Contacts of the helix formed by residues 471 - 493 (chain C) in PDB entry 2W4T
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 SER 471 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C PHE* 3.8 20.0 - - - -
470C ASN* 1.3 74.3 - - - +
472C PHE* 1.3 67.3 + - - +
473C GLU* 3.2 6.0 + - - +
474C GLN* 3.0 15.6 + - - +
475C LEU 3.1 9.4 + - - -
589C TYR* 4.0 7.2 - - - -
590C SER 3.7 13.7 - - - -
592C THR 5.5 4.7 - - - -
594C TRP* 3.9 3.6 - - - -
597C LYS* 3.3 15.4 + - - -
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Residues in contact with PHE 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LEU* 5.7 1.3 - - + -
471C SER* 1.3 76.8 - - - +
473C GLU* 1.3 65.8 + - - +
475C LEU* 3.3 1.4 + - - +
476C CYS* 2.8 55.5 + - - -
530C LEU* 4.1 4.0 - - + -
594C TRP* 2.3 85.2 - + + -
597C LYS* 2.9 47.1 - - + -
598C ASN* 3.8 10.8 - - + -
645C ILE* 3.0 35.9 - - + -
646C SER* 4.0 4.9 - - - -
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Residues in contact with GLU 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LEU* 6.2 0.2 - - - +
268C GLU* 3.6 25.1 - - - +
269C LYS* 4.2 1.5 + - - +
270C SER* 2.9 32.5 + - - +
471C SER* 3.1 6.0 + - - +
472C PHE* 1.3 79.5 - - - +
474C GLN* 1.3 55.6 + - - +
476C CYS* 3.3 6.1 - - - +
477C ILE* 2.7 34.2 + - + +
597C LYS* 2.2 57.8 - - - +
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Residues in contact with GLN 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C PHE* 3.8 8.3 - - - -
465C GLU* 2.6 36.8 + - + +
466C ILE* 4.7 0.2 - - - +
470C ASN* 3.8 20.9 - - + +
471C SER 3.0 11.6 + - - +
473C GLU* 1.3 76.1 - - - +
475C LEU* 1.3 67.2 + - - +
476C CYS 3.0 1.8 - - - -
477C ILE* 2.9 14.6 + - + +
478C ASN* 2.7 39.2 + - - +
587C VAL* 4.0 5.3 - - - +
589C TYR* 2.4 39.6 + - + -
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Residues in contact with LEU 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C SER 3.1 3.6 + - - -
472C PHE 3.3 0.6 + - - +
474C GLN* 1.3 79.3 + - - +
476C CYS* 1.3 54.1 + - - +
478C ASN* 3.8 2.4 - - + +
479C TYR* 2.7 38.3 + - + +
523C ILE* 5.7 5.6 - - + +
529C ILE* 4.3 18.2 - - + -
578C PHE* 3.8 24.2 - - + -
580C LEU* 4.0 16.4 - - + -
589C TYR* 2.9 47.3 - - + +
594C TRP* 3.5 37.7 - - + -
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Residues in contact with CYS 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C TYR* 5.3 0.3 + - - -
266C LEU* 3.5 29.5 - - + +
472C PHE* 2.8 65.9 + - - -
473C GLU* 3.3 10.8 - - - +
474C GLN 3.0 0.6 - - - -
475C LEU* 1.3 75.2 - - - +
477C ILE* 1.3 56.3 + - + +
479C TYR* 3.9 6.0 - - - +
480C THR* 2.5 34.2 + - - -
530C LEU* 6.0 4.3 - - - -
594C TRP* 5.0 0.2 - - - -
645C ILE* 4.6 1.3 - - - -
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Residues in contact with ILE 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LEU* 5.8 0.9 - - + -
462C ALA* 4.4 15.4 - - + +
463C GLY 2.9 30.5 - - - +
464C PHE* 3.7 8.1 - - - -
465C GLU* 3.9 11.2 - - + +
473C GLU* 2.7 24.2 - - + +
474C GLN* 2.9 20.6 - - + +
476C CYS* 1.3 75.0 - - + +
478C ASN* 1.3 68.2 + - + +
480C THR* 2.9 10.7 - - - -
481C ASN* 2.7 49.8 + - - +
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Residues in contact with ASN 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C PHE* 2.5 26.7 - - - +
474C GLN* 2.7 27.3 + - - +
475C LEU* 3.8 3.4 - - + +
477C ILE* 1.3 78.5 - - - +
479C TYR* 1.3 68.6 + - - +
480C THR 3.0 1.5 + - - -
481C ASN* 3.1 1.5 + - - -
482C GLU* 2.9 28.6 + - - +
580C LEU* 5.7 1.0 - - - +
582C HIS* 2.0 62.1 + - - +
587C VAL* 4.2 1.6 - - - +
589C TYR* 3.1 15.9 + - - +
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Residues in contact with TYR 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C LEU* 2.7 25.4 + - + +
476C CYS* 3.9 6.3 - - - +
478C ASN* 1.3 74.7 - - - +
480C THR* 1.3 63.7 + - - +
482C GLU* 3.4 9.9 - - + +
483C ARG* 3.3 30.7 + - + +
520C ILE* 3.4 16.0 + - + +
523C ILE* 2.3 61.7 - - + -
524C GLU* 2.3 39.7 - - + +
530C LEU* 5.5 9.4 - - + -
650C ARG* 5.3 8.5 - - + -
653C LEU* 4.3 20.9 - - + -
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Residues in contact with THR 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C TYR* 3.8 18.4 + - + -
461C ILE* 4.2 21.5 - - + -
462C ALA 5.2 2.9 - - - +
476C CYS 2.5 22.1 + - - -
477C ILE* 2.9 15.7 + - - +
478C ASN 3.0 0.4 - - - -
479C TYR* 1.3 77.5 - - - +
481C ASN* 1.3 57.3 + - - +
483C ARG* 3.0 44.4 + - - +
484C LEU* 3.4 4.2 + - - +
653C LEU* 3.7 26.9 - - + +
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Residues in contact with ASN 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLY 5.2 0.6 + - - -
182C LYS* 3.7 1.0 - - - +
461C ILE* 3.3 15.5 + - - +
462C ALA 2.4 30.1 + - - +
463C GLY* 2.9 23.7 - - - -
464C PHE 3.1 8.2 + - - -
477C ILE* 2.7 30.8 + - - +
478C ASN 3.1 5.6 + - - +
480C THR* 1.3 70.3 - - - +
482C GLU* 1.3 67.2 + - - +
484C LEU* 3.4 10.4 + - - +
485C GLN* 3.3 17.3 + - - +
582C HIS* 4.1 1.1 - - + -
583C TYR* 3.5 23.9 - - + +
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Residues in contact with GLU 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C ASN* 2.9 28.5 + - - +
479C TYR* 3.4 12.6 - - + +
481C ASN* 1.3 71.9 - - - +
483C ARG* 0.9 96.6 - - - +
484C LEU 2.7 2.4 + - - -
485C GLN* 2.8 13.9 + - - +
486C GLN* 3.0 9.9 + - - +
516C LEU* 3.4 9.0 - - - +
519C CYS* 3.2 26.2 - - + +
520C ILE* 4.4 17.1 - - + +
582C HIS* 3.0 17.0 - - - +
583C TYR* 1.6 59.2 + - - -
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Residues in contact with ARG 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C LEU* 6.0 2.6 - - - +
461C ILE* 4.4 16.6 - - - +
479C TYR* 3.3 17.5 - - + +
480C THR* 3.0 31.6 + - - +
482C GLU* 0.9 106.4 - - - +
484C LEU* 1.3 71.4 + - - +
486C GLN* 3.1 17.2 + - - +
487C PHE* 3.3 6.3 + - - +
520C ILE* 4.4 15.9 - - + -
653C LEU* 3.3 52.9 + - - +
654C ASN* 6.1 0.4 - - - +
656C LEU* 5.3 5.0 - - - +
657C MET* 4.3 42.1 - - - +
660C LEU* 5.3 8.1 - - - +
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Residues in contact with LEU 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C LEU* 4.1 24.5 - - + -
175C THR* 2.9 39.9 - - + -
461C ILE* 3.5 33.7 - - + +
480C THR 3.4 7.0 + - - +
481C ASN* 3.4 12.5 + - - +
482C GLU 2.7 4.4 - - - -
483C ARG* 1.3 87.1 - - - +
485C GLN* 1.3 63.0 + - + +
487C PHE* 2.6 35.8 + - - +
488C PHE* 3.3 8.4 + - + +
667C PHE* 4.9 2.2 - - + -
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Residues in contact with GLN 485 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C ASN 3.3 8.4 + - - +
482C GLU* 2.8 14.1 + - - +
484C LEU* 1.3 83.2 - - + +
486C GLN* 1.3 54.9 + - - +
488C PHE* 2.8 28.3 + - + +
489C ASN* 2.4 25.3 + - - +
514C MET* 3.8 14.1 - - - +
516C LEU* 5.3 4.9 - - + -
583C TYR* 4.7 22.4 - - + -
693C CYS 3.5 19.9 + - - +
694C ASN* 3.3 28.5 + - - +
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Residues in contact with GLN 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C GLU 3.0 5.7 + - - +
483C ARG* 3.2 11.6 - - - +
485C GLN* 1.3 79.9 - - - +
487C PHE* 1.3 65.9 + - - +
489C ASN* 3.1 15.7 + - + +
490C HIS* 2.9 31.9 + - - +
494C ILE* 5.9 2.2 - - - +
514C MET 5.8 0.2 + - - -
515C ASP* 4.1 17.1 + - - +
516C LEU* 4.2 22.5 - - + +
517C GLN* 4.3 10.9 - - - +
520C ILE* 4.1 18.8 - - + -
657C MET* 4.8 10.7 - - - +
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Residues in contact with PHE 487 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C LEU* 3.9 26.0 - - + -
483C ARG* 3.3 5.5 + - - +
484C LEU* 2.6 28.4 + - + +
486C GLN* 1.3 77.9 + - - +
488C PHE* 1.3 64.2 + - - -
490C HIS* 3.0 10.4 + + + +
491C HIS* 2.9 38.8 + - + +
495C LEU* 6.2 0.4 - - + -
657C MET* 4.5 27.1 - - + -
660C LEU* 4.4 16.6 - - + -
661C TYR* 4.1 41.5 - + + -
663C THR* 4.8 0.9 - - - -
665C PRO* 4.4 24.5 - - + -
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Residues in contact with PHE 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE* 3.7 41.5 - + + -
484C LEU* 3.3 7.9 + - + +
485C GLN* 2.8 16.5 + - - +
487C PHE* 1.3 86.0 - - + +
489C ASN* 1.3 57.4 + - - +
491C HIS* 3.9 3.5 - + - -
492C MET* 2.4 95.5 + - + +
667C PHE* 4.1 33.4 - + + -
694C ASN 4.3 19.3 - - - -
695C GLY 4.5 3.8 - - - -
696C VAL* 6.4 0.2 - - - -
699C GLY* 4.8 3.4 - - - -
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Residues in contact with ASN 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C GLN* 2.4 34.5 + - - +
486C GLN* 3.3 20.2 - - + +
488C PHE* 1.3 77.0 - - - +
490C HIS* 1.3 62.5 + - - +
492C MET* 4.0 10.6 - - - +
493C PHE* 3.0 23.3 + - - +
494C ILE* 3.4 10.1 + - + +
514C MET* 2.3 69.9 - - - +
515C ASP* 4.8 1.4 + - - -
516C LEU* 5.3 4.9 + - - +
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Residues in contact with HIS 490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C GLN* 2.9 26.4 + - - +
487C PHE* 3.0 13.9 + + + +
489C ASN* 1.3 76.7 - - - +
491C HIS* 1.3 58.7 + - + +
492C MET 3.2 0.9 + - - -
494C ILE* 2.3 59.2 + - + +
495C LEU* 2.6 58.6 + - + +
657C MET* 6.2 2.9 - - + +
661C TYR* 4.1 20.6 + + - -
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Residues in contact with HIS 491 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE* 4.5 17.8 - + - -
487C PHE* 2.9 27.5 + + + +
488C PHE* 4.4 4.3 - + - +
490C HIS* 1.3 79.3 - - + +
492C MET* 1.3 60.6 + - + +
495C LEU* 2.7 39.9 - - + +
496C GLU* 3.9 15.3 + - - +
663C THR 4.7 1.8 + - - -
664C HIS* 6.5 0.2 - + - -
665C PRO* 3.0 52.4 + - + +
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Residues in contact with MET 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE* 5.2 7.0 - - + -
488C PHE* 2.4 80.3 + - + +
489C ASN* 4.0 7.9 - - - +
490C HIS 3.1 0.2 - - - -
491C HIS* 1.3 84.4 - - + +
493C PHE* 1.3 100.5 + - + +
496C GLU* 2.6 27.3 - - - +
514C MET* 4.7 1.3 - - + -
695C GLY 4.4 3.6 - - - +
699C GLY* 3.3 24.0 - - - +
702C ILE* 4.2 16.7 - - + +
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Residues in contact with PHE 493 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C ASN* 3.0 16.4 + - - +
492C MET* 1.3 119.5 - - + +
494C ILE* 1.3 72.8 + - + +
495C LEU 3.1 1.4 + - - -
496C GLU* 3.6 9.3 + - - +
497C GLN* 3.7 13.7 + - - +
509C PHE* 5.5 5.3 - - + -
510C ILE* 5.6 1.6 - - - +
512C PHE* 2.5 78.2 - + + -
514C MET* 4.1 14.4 - - + -
698C GLU* 3.1 35.2 - - + -
699C GLY* 4.2 0.2 - - - -
702C ILE* 3.3 13.7 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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