LEU* 3.7 8.5 - - + +
515A SER* 3.0 28.6 + - - -
542A LEU* 3.4 43.1 - - + +
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Residues in contact with LEU 512 (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 LEU* 3.9 19.3 - - + -
477A VAL* 3.9 12.6 - - + -
478A GLU* 3.8 48.5 - - + +
481A LEU* 4.1 7.4 - - + -
508A ASP 3.1 16.3 + - - +
509A ILE* 3.8 4.7 - - - +
510A VAL 3.3 0.4 - - - -
511A LYS* 1.3 74.0 - - - +
513A LEU* 1.3 66.7 + - - +
515A SER* 2.8 25.8 + - - +
516A TYR* 3.3 34.3 + - + -
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Residues in contact with LEU 513 (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 LEU* 4.5 5.2 - - + -
469A CYS* 3.7 21.5 - - - -
477A VAL* 4.3 3.4 - - + -
481A LEU* 4.2 15.7 - - + -
487A VAL* 3.6 21.2 - - + +
497A PRO* 3.5 41.1 - - + +
498A LEU* 3.6 15.9 - - + +
501A ALA* 4.0 3.1 - - + -
509A ILE* 2.9 30.4 + - + +
510A VAL 3.7 3.4 - - - +
512A LEU* 1.3 75.5 - - - +
514A LEU* 1.3 59.1 + - - +
516A TYR* 3.0 21.7 + - - +
517A GLY 3.3 0.7 + - - -
518A ALA* 3.1 27.5 + - + +
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Residues in contact with LEU 514 (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 LEU* 4.1 22.4 - - + -
510A VAL* 3.0 36.3 + - + +
511A LYS* 3.7 7.0 - - - +
513A LEU* 1.3 75.8 - - - +
515A SER* 1.3 54.1 + - - +
517A GLY* 2.8 23.6 + - - -
518A ALA* 3.8 21.6 - - - +
520A ARG* 4.2 21.5 - - + -
542A LEU* 3.7 28.9 - - + +
543A LEU* 4.6 1.3 - - + -
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Residues in contact with SER 515 (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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511A LYS 3.0 14.6 + - - -
512A LEU* 2.8 27.4 + - - +
514A LEU* 1.3 73.7 - - - +
516A TYR* 1.3 66.8 + - - +
517A GLY 3.4 1.3 + - - -
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Residues in contact with TYR 516 (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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478A GLU* 4.8 3.9 + - + +
481A LEU* 3.6 46.2 - - + -
482A GLN* 3.8 25.3 + - - +
487A VAL* 3.6 24.8 - - + +
512A LEU* 3.3 39.3 + - + +
513A LEU 3.0 10.5 + - - +
515A SER* 1.3 82.5 - - - +
517A GLY* 1.3 58.8 + - - +
518A ALA 3.5 0.4 - - - -
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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