Contacts of the helix formed by residues 462 - 474 (chain B) in PDB entry 5C16
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 462 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458B SER 4.1 7.2 - - - +
459B TYR* 2.7 30.8 + - + +
461B ARG* 1.3 82.9 - - - +
463B ILE* 1.3 59.8 + - - +
464B LYS* 3.9 3.5 + - - +
465B GLY* 3.0 13.5 + - - -
466B PHE* 2.9 27.7 + - - +
520B GLU* 3.1 20.0 - - - +
521B PHE* 4.6 1.3 - - - -
577B PHE* 4.5 14.8 - - + -
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Residues in contact with ILE 463 (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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462B THR* 1.3 73.7 - - - +
464B LYS* 1.3 65.3 + - + +
466B PHE* 3.7 3.8 - - - +
467B GLU* 3.1 50.2 + - - +
520B GLU* 3.1 33.6 + - + +
521B PHE* 3.8 24.7 - - + -
525B PHE* 4.3 11.8 - - + -
565B ILE* 4.8 1.3 - - + -
566B ASN* 4.2 1.6 - - - +
569B LEU* 3.9 31.9 - - + -
572B PHE* 3.9 13.5 - - + +
573B SER* 3.8 22.0 - - - +
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Residues in contact with LYS 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ILE* 5.2 8.3 - - - +
229B VAL* 3.9 11.1 - - + +
459B TYR* 4.4 8.1 - - + +
462B THR* 3.4 3.4 + - - +
463B ILE* 1.3 78.1 - - + +
465B GLY* 1.3 62.7 + - - +
467B GLU* 3.3 10.2 + - - +
468B THR* 2.8 34.1 + - - -
520B GLU* 4.8 0.6 + - - -
566B ASN* 3.4 36.1 - - - +
569B LEU* 5.5 10.6 - - + +
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Residues in contact with GLY 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B TYR* 3.2 42.5 - - - -
460B TYR* 3.3 16.1 - - - -
462B THR* 3.0 10.4 + - - -
464B LYS* 1.3 76.5 - - - +
466B PHE* 1.3 51.3 + - - +
468B THR* 3.2 3.5 + - - -
469B LEU 2.7 29.6 + - - -
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Residues in contact with PHE 466 (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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454B LEU* 4.0 27.6 - - + -
460B TYR 3.3 16.9 + - - +
462B THR 2.9 19.1 + - - +
463B ILE 3.7 4.0 - - - +
465B GLY* 1.3 72.0 - - - +
467B GLU* 1.3 68.6 + - - +
468B THR 3.0 1.3 - - - -
469B LEU* 3.0 10.4 + - + +
470B VAL* 2.9 41.6 + - + +
501B PHE* 6.1 1.1 - + - -
504B PHE* 3.9 27.8 - + - -
505B VAL* 5.9 2.9 - - + -
508B VAL* 4.0 21.8 - - + -
521B PHE* 3.9 16.2 - + + -
525B PHE* 3.8 28.3 - + + -
526B LEU* 4.3 7.6 - - + -
529B ILE* 4.3 11.0 - - + -
562B TRP* 6.0 0.2 - + - -
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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
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229B VAL* 3.7 18.4 - - + +
463B ILE* 3.1 25.4 - - - +
464B LYS* 3.5 8.9 - - - +
466B PHE* 1.3 79.3 - - - +
468B THR* 1.3 57.8 + - - +
470B VAL* 3.4 3.5 + - - +
471B GLU* 2.9 34.1 + - - +
525B PHE* 4.2 6.6 - - + -
562B TRP* 3.5 49.9 + - + -
565B ILE* 4.0 7.1 - - - +
566B ASN* 2.8 41.0 + - - +
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Residues in contact with THR 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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229B VAL* 3.6 22.7 + - - +
230B TYR* 3.7 24.2 - - + -
235B GLU* 4.1 26.2 - - + +
459B TYR* 3.6 16.8 + - + +
460B TYR* 4.7 1.6 - - + -
464B LYS 2.8 16.2 + - - -
465B GLY 3.2 10.1 - - - +
467B GLU* 1.3 74.9 - - - +
469B LEU* 1.3 66.8 + - - +
471B GLU* 3.2 6.9 + - - +
472B LYS* 2.9 23.9 + - + +
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Residues in contact with LEU 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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450B SER* 3.6 32.1 - - - +
453B MET* 3.6 37.2 - - + -
454B LEU* 3.9 25.8 - - + +
460B TYR* 3.7 19.1 - - + -
465B GLY 2.7 18.2 + - - +
466B PHE* 3.0 22.6 + - + +
468B THR* 1.3 74.6 - - - +
470B VAL* 1.3 57.1 + - + +
472B LYS* 4.8 2.0 - - - -
473B GLU* 2.9 37.4 + - + +
474B TRP* 5.3 0.2 - - - -
504B PHE* 4.4 4.5 - - + -
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Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B PHE* 2.9 46.6 + - + +
467B GLU* 3.7 9.2 - - - +
469B LEU* 1.3 70.8 - - + +
471B GLU* 1.3 64.8 + - - +
474B TRP* 3.3 16.5 + - + -
475B ILE* 3.1 35.4 + - + +
501B PHE* 4.1 16.6 - - + -
504B PHE* 4.5 14.4 - - + -
529B ILE* 5.9 1.1 - - + -
541B PHE* 4.1 19.3 - - + -
562B TRP* 4.5 11.0 - - + -
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Residues in contact with GLU 471 (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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226B GLY 6.0 0.2 - - - -
227B TRP* 4.9 14.9 - - - -
229B VAL* 5.6 0.2 - - + -
230B TYR* 3.5 40.7 - - + +
467B GLU 2.9 22.9 + - - +
468B THR 3.2 1.5 + - - +
470B VAL* 1.3 75.9 - - - +
472B LYS* 1.3 57.1 + - - +
475B ILE* 3.2 34.1 - - + +
476B SER* 3.0 30.5 + - - -
540B THR* 4.1 8.3 + - - +
560B SER* 4.8 1.0 + - - -
562B TRP* 2.5 35.0 + - + +
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Residues in contact with LYS 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B TYR* 3.3 27.1 - - + +
235B GLU* 3.7 29.6 - - + -
236B TYR* 4.5 13.9 + - + +
239B GLN* 4.1 2.3 - - - +
291B LEU 4.5 3.8 + - - -
292B SER* 2.7 34.2 + - - +
453B MET* 4.0 12.6 - - - -
460B TYR* 4.1 7.6 - - - -
468B THR* 2.9 16.1 + - - +
469B LEU* 3.8 2.7 - - - +
471B GLU* 1.3 77.0 - - - +
473B GLU* 1.3 87.5 + - + +
474B TRP 3.4 0.6 + - - -
476B SER* 2.5 23.2 + - - +
477B PHE* 3.3 22.3 + - + -
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Residues in contact with GLU 473 (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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292B SER* 3.1 21.3 + - - -
304B ARG* 3.0 38.1 + - - +
446B ALA* 3.8 10.5 - - - +
449B THR* 2.8 22.5 + - - +
450B SER* 4.1 17.7 - - - -
453B MET* 3.7 26.9 - - + +
469B LEU* 2.9 23.4 + - + +
472B LYS* 1.3 106.0 + - + +
474B TRP* 1.3 61.5 + - + +
477B PHE* 3.7 10.7 - - - +
479B HIS 5.3 0.7 + - - -
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Residues in contact with TRP 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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446B ALA* 3.8 9.1 + - + -
447B GLN* 3.5 39.0 - - + -
450B SER* 3.0 28.7 + - - -
469B LEU 4.8 0.4 - - - -
470B VAL* 3.3 24.2 + - + +
473B GLU* 1.3 84.2 - - + +
475B ILE* 1.3 62.3 + - - +
477B PHE 4.4 0.7 - - - -
478B GLY 3.8 0.3 + - - -
479B HIS* 2.9 78.7 + + + +
481B PHE* 3.3 14.5 - + + -
500B ILE* 3.6 7.4 - - + -
501B PHE* 3.6 38.1 - + - -
504B PHE* 3.4 36.6 - + + -
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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