Contacts of the helix formed by residues 462 - 473 (chain B) in PDB entry 2C0O
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 PRO 462 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A GLU* 5.0 9.2 - - + +
503A GLU* 3.5 19.5 - - - +
334B LEU* 3.6 33.9 - - + -
338B ILE* 4.9 0.9 - - + -
460B ASN 3.5 8.3 - - - +
461B CYS* 1.3 92.5 - - - +
463B GLU* 1.3 59.8 + - - +
464B GLU* 4.3 8.1 - - - +
465B LEU* 3.2 20.3 + - + +
466B TYR* 2.9 24.6 + - - +
493B PHE* 4.4 15.3 - - + -
494B TYR* 5.4 1.1 - - + +
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Residues in contact with GLU 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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155A THR* 5.1 1.0 + - - -
178A LYS* 3.3 31.0 - - + +
180A ARG* 2.7 29.9 + - - -
501A PTR 4.7 13.0 - - + +
502A GLU 6.1 1.1 - - - +
503A GLU* 4.6 14.2 + - + +
457B ARG* 3.0 38.7 + - - +
461B CYS 3.5 1.6 + - - -
462B PRO* 1.3 70.9 - - - +
464B GLU* 1.3 69.7 + - + +
466B TYR* 3.1 16.6 + - - +
467B ASN* 3.0 22.7 + - - +
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Residues in contact with GLU 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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497A THR* 3.0 34.8 - - + +
498A GLU* 3.1 7.9 - - - +
500A GLN* 3.5 23.6 - - + +
501A PTR 2.9 27.5 + - + +
1507A CA 2.6 29.7 - - - -
462B PRO* 4.3 5.5 - - - +
463B GLU* 1.3 80.1 + - + +
465B LEU* 1.3 64.8 + - - +
466B TYR 3.2 0.2 - - - -
467B ASN* 3.4 14.1 + - + +
468B ILE* 3.3 22.9 + - - +
493B PHE* 4.3 6.2 - - + -
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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
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334B LEU* 4.5 0.2 - - + -
338B ILE* 4.3 21.3 - - + -
341B SER* 5.8 0.2 - - - +
426B LEU* 4.2 20.4 - - + -
430B VAL* 3.6 31.2 - - + -
461B CYS* 3.9 6.3 - - - -
462B PRO* 3.2 32.0 + - + +
464B GLU* 1.3 80.3 - - - +
466B TYR* 1.3 61.6 + - - +
468B ILE* 3.2 18.2 + - + +
469B MET* 3.4 21.8 + - + +
490B LEU* 4.1 26.5 - - + -
493B PHE* 3.9 12.2 - - + -
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Residues in contact with TYR 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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427B MET* 4.5 5.2 - - + -
454B ARG* 4.7 2.3 + - - +
455B MET 2.6 31.1 + - - -
456B PRO* 3.6 5.7 - - - +
457B ARG* 3.3 52.7 - - + -
458B PRO* 4.6 3.6 - - + -
461B CYS* 4.1 2.7 - - - -
462B PRO 2.9 9.7 + - - +
463B GLU* 3.1 16.4 - - - +
465B LEU* 1.3 77.4 - - - +
467B ASN* 1.3 60.7 + - - +
469B MET* 3.3 20.9 + - - +
470B MET* 3.0 49.2 + - + +
473B TRP* 4.8 4.3 - + - -
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Residues in contact with ASN 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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154A THR* 3.3 51.9 - - - +
463B GLU 3.0 12.2 + - - +
464B GLU* 3.4 12.1 + - + +
465B LEU 3.1 1.0 - - - -
466B TYR* 1.3 77.1 - - - +
468B ILE* 1.3 55.8 + - + +
470B MET* 3.9 13.4 - - - +
471B ARG* 2.8 53.1 + - - +
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Residues in contact with ILE 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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497A THR* 5.6 2.2 - - + -
426B LEU* 4.0 17.7 - - + -
464B GLU 3.3 16.8 - - - +
465B LEU* 3.2 18.1 + - + +
467B ASN* 1.3 74.6 - - + +
469B MET* 1.3 62.0 + - - +
471B ARG* 3.1 12.6 + - + +
472B CYS* 2.8 34.5 + - - -
481B PRO* 5.7 1.6 - - + -
485B TYR* 5.6 4.5 - - + -
486B ILE* 4.3 28.0 - - + -
489B VAL* 3.8 33.4 - - + -
490B LEU* 4.9 9.2 - - + -
493B PHE* 5.2 2.5 - - + -
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Residues in contact with MET 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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423B GLY* 4.2 4.5 - - - +
426B LEU* 3.8 21.8 - - + +
427B MET* 3.6 36.6 - - + -
430B VAL* 3.5 33.0 - - + -
461B CYS* 3.8 19.3 - - - -
465B LEU* 3.4 23.1 - - + +
466B TYR* 3.5 13.2 - - + +
467B ASN 3.3 0.2 - - - -
468B ILE* 1.3 76.0 - - - +
470B MET* 1.3 57.3 + - - +
472B CYS* 2.9 11.2 + - - +
473B TRP* 2.9 53.2 + - + -
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Residues in contact with MET 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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154A THR 5.8 3.1 - - - +
454B ARG* 3.9 30.5 - - + +
466B TYR* 3.0 52.4 + - + +
467B ASN* 3.6 19.5 - - - +
469B MET* 1.3 75.2 - - - +
471B ARG* 1.3 62.0 + - + +
473B TRP* 3.2 17.3 + - + +
474B LYS* 3.4 21.4 + - - +
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Residues in contact with ARG 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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484A GLU* 5.2 8.9 + - - -
467B ASN* 2.8 42.3 + - - +
468B ILE* 3.1 13.1 + - - +
470B MET* 1.3 73.6 - - + +
472B CYS* 1.3 60.6 + - - +
474B LYS* 3.4 34.2 + - + +
479B GLU 4.1 5.3 + - - +
480B ARG* 3.8 4.0 - - - -
481B PRO* 3.6 44.8 - - + +
485B TYR* 3.3 37.2 + - - -
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Residues in contact with CYS 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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419B VAL* 3.5 35.2 - - - +
420B TRP* 3.8 7.1 - - - -
422B PHE* 4.4 4.0 - - - -
423B GLY* 3.8 22.2 - - - -
468B ILE* 2.8 27.4 + - - -
469B MET 3.3 6.7 - - - +
471B ARG* 1.3 72.7 - - - +
473B TRP* 1.3 62.4 + - + +
474B LYS 3.1 4.7 + - - -
480B ARG* 3.3 24.1 + - - -
481B PRO* 4.3 1.6 - - - -
486B ILE* 3.7 29.2 - - - -
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Residues in contact with TRP 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B TRP* 3.2 44.1 + + + -
423B GLY 3.1 29.4 - - - -
424B ILE* 3.1 31.4 - - + +
427B MET* 3.7 27.1 - - + -
437B TYR* 5.7 1.8 - - - -
454B ARG* 2.5 68.8 + - + +
455B MET* 4.2 28.9 - - + -
466B TYR* 4.8 4.5 - + - -
469B MET* 2.9 39.9 + - + +
470B MET* 3.2 12.4 + - - +
472B CYS* 1.3 79.8 - - + +
474B LYS* 1.3 58.1 + - - +
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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