Contacts of the helix formed by residues 506 - 516 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469B CYS 3.2 23.1 - - - -
470B ASN 3.2 15.8 + - - -
471B HIS 3.7 5.0 - - - -
472B GLY* 3.5 22.0 + - - -
501B ALA* 2.9 12.3 + - - +
504B ASN* 3.5 33.6 + - + +
505B GLY* 1.3 76.4 + - - +
507B VAL* 1.3 57.4 + - - +
508B ASP 3.4 2.9 - - - -
509B ILE* 3.2 21.4 + - + +
510B VAL* 3.0 28.6 + - - +
539B MET* 3.7 2.2 - - - +
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Residues in contact with VAL 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B GLY* 3.1 9.2 + - - +
506B HIS* 1.3 68.1 - - - +
508B ASP* 1.3 73.6 + - - +
510B VAL* 3.6 3.8 - - - +
511B LYS* 2.9 38.2 + - + +
536B ASP* 4.6 13.9 - - - +
538B SER* 4.6 13.2 - - - +
539B MET* 3.5 26.9 - - + -
542B LEU* 4.0 14.2 - - + +
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Residues in contact with ASP 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B LEU* 3.8 31.8 - - + +
506B HIS 3.4 0.4 - - - -
507B VAL* 1.3 88.5 - - - +
509B ILE* 1.3 58.8 + - + +
511B LYS* 3.3 15.4 + - - +
512B LEU* 2.9 27.0 + - - +
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Residues in contact with ILE 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B CYS* 3.7 33.2 - - - +
472B GLY* 3.4 42.8 - - - +
473B HIS 3.8 4.5 - - - +
474B LEU* 3.5 31.4 - - + +
477B VAL* 3.9 13.5 - - + -
501B ALA* 3.8 12.1 - - + -
506B HIS* 3.2 18.4 + - + +
508B ASP* 1.3 72.5 - - + +
510B VAL* 1.3 56.2 + - - +
512B LEU* 3.2 2.9 + - - +
513B LEU* 2.8 43.1 + - + +
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Residues in contact with VAL 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B LEU* 3.9 22.8 - - + +
501B ALA* 3.6 18.6 - - + -
502B ALA* 3.6 11.4 - - + +
506B HIS 3.0 18.1 + - - +
507B VAL 3.6 7.0 - - - +
508B ASP 3.4 0.2 - - - -
509B ILE* 1.3 75.0 - - - +
511B LYS* 1.3 62.7 + - - +
513B LEU* 3.2 2.0 + - - +
514B LEU* 3.0 39.3 + - + +
539B MET* 3.6 31.9 - - - -
542B LEU* 4.3 11.0 - - + -
543B LEU* 4.3 9.4 - - + -
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Residues in contact with LYS 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B VAL* 2.9 27.4 + - + +
508B ASP* 3.5 14.9 + - - +
509B ILE 3.3 0.2 - - - -
510B VAL* 1.3 76.2 - - - +
512B LEU* 1.3 61.4 + - - +
514B LEU* 3.6 8.8 + - + +
515B SER* 3.1 23.4 + - - -
542B LEU* 3.8 39.4 - - + +
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B LEU* 4.2 16.2 - - + -
477B VAL* 3.8 22.7 - - + -
478B GLU* 3.7 42.8 - - + +
481B LEU* 3.9 7.9 - - + -
508B ASP 2.9 16.8 + - - +
509B ILE* 3.2 6.3 + - - +
511B LYS* 1.3 72.4 - - - +
513B LEU* 1.3 66.0 + - - +
515B SER* 2.8 23.9 + - - +
516B TYR* 3.2 41.1 + - + -
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Residues in contact with LEU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B LEU* 4.4 4.0 - - + -
469B CYS* 3.8 23.3 - - - -
477B VAL* 4.2 13.0 - - + -
481B LEU* 4.3 5.8 - - + -
487B VAL* 3.7 19.8 - - + +
497B PRO* 3.5 34.5 - - + +
498B LEU* 3.6 19.5 - - + -
501B ALA* 3.9 6.5 - - + -
509B ILE* 2.8 32.8 + - + +
510B VAL 3.2 3.3 + - - +
512B LEU* 1.3 73.3 - - - +
514B LEU* 1.3 63.1 + - - +
516B TYR* 3.0 15.4 + - - +
517B GLY 3.3 0.7 + - - -
518B ALA* 3.1 27.6 + - + +
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Residues in contact with LEU 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B LEU* 4.1 21.8 - - + -
510B VAL* 3.0 36.6 + - + +
511B LYS* 4.0 7.6 - - + +
513B LEU* 1.3 75.7 - - - +
515B SER* 1.3 55.7 + - - +
516B TYR 3.1 0.2 - - - -
517B GLY* 2.9 19.8 + - - -
518B ALA* 3.8 22.9 + - - +
520B ARG* 4.1 22.7 - - + -
542B LEU* 3.8 25.6 - - + +
543B LEU* 4.7 1.8 - - + -
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Residues in contact with SER 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511B LYS 3.1 15.3 + - - -
512B LEU* 2.8 27.0 + - - +
514B LEU* 1.3 75.6 - - - +
516B TYR* 1.3 66.7 + - - +
517B GLY 3.4 1.1 + - - -
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Residues in contact with TYR 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B GLU* 5.0 4.3 + - + +
481B LEU* 3.6 44.4 - - + -
482B GLN* 3.9 23.3 + - - +
487B VAL* 3.4 26.9 - - + +
512B LEU* 3.2 39.5 + - + +
513B LEU 3.0 10.5 + - - +
515B SER* 1.3 81.0 - - - +
517B GLY* 1.3 57.5 + - - +
518B ALA 3.6 0.2 - - - -
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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