Contacts of the helix formed by residues 463 - 472 (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 THR 463 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B HIS* 4.1 3.4 - - - -
454B PRO 4.3 5.2 - - - +
455B ASN* 5.4 3.4 - - - +
456B VAL 3.4 14.4 - - - +
457B LYS* 3.9 16.2 - - + -
461B GLY 4.3 0.7 - - - +
462B TRP* 1.3 76.5 - - - +
464B PRO* 1.3 75.4 - - - +
465B LEU* 3.3 11.2 + - - +
466B HIS* 2.8 44.3 + - + +
467B GLU* 3.0 23.6 + - - +
489B THR* 4.2 15.4 - - + -
497B PRO* 5.2 0.2 - - - +
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Residues in contact with PRO 464 (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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432B LEU* 3.8 26.0 - - + +
433B HIS* 3.8 19.0 - - + +
436B SER* 3.3 27.4 - - - +
454B PRO 3.4 18.8 - - - +
456B VAL* 3.5 17.5 - - + +
463B THR* 1.3 88.3 - - - +
465B LEU* 1.3 55.5 + - - +
467B GLU* 3.2 6.3 + - + +
468B ALA* 2.8 31.2 + - - +
480B LEU* 3.6 11.7 - - + -
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Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B PRO* 5.2 1.0 + - - +
463B THR* 3.1 9.0 + - - +
464B PRO* 1.3 79.1 - - - +
466B HIS* 1.3 56.7 + - - +
468B ALA* 3.3 0.3 + - - -
469B CYS* 2.9 40.9 + - - -
477B VAL* 3.8 42.2 - - + +
480B LEU* 3.6 13.5 - - + +
481B LEU* 4.0 23.3 - - + -
485B ALA* 4.3 13.2 - - + -
486B LEU 3.5 25.8 - - - +
487B VAL* 4.0 3.6 - - - -
497B PRO* 3.7 22.9 - - + -
513B LEU* 4.4 2.2 - - + -
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Residues in contact with HIS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B TRP* 3.7 22.0 - + + -
463B THR* 2.8 50.8 + - + +
465B LEU* 1.3 74.8 - - - +
467B GLU* 1.3 58.3 + - - +
469B CYS* 3.7 4.9 - - - +
470B ASN* 2.9 31.0 + - - +
489B THR* 3.1 26.9 + - - -
490B THR 4.0 0.2 - - - -
491B GLY* 3.4 18.3 + - - -
492B TYR 5.4 0.9 - - - -
495B ASP* 2.7 30.2 + - + -
497B PRO* 3.5 20.5 - - + +
500B ASP* 3.4 21.5 - - - +
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Residues in contact with GLU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B GLU* 5.3 2.3 - - - +
433B HIS* 4.7 8.1 - - + +
436B SER* 4.3 2.2 - - - -
437B ILE* 3.4 38.9 - - + +
458B ASP* 4.3 5.2 - - - +
462B TRP* 3.4 38.6 - - + +
463B THR 3.0 17.2 + - - +
464B PRO* 3.5 11.7 - - + +
465B LEU 3.2 0.2 - - - -
466B HIS* 1.3 77.0 - - - +
468B ALA* 1.3 62.5 + - - +
470B ASN 3.4 0.5 + - - -
471B HIS* 2.8 54.7 + - - +
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Residues in contact with ALA 468 (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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436B SER* 3.8 11.6 + - - +
464B PRO 2.8 19.3 + - - +
465B LEU 3.9 1.6 - - - +
467B GLU* 1.3 73.0 - - - +
469B CYS* 1.3 56.3 + - - +
471B HIS 3.5 0.3 + - - -
472B GLY* 3.0 9.7 + - - -
473B HIS* 2.9 29.5 + - + +
476B VAL* 3.6 33.0 - - + -
477B VAL* 3.6 18.9 - - + +
480B LEU* 4.0 4.7 - - + -
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Residues in contact with CYS 469 (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* 2.9 24.6 + - - +
466B HIS 3.7 3.6 - - - +
468B ALA* 1.3 76.1 - - - +
470B ASN* 1.3 62.6 + - - +
472B GLY* 3.4 2.8 + - - -
477B VAL* 3.8 12.1 - - - -
497B PRO* 3.5 25.6 - - + +
500B ASP* 4.1 2.0 - - + -
501B ALA* 3.7 12.5 - - + +
506B HIS* 3.2 20.6 - - - -
509B ILE* 3.7 23.0 - - - +
513B LEU* 3.8 26.0 - - - -
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Residues in contact with ASN 470 (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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507A VAL* 5.6 5.9 - - - +
462B TRP* 3.7 21.6 - - + -
466B HIS 2.9 18.6 + - - +
467B GLU 3.7 4.3 - - - +
468B ALA 3.4 0.2 - - - -
469B CYS* 1.3 75.6 - - - +
471B HIS* 1.3 73.9 + - - +
500B ASP* 2.7 34.2 + - - +
503B LYS* 5.1 5.7 - - - +
504B ASN* 2.7 41.5 + - - +
506B HIS* 3.2 12.1 + - - -
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Residues in contact with HIS 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A VAL* 5.8 7.0 - - + +
538A SER* 3.7 22.9 + - - -
437B ILE* 3.9 26.9 - - + +
462B TRP* 5.6 0.4 - + - -
467B GLU* 2.8 45.7 + - - +
470B ASN* 1.3 88.6 + - - +
472B GLY* 1.3 61.8 + - - +
473B HIS* 3.4 34.4 + - + +
506B HIS* 3.7 6.8 + - - -
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Residues in contact with GLY 472 (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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468B ALA 3.0 4.0 + - - -
469B CYS 3.4 0.6 + - - -
470B ASN 3.3 3.6 - - - -
471B HIS* 1.3 79.8 - - - +
473B HIS* 1.3 61.8 + - - +
474B LEU* 3.2 7.6 + - - +
506B HIS* 3.5 22.3 + - - -
509B ILE* 3.4 23.2 - - - +
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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