Contacts of the helix formed by residues 471 - 490 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B THR* 5.6 0.2 - - - -
470C GLY* 1.3 76.8 - - - +
472C HIS* 1.3 65.9 + - - +
473C HIS 3.4 3.0 + - - -
474C LYS* 3.4 35.3 + - - +
475C ILE* 3.2 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 472 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 2.8 25.8 + - - +
237B GLY* 3.7 20.6 - - - +
240B ILE* 4.0 9.9 - - + -
268B THR* 3.6 27.6 - - + +
269B ASN* 3.2 25.8 - - - -
272B SER* 2.8 29.2 + - - -
467C ASN 5.9 0.2 - - - +
469C ILE* 3.0 35.2 + - + +
470C GLY* 3.4 1.5 - - - -
471C ASP* 1.3 79.3 - - - +
473C HIS* 1.3 58.0 + - - +
475C ILE* 3.4 8.2 + - - +
476C PHE* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 473 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ASP* 5.0 4.5 - - - -
237B GLY 5.1 2.6 - - - +
601B PHE* 4.0 6.6 - + - -
462C ALA* 3.1 24.0 + - - +
463C ILE 2.8 32.2 + - - -
464C GLN* 3.9 2.6 - - - -
465C SER* 3.6 36.2 + - - -
467C ASN 5.6 2.2 + - - +
469C ILE 4.6 0.8 + - - -
470C GLY 5.2 1.0 + - - -
471C ASP 3.4 0.6 - - - -
472C HIS* 1.3 78.0 - - - +
474C LYS* 1.3 57.6 + - - +
476C PHE* 3.4 20.7 + + - +
477C MET* 2.9 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 474 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B LEU* 3.5 25.7 + - + +
579B PRO* 6.2 0.6 - - - +
581B LEU* 3.3 44.1 + - + +
582B ARG* 5.4 12.3 - - - +
601B PHE* 4.9 7.4 - - + -
471C ASP* 3.4 44.7 + - + +
473C HIS* 1.3 74.2 - - - +
475C ILE* 1.3 64.8 + - + +
477C MET* 4.7 0.9 - - - -
478C SER* 3.0 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 475 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 3.8 20.0 - - + -
264B GLN* 3.4 34.1 - - + +
265B GLU* 6.3 0.2 - - + -
268B THR* 3.8 29.4 - - + +
578B LEU* 3.7 25.8 - - + -
471C ASP* 3.2 31.7 + - + +
472C HIS 3.7 3.6 - - - +
474C LYS* 1.3 74.8 - - + +
476C PHE* 1.3 59.4 + - - +
478C SER* 2.7 22.1 + - - -
479C ASN* 2.9 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 476 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ASN* 3.4 19.3 - - - -
235B VAL* 3.7 18.8 - - + +
236B ASP* 3.6 33.4 - - + -
394C TYR* 3.2 49.4 - + + -
395C ASP* 3.7 1.8 - - - -
437C GLY 3.4 14.8 - - - -
438C THR* 3.6 16.6 - - + +
472C HIS 2.9 17.9 + - - +
473C HIS* 3.4 26.7 - + - +
475C ILE* 1.3 77.2 - - - +
477C MET* 1.3 68.1 + - - +
479C ASN* 3.2 22.2 + - - +
480C PHE* 3.6 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 477 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B LEU* 4.0 4.5 - - + -
601B PHE* 3.7 33.4 - - + -
394C TYR* 4.8 4.5 - - - +
461C GLY 4.4 0.2 - - - -
462C ALA 3.2 34.3 - - - +
473C HIS* 2.9 37.4 + - + +
474C LYS 4.3 2.0 - - - +
476C PHE* 1.3 83.2 - - + +
478C SER* 1.3 64.0 + - - +
479C ASN 3.1 2.0 - - - -
480C PHE* 3.2 45.2 + - + +
481C PHE* 3.1 27.7 + - + -
530C LEU* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 478 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B GLN* 4.6 4.9 + - - -
574B ALA* 3.5 31.4 + - - +
577B ILE* 4.2 9.1 - - - +
578B LEU* 3.9 20.8 - - - +
581B LEU* 3.8 7.4 - - - +
474C LYS 3.0 15.7 + - - -
475C ILE* 2.7 20.4 + - - -
477C MET* 1.3 77.2 - - - +
479C ASN* 1.3 60.6 + - - +
482C ALA* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 479 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 4.7 4.2 - - - +
264B GLN* 4.4 11.7 + - - +
265B GLU* 4.6 6.0 + - - +
570B GLY 5.0 2.3 - - - +
571B LYS* 5.5 4.0 - - - +
574B ALA* 4.0 15.9 - - - +
394C TYR* 4.2 2.9 - - + -
438C THR* 3.8 15.6 - - + +
441C GLN* 3.0 35.9 + - - +
475C ILE 2.9 27.1 + - - -
476C PHE* 3.2 9.0 + - - +
478C SER* 1.3 81.2 + - - +
480C PHE* 1.3 58.3 + - - +
482C ALA* 4.3 1.3 - - - -
483C GLN* 2.9 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 480 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C TYR* 3.6 38.3 - + + -
459C PHE* 3.6 23.0 - + + -
460C ILE 3.5 22.0 - - - -
461C GLY* 3.5 15.5 - - - -
476C PHE 3.6 1.8 + - - -
477C MET* 3.2 37.2 + - + +
479C ASN* 1.3 80.8 - - - +
481C PHE* 1.3 78.3 + + - +
483C GLN 4.0 3.3 + - - -
484C THR* 3.9 17.7 + - - +
528C THR* 3.6 32.3 - - + -
529C LEU 3.8 5.4 - - - -
530C LEU* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 481 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B ILE* 4.1 19.3 - - + -
581B LEU* 4.2 13.0 - - + -
594B THR* 4.5 7.7 - - + +
597B LEU* 3.7 44.4 - - + +
598B ILE* 4.1 18.2 - - + -
601B PHE* 3.7 44.9 - + + -
477C MET* 3.1 34.3 + - + +
478C SER 4.4 0.7 - - - +
480C PHE* 1.3 100.7 - + - +
482C ALA* 1.3 62.4 + - - +
484C THR* 3.1 20.4 + - - -
485C GLU* 3.3 12.0 + - - +
528C THR* 5.6 0.2 - - + -
530C LEU* 4.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 482 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B GLY 3.7 9.4 - - - +
573B LEU* 3.7 10.1 - - + +
574B ALA* 3.5 29.6 - - + +
577B ILE* 3.8 8.2 - - + +
478C SER 3.1 19.4 + - - +
479C ASN* 3.8 3.1 - - - +
481C PHE* 1.3 77.3 - - - +
483C GLN* 1.3 59.9 + - - +
485C GLU* 3.3 5.9 + - - +
486C ALA* 2.8 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 483 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B VAL* 5.2 3.6 + - - +
570B GLY* 3.5 27.0 + - - -
571B LYS* 4.7 0.8 - - - +
394C TYR* 3.7 5.8 - - - +
441C GLN* 3.5 36.2 - - - +
445C TYR* 3.3 17.8 - - + -
449C HIS* 2.9 29.7 + - - -
459C PHE* 3.6 22.2 - - + -
479C ASN* 2.9 21.6 + - - +
480C PHE 4.4 0.7 - - - +
482C ALA* 1.3 76.0 - - + +
484C THR* 1.3 58.4 + - - +
486C ALA* 3.3 4.0 + - - +
487C LEU* 3.0 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 484 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B LEU* 4.9 2.3 - - - +
105C LYS* 3.3 32.0 + - - +
459C PHE* 3.6 33.2 - - + -
480C PHE 3.9 8.0 + - - +
481C PHE* 3.1 16.3 + - - -
483C GLN* 1.3 73.6 - - - +
485C GLU* 1.3 63.8 + - - +
487C LEU* 3.5 7.3 + - - +
488C MET 3.3 16.3 + - - -
524C ARG 5.1 0.2 - - - +
526C SER* 3.4 24.9 + - - +
528C THR* 3.6 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 485 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B LEU* 3.6 25.0 - - + +
577B ILE* 3.6 16.6 - - - +
590B HIS* 2.6 41.6 + - - +
591B ASP* 4.0 9.6 + - - +
594B THR* 3.6 20.6 - - - +
105C LYS* 4.3 3.8 - - - +
481C PHE 3.3 10.2 + - - +
482C ALA 3.5 5.6 - - - +
483C GLN 3.3 0.2 - - - -
484C THR* 1.3 81.1 + - - +
486C ALA* 1.3 57.1 + - - +
488C MET* 3.2 4.3 + - - +
489C ILE* 2.9 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 486 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B LEU* 3.6 28.5 - - + +
570B GLY* 4.2 8.7 - - - -
573B LEU* 3.7 12.8 - - + +
449C HIS* 3.6 19.2 + - + -
482C ALA 2.8 18.4 + - - +
483C GLN* 3.5 7.9 - - - +
485C GLU* 1.3 76.7 - - - +
487C LEU* 1.3 62.2 - - - +
489C ILE* 4.4 0.9 - - - -
490C GLY* 3.1 22.0 + - - -
520C PHE* 5.5 0.5 - - - +
522C GLY* 4.7 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 487 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C TYR* 6.4 0.9 - - + -
448C ILE* 3.7 29.6 - - + +
449C HIS* 3.7 26.0 - - + +
455C ILE 5.9 0.2 - - - +
457C CYS* 4.4 9.2 - - - -
459C PHE* 3.9 29.6 - - + -
483C GLN* 3.0 20.4 + - + +
484C THR* 3.8 5.2 - - - +
485C GLU 3.4 0.2 - - - -
486C ALA* 1.3 76.0 - - - +
488C MET* 1.3 57.3 + - - +
522C GLY* 3.3 8.7 - - - -
523C GLY 3.2 6.8 + - - -
524C ARG* 3.0 48.6 + - + +
525C PRO 4.4 14.6 - - - +
526C SER* 4.4 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 488 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B ASP* 3.1 46.9 - - + +
71C ILE* 3.7 19.1 - - + -
72C LYS* 4.5 16.7 + - - +
75C PHE* 3.2 34.8 - - + -
105C LYS* 3.6 25.4 - - + -
484C THR 3.3 11.1 + - - +
485C GLU 3.2 3.4 + - - +
487C LEU* 1.3 79.8 - - - +
489C ILE* 1.3 70.1 + - + +
523C GLY* 2.9 25.3 + - - +
524C ARG 3.9 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B LEU* 5.5 0.7 - - + -
573B LEU* 3.9 28.7 - - + -
591B ASP* 4.7 6.5 - - + +
72C LYS* 3.1 42.6 + - + +
485C GLU* 2.9 41.4 + - + +
486C ALA* 4.4 0.9 - - - -
488C MET* 1.3 91.0 - - + +
490C GLY* 1.3 74.8 + - - +
491C LYS 3.9 0.2 + - - -
492C SER 5.6 0.2 + - - -
495C GLU* 5.5 1.0 - - - +
521C ILE 4.9 2.3 - - - +
522C GLY* 4.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B LEU* 3.6 18.5 - - - +
486C ALA 3.1 19.1 + - - -
488C MET 3.5 1.4 - - - -
489C ILE* 1.3 92.0 - - - +
491C LYS* 1.3 62.9 + - - +
495C GLU* 4.5 4.6 - - - +
520C PHE* 3.5 13.9 - - - -
521C ILE 4.5 0.2 - - - -
522C GLY* 3.8 10.7 - - - -
----------------------------------------------------------
Back to top of page
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