Contacts of the helix formed by residues 471 - 490 (chain B) in PDB entry 2O2C
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 ASP 471 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B ILE 3.3 0.2 + - - -
470B GLY* 1.3 77.0 - - - +
472B HIS* 1.3 65.0 + - - +
473B HIS 3.3 3.3 + - - -
474B LYS* 3.4 32.2 + - - +
475B ILE* 3.3 37.0 + - + +
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Residues in contact with HIS 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B ILE* 3.1 34.2 + - + +
470B GLY* 3.4 1.1 - - - -
471B ASP* 1.3 78.5 - - - +
473B HIS* 1.3 57.6 + - - +
475B ILE* 3.4 8.6 + - - +
476B PHE* 2.9 31.3 + - - +
235C VAL* 2.8 25.3 + - + +
237C GLY* 3.7 20.7 - - - +
240C ILE* 4.0 11.2 - - + -
268C THR* 3.6 26.5 - - + +
269C ASN* 3.2 26.0 + - - -
272C SER* 2.8 29.7 + - - -
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Residues in contact with HIS 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B TYR 5.7 0.2 + - - -
462B ALA* 3.0 31.1 + - - +
463B ILE 3.1 23.0 + - - -
464B GLN* 4.4 0.6 + - - -
465B SER* 3.6 38.0 + - - -
467B ASN 5.6 2.0 - - - +
468B LYS* 6.4 0.2 - - - -
469B ILE 4.7 0.6 + - - -
470B GLY 5.3 0.6 + - - -
471B ASP 3.4 1.2 - - - -
472B HIS* 1.3 77.9 - - - +
474B LYS* 1.3 58.2 + - - +
476B PHE* 3.4 24.6 + + - +
477B MET* 2.8 50.3 + - + +
236C ASP* 4.7 5.4 - - - -
237C GLY 5.1 1.8 - - - +
601C PHE* 4.1 5.8 - - + -
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Residues in contact with LYS 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ASP* 3.4 38.2 + - + +
473B HIS* 1.3 74.6 - - - +
475B ILE* 1.3 62.2 + - + +
478B SER* 3.0 26.3 + - - -
578C LEU* 3.6 26.7 + - + +
579C PRO* 5.9 1.8 - - - +
581C LEU* 3.2 48.3 + - + +
582C ARG* 5.4 5.1 - - - +
601C PHE* 4.6 10.7 - - + -
606C HIS* 6.2 4.7 - - + -
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Residues in contact with ILE 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ASP* 3.3 27.7 + - + +
472B HIS 3.7 6.1 - - - +
474B LYS* 1.3 76.9 - - + +
476B PHE* 1.3 59.3 - - - +
478B SER* 2.6 21.8 + - - -
479B ASN* 3.0 12.9 + - - -
235C VAL* 3.8 20.9 - - + -
264C GLN* 3.5 33.9 - - + +
265C GLU* 6.3 0.2 - - + -
268C THR* 3.9 27.1 - - + +
578C LEU* 3.9 26.5 - - + -
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Residues in contact with PHE 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B TYR* 3.2 52.7 - + + -
395B ASP* 3.6 3.6 - - - -
437B GLY 3.4 26.2 - - - -
438B THR* 3.8 4.3 - - + -
472B HIS 2.9 18.7 + - - +
473B HIS* 3.4 29.2 - + - +
475B ILE* 1.3 74.9 - - - +
477B MET* 1.3 67.8 + - - +
479B ASN* 3.2 22.7 + - - +
480B PHE* 3.6 4.2 + - - +
234C ASN* 3.5 9.4 - - - -
235C VAL* 3.7 27.1 - - + +
236C ASP* 3.7 30.3 - - + -
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Residues in contact with MET 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B TYR* 4.8 3.4 - - - +
461B GLY 4.4 0.2 - - - -
462B ALA 3.2 35.0 - - - +
473B HIS* 2.8 41.7 + - + +
474B LYS 4.2 1.6 - - - +
476B PHE* 1.3 87.2 - - + +
478B SER* 1.3 65.1 + - - +
479B ASN 3.1 2.2 - - - -
480B PHE* 3.2 49.4 + - + +
481B PHE* 3.0 32.3 + - + -
530B LEU* 4.1 7.9 - - + -
581C LEU* 4.2 2.0 - - + -
601C PHE* 3.7 24.7 - - + -
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Residues in contact with SER 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 LYS 3.0 15.9 + - - -
475B ILE* 2.6 22.0 + - - -
477B MET* 1.3 77.5 - - - +
479B ASN* 1.3 56.9 + - - +
481B PHE* 3.8 0.5 + - - -
482B ALA* 3.1 29.1 + - - +
264C GLN* 4.6 5.0 + - - -
574C ALA* 3.5 32.6 + - - +
577C ILE* 4.2 9.0 - - - +
578C LEU* 4.0 21.3 - - - +
581C LEU* 4.0 6.1 - - - -
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Residues in contact with ASN 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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394B TYR* 4.1 2.5 - - + -
438B THR* 3.8 15.8 - - + +
441B GLN* 3.2 34.6 - - - +
475B ILE 3.0 26.3 + - - -
476B PHE* 3.2 9.2 + - - +
477B MET 3.1 0.2 - - - -
478B SER* 1.3 78.3 + - - +
480B PHE* 1.3 59.4 + - - +
482B ALA* 4.3 1.3 - - - -
483B GLN* 3.0 38.4 + - - +
235C VAL* 4.5 4.0 - - - +
264C GLN* 4.5 11.4 + - - +
265C GLU* 4.7 6.1 + - - +
570C GLY 4.9 3.3 - - - +
571C LYS* 5.4 3.1 - - - +
574C ALA* 3.9 17.9 - - - +
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Residues in contact with PHE 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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394B TYR* 3.6 40.3 - + + -
459B PHE* 3.6 24.4 - - + -
460B ILE 3.5 20.9 - - - -
461B GLY* 3.5 16.2 - - - -
476B PHE 3.6 1.4 + - - -
477B MET* 3.2 35.1 + - + +
479B ASN* 1.3 80.4 - - - +
481B PHE* 1.3 81.2 + + - +
483B GLN 4.1 1.6 + - - -
484B THR* 3.8 18.9 + - - +
528B THR* 3.6 33.8 + - + +
529B LEU 3.8 3.4 - - - -
530B LEU* 3.9 13.7 - - + -
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Residues in contact with PHE 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B MET* 3.0 30.8 + - + +
478B SER 4.3 1.1 - - - +
480B PHE* 1.3 102.4 - + - +
482B ALA* 1.3 62.3 + - - +
484B THR* 3.0 20.2 + - - -
485B GLU* 3.4 11.6 + - - +
528B THR* 5.7 0.2 - - + -
530B LEU* 4.6 7.0 - - + -
577C ILE* 4.1 18.4 - - + -
581C LEU* 4.2 14.8 - - + -
594C THR* 4.4 8.8 - - + +
597C LEU* 3.7 39.7 - - + -
598C ILE* 4.1 17.5 - - + -
601C PHE* 3.7 45.5 - + + -
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Residues in contact with ALA 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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478B SER 3.1 20.7 + - - +
479B ASN 3.3 3.6 + - - +
481B PHE* 1.3 75.6 - - - +
483B GLN* 1.3 60.2 + - - +
485B GLU* 3.3 4.1 + - - +
486B ALA* 2.8 30.8 + - - +
570C GLY 3.8 9.4 - - - +
573C LEU* 3.7 12.4 - - + +
574C ALA* 3.5 28.5 - - + +
577C ILE* 3.9 8.0 - - + +
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Residues in contact with GLN 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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394B TYR* 3.7 4.0 - - - +
441B GLN* 3.5 35.5 + - - +
445B TYR* 3.2 16.5 - - + -
449B HIS* 2.9 30.5 + - - -
459B PHE* 3.6 21.8 - - + -
479B ASN* 3.0 22.0 + - - +
480B PHE 4.6 0.2 - - - +
482B ALA* 1.3 75.0 - - - +
484B THR* 1.3 58.8 + - - +
486B ALA* 3.4 4.0 + - - +
487B LEU* 3.0 36.0 + - - +
567C VAL* 5.2 3.4 + - - +
570C GLY* 3.4 28.8 + - - -
571C LYS* 6.0 0.8 - - - +
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Residues in contact with THR 484 (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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105B LYS* 3.4 32.9 + - - +
459B PHE* 3.6 32.8 - - + -
480B PHE 3.8 8.0 + - - +
481B PHE* 3.0 19.6 + - - -
483B GLN* 1.3 73.0 - - - +
485B GLU* 1.3 63.8 + - - +
487B LEU* 3.5 6.6 + - - +
488B MET* 3.3 15.9 + - - +
524B ARG 5.1 0.3 - - - +
526B SER* 3.4 24.0 + - - +
528B THR* 3.5 18.8 + - - +
597C LEU* 5.0 2.3 - - - +
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Residues in contact with GLU 485 (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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105B LYS* 4.1 4.7 - - - +
481B PHE 3.4 9.6 + - - +
482B ALA 3.3 6.2 + - - +
483B GLN 3.3 0.2 - - - -
484B THR* 1.3 81.5 + - - +
486B ALA* 1.3 57.2 + - - +
488B MET* 3.2 4.0 + - - +
489B ILE* 2.9 48.5 + - + +
573C LEU* 3.8 25.8 - - + +
577C ILE* 3.5 23.4 - - - +
590C HIS* 2.8 35.9 + - - +
591C ASP* 3.9 8.6 + - - +
594C THR* 3.7 21.8 - - + +
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Residues in contact with ALA 486 (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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449B HIS* 3.8 19.3 + - + -
482B ALA 2.8 17.5 + - - +
483B GLN* 3.5 7.6 - - - +
484B THR 3.3 0.2 - - - -
485B GLU* 1.3 77.2 - - - +
487B LEU* 1.3 60.4 - - - +
489B ILE* 4.5 0.9 - - - -
490B GLY* 3.1 21.1 + - - -
520B PHE* 5.5 0.3 - - - +
522B GLY* 4.7 0.5 - - - -
569C LEU* 3.6 27.7 - - + +
570C GLY* 4.3 9.6 - - - -
573C LEU* 3.8 12.1 - - + +
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Residues in contact with LEU 487 (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 TYR* 6.4 0.7 - - + -
448B ILE* 3.7 24.7 - - + +
449B HIS* 3.6 25.6 - - + +
457B CYS* 4.4 10.5 - - - -
459B PHE* 3.9 28.9 - - + -
483B GLN* 3.0 20.6 + - + +
484B THR 3.7 4.9 - - - +
485B GLU 3.4 0.2 - - - -
486B ALA* 1.3 74.8 - - - +
488B MET* 1.3 56.8 + - - +
522B GLY* 3.3 7.8 - - - -
523B GLY 3.2 6.2 + - - -
524B ARG* 2.9 54.4 + - + +
525B PRO 4.3 7.0 - - - +
526B SER* 4.3 13.7 - - - +
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Residues in contact with MET 488 (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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71B ILE* 3.7 24.0 - - + -
72B LYS* 4.4 16.0 + - + +
75B PHE* 3.1 34.8 - - + -
105B LYS* 3.8 20.0 - - + -
484B THR 3.3 12.2 + - - +
485B GLU 3.2 3.6 + - - +
487B LEU* 1.3 79.4 - - - +
489B ILE* 1.3 78.3 + - + +
523B GLY* 2.9 22.8 + - - +
524B ARG 3.7 8.7 + - - +
591C ASP* 3.3 41.3 - - + +
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Residues in contact with ILE 489 (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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72B LYS* 3.2 39.2 + - + +
485B GLU* 2.9 42.4 + - + +
486B ALA* 4.5 1.1 - - - -
488B MET* 1.3 93.9 - - + +
490B GLY* 1.3 73.2 + - - +
491B LYS 3.9 0.2 + - - -
495B GLU* 5.6 1.6 - - - +
521B ILE 4.9 2.4 - - - +
522B GLY* 4.4 2.6 - - - -
569C LEU* 5.6 1.1 - - + -
573C LEU* 3.9 28.3 - - + -
591C ASP* 4.7 4.3 - - + +
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Residues in contact with GLY 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B ALA 3.1 19.1 + - - -
488B MET 3.6 1.2 - - - -
489B ILE* 1.3 92.9 - - - +
491B LYS* 1.3 62.9 + - - +
495B GLU* 4.5 5.1 - - - +
520B PHE* 3.5 14.4 - - - -
522B GLY* 3.8 11.4 - - - -
569C LEU* 3.5 17.8 - - - +
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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
------------------------------------------------------------
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