Contacts of the helix formed by residues 473 - 483 (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 473 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436B SER 3.0 25.6 - - - -
437B ILE 2.8 20.4 + - - -
438B LYS 3.9 4.0 - - - -
439B GLY* 3.0 23.5 + - - +
468B ALA* 2.9 12.6 + - + +
471B HIS* 3.4 29.6 - - + +
472B GLY* 1.3 75.1 + - - +
474B LEU* 1.3 54.4 + - - +
475B LYS 3.5 2.0 - - - -
476B VAL* 3.1 21.6 + - + +
477B VAL* 2.8 36.5 + - - +
509B ILE* 3.8 0.2 - - - +
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Residues in contact with LEU 474 (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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472B GLY 3.2 6.5 + - - +
473B HIS* 1.3 72.4 - - - +
475B LYS* 1.3 64.5 + - - +
477B VAL* 3.1 5.6 + - - +
478B GLU* 2.9 23.0 + - + +
508B ASP* 3.8 31.2 - - + +
509B ILE* 3.5 43.3 - - + +
512B LEU* 4.2 15.9 - - + +
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Residues in contact with LYS 475 (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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441B ILE* 3.7 43.1 - - + -
445B GLU* 5.0 7.8 + - - -
473B HIS 3.5 0.2 - - - -
474B LEU* 1.3 78.5 - - - +
476B VAL* 1.3 58.5 + - - +
478B GLU* 3.3 20.9 + - - +
479B LEU* 2.9 57.9 + - + +
482B GLN* 5.0 4.2 + - - +
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B SER* 4.0 16.4 - - - +
439B GLY* 4.1 17.7 - - - -
441B ILE* 4.0 25.1 - - + -
444B VAL* 4.0 20.9 - - + -
468B ALA* 3.6 20.4 - - + -
473B HIS* 3.1 23.3 + - + +
475B LYS* 1.3 72.8 - - - +
477B VAL* 1.3 66.4 + - - +
479B LEU* 3.2 9.8 + - + +
480B LEU* 3.0 32.8 + - + +
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Residues in contact with VAL 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B LEU* 3.8 18.6 - - + +
468B ALA* 3.6 22.7 - - + +
469B CYS* 3.7 21.5 - - - +
473B HIS 2.8 22.1 + - - +
474B LEU* 3.1 10.3 + - - +
476B VAL* 1.3 71.9 - - - +
478B GLU* 1.3 56.8 + - - +
480B LEU* 3.1 4.8 + - - +
481B LEU* 2.9 36.4 + - + +
509B ILE* 3.9 22.7 - - + -
512B LEU* 3.8 17.5 - - + -
513B LEU* 4.2 4.7 - - + -
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Residues in contact with GLU 478 (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* 2.9 13.2 + - + +
475B LYS* 3.5 26.2 + - + +
477B VAL* 1.3 76.1 - - - +
479B LEU* 1.3 53.1 + - - +
481B LEU* 3.2 5.0 + - - +
482B GLN* 2.7 65.0 + - + +
512B LEU* 3.7 31.1 - - + +
516B TYR* 5.1 4.0 - - + +
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Residues in contact with LEU 479 (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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441B ILE* 4.0 17.7 - - + -
444B VAL* 4.1 15.7 - - + -
445B GLU* 3.8 39.9 - - + +
448B LEU* 3.7 11.7 - - + -
475B LYS* 2.9 46.7 + - + +
476B VAL* 3.2 8.7 + - - +
478B GLU* 1.3 74.7 - - - +
480B LEU* 1.3 57.7 + - - +
482B GLN* 3.4 16.0 + - - +
483B HIS* 2.9 46.8 + - + +
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Residues in contact with LEU 480 (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* 4.1 19.1 - - + -
436B SER* 3.9 2.7 - - - +
444B VAL* 4.7 0.9 - - + -
448B LEU* 3.9 17.9 - - + -
454B PRO* 3.9 23.0 - - + +
464B PRO* 3.6 37.5 - - + +
465B LEU* 3.6 12.6 - - + +
468B ALA* 4.0 4.7 - - + -
476B VAL* 3.0 35.4 + - + +
477B VAL 3.1 6.3 + - - +
479B LEU* 1.3 74.6 - - - +
481B LEU* 1.3 63.4 + - - +
483B HIS* 3.1 10.6 + - - +
484B LYS 3.2 0.7 + - - -
485B ALA* 3.0 33.5 + - + +
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Residues in contact with LEU 481 (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* 4.0 23.3 - - + -
477B VAL* 2.9 29.3 + - + +
478B GLU 3.6 3.8 - - - +
480B LEU* 1.3 74.5 - - - +
482B GLN* 1.3 65.0 + - - +
484B LYS* 3.0 14.2 + - - -
485B ALA 3.8 19.3 - - - +
487B VAL* 4.1 18.2 - - + -
512B LEU* 3.9 20.0 - - + +
513B LEU* 4.3 9.0 - - + -
516B TYR* 3.6 52.3 - - + -
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Residues in contact with GLN 482 (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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475B LYS* 5.0 3.8 + - - +
478B GLU* 2.7 46.8 + - + +
479B LEU* 3.5 26.4 + - - +
481B LEU* 1.3 72.2 - - - +
483B HIS* 1.3 65.6 + - + +
484B LYS* 3.4 9.0 + - - +
516B TYR* 3.9 18.9 + - - +
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Residues in contact with HIS 483 (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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445B GLU* 5.1 2.0 - - + -
448B LEU* 3.6 59.1 + - + +
449B GLN* 4.2 13.9 + - + +
454B PRO* 3.4 18.4 - - - +
479B LEU* 2.9 41.5 + - + +
480B LEU 3.3 7.6 - - - +
481B LEU 3.1 0.2 - - - -
482B GLN* 1.3 81.9 - - + +
484B LYS* 1.3 65.4 + - - +
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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