Contacts of the helix formed by residues 460 - 469 (chain A) in PDB entry 3RC3
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 THR 460 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A PRO 4.7 4.0 - - - +
459A ILE* 1.3 77.7 - - - +
461A THR* 1.3 65.2 + - - +
462A SER* 3.5 9.1 + - - -
463A GLN* 2.9 48.5 + - - +
464A ALA* 3.0 22.0 + - - +
497A ILE* 4.0 1.1 - - - -
500A ARG* 5.3 3.4 - - - +
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Residues in contact with THR 461 (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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460A THR* 1.3 74.0 - - - +
462A SER* 1.3 63.4 + - - +
464A ALA* 3.3 2.1 + - - +
465A LEU* 3.0 38.8 + - + +
497A ILE* 2.7 33.9 + - - +
498A LEU 4.2 2.9 - - - +
500A ARG* 3.4 40.0 + - - +
501A PRO 4.9 1.5 + - - -
502A VAL* 3.4 29.2 - - + -
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Residues in contact with SER 462 (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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322A GLU* 3.1 34.9 + - - -
460A THR* 3.2 8.3 + - - -
461A THR* 1.3 79.6 - - - +
463A GLN* 1.3 62.4 + - - +
465A LEU* 3.4 7.8 + - - +
466A GLN* 3.0 25.1 + - - +
502A VAL* 3.7 17.0 - - - +
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Residues in contact with GLN 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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373A PHE* 6.1 0.2 - - + -
425A ASP* 5.8 6.1 - - + +
445A LYS* 5.4 6.6 - - - +
459A ILE* 3.4 19.1 - - + +
460A THR* 2.9 48.2 + - - +
462A SER* 1.3 78.1 - - - +
464A ALA* 1.3 64.2 + - - +
466A GLN* 3.2 6.3 + - - +
467A ILE* 2.9 38.3 + - + +
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Residues in contact with ALA 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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440A PHE* 3.6 15.3 - - + -
459A ILE* 3.8 20.5 - - + +
460A THR 3.0 12.7 + - - +
461A THR 3.6 6.7 - - - +
463A GLN* 1.3 75.1 - - - +
465A LEU* 1.3 57.0 + - - +
468A ALA* 2.8 34.5 + - - +
494A LEU* 4.6 2.2 - - + -
497A ILE* 3.9 14.1 - - + -
498A LEU* 3.6 21.5 - - + -
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Residues in contact with LEU 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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209A THR* 4.3 3.2 - - - +
461A THR* 3.0 36.2 + - + +
462A SER* 3.9 6.3 - - - +
463A GLN 3.2 0.2 - - - -
464A ALA* 1.3 74.1 - - - +
466A GLN* 1.3 68.0 + - - +
468A ALA* 3.9 2.6 - - + +
469A GLY* 3.0 21.7 + - - -
498A LEU* 3.7 36.8 - - + +
502A VAL* 5.0 5.4 - - + -
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Residues in contact with GLN 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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209A THR* 3.4 22.8 + - - +
213A LYS* 5.3 1.6 + - - -
294A GLN* 5.8 2.0 + - - -
428A GLY* 2.8 34.4 + - - +
429A MSE 3.7 13.8 - - + +
462A SER 3.0 18.1 + - - +
463A GLN* 3.7 5.8 - - - +
465A LEU* 1.3 80.7 - - - +
467A ILE* 1.3 63.6 + - + +
469A GLY 3.6 3.1 + - - -
470A ARG* 3.2 28.4 + - - +
801A ANP 3.1 24.2 + - - -
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Residues in contact with ILE 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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371A VAL* 3.8 28.9 - - + -
373A PHE* 4.1 20.9 - - + -
425A ASP* 3.7 34.8 - - + -
427A ILE* 4.8 4.0 - - + -
428A GLY* 4.7 11.7 - - - +
438A ILE* 3.5 9.5 - - + +
440A PHE* 3.5 25.1 - - + -
459A ILE* 5.4 0.4 - - + -
463A GLN* 2.9 32.7 + - + +
466A GLN* 1.3 77.8 - - + +
468A ALA* 1.3 62.5 + - - +
470A ARG* 3.0 26.6 + - - +
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Residues in contact with ALA 468 (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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351A ILE* 3.4 14.0 - - + +
438A ILE* 3.8 10.7 - - - +
440A PHE* 3.8 5.3 - - + -
464A ALA 2.8 22.4 + - - +
465A LEU* 3.9 4.7 - - + +
467A ILE* 1.3 73.6 - - - +
469A GLY* 1.3 60.9 + - - +
470A ARG 3.1 1.8 + - - -
471A ALA* 3.2 16.5 + - - +
483A VAL* 3.9 27.2 - - + +
498A LEU* 4.3 14.8 - - + -
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Residues in contact with GLY 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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209A THR* 3.7 21.2 + - - +
210A ASN* 4.1 6.1 - - - +
347A ARG* 2.4 38.2 + - - -
351A ILE* 4.1 3.8 - - - -
465A LEU 3.0 18.1 + - - -
466A GLN 3.6 0.2 + - - -
467A ILE 3.2 0.4 - - - -
468A ALA* 1.3 75.7 - - - +
470A ARG* 1.3 60.2 + - - +
471A ALA 3.4 0.7 - - - +
473A ARG* 4.3 2.1 - - - +
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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