Contacts of the helix formed by residues 453 - 475 (chain F) in PDB entry 7C17
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 453 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601 A 3.3 41.1 - - + +
611 G 4.2 20.0 - - + +
46D TYR* 3.7 11.4 - - + +
444F ALA* 4.6 0.4 - - - -
445F ASP* 5.4 3.4 - - - +
451F ARG* 3.9 11.2 - - - +
452F ILE* 1.3 95.3 - - + +
454F VAL* 1.3 62.0 + - + +
455F HIS* 3.3 21.0 + - + +
456F MET* 3.4 3.2 + - + -
457F ILE* 2.9 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 454 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611 G 5.1 6.1 - - + +
621 G 4.8 21.3 - - - +
631 T 5.6 5.2 - - + +
272 A 6.2 1.8 - - - +
440F THR* 4.5 12.6 - - - +
441F ARG* 4.8 9.2 - - + -
444F ALA* 3.8 25.7 - - + +
445F ASP* 5.0 6.1 + - - +
453F PRO* 1.3 74.2 - - + +
455F HIS* 1.3 70.1 + - + +
457F ILE* 3.6 3.4 - - + +
458F GLU* 2.9 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 455 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591 A 3.8 13.2 - + + -
601 A 3.2 45.6 + + - -
611 G 4.1 17.3 - - - +
282 C 6.4 0.2 - - - +
453F PRO* 3.5 18.8 - - + +
454F VAL* 1.3 80.8 - - + +
456F MET* 1.3 95.0 + - + +
458F GLU* 3.2 7.3 + - - +
459F THR* 3.0 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 456 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591 A 3.9 27.4 - - + +
46D TYR* 3.4 27.4 - - + +
452F ILE* 3.7 28.2 - - + +
453F PRO* 3.4 4.3 + - + +
455F HIS* 1.3 107.0 + - + +
457F ILE* 1.3 59.4 + - - +
459F THR* 2.9 17.3 + - + +
460F ILE* 2.9 31.2 + - - +
497F VAL* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 457 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440F THR* 4.9 2.7 - - - +
443F ILE* 4.4 14.8 - - + +
444F ALA* 3.8 37.2 - - + +
448F ARG* 4.0 14.6 - - + +
452F ILE* 3.7 28.0 - - + +
453F PRO 2.9 20.5 + - - +
454F VAL* 3.6 7.6 - - + +
455F HIS 3.2 0.2 - - - -
456F MET* 1.3 76.9 - - - +
458F GLU* 1.3 58.9 + - + +
460F ILE* 3.3 12.6 - - + +
461F ASN* 2.9 47.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 458 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252 A 3.4 25.0 - - - +
262 A 3.3 45.9 + - + +
272 A 5.6 4.3 - - - +
440F THR* 5.5 4.9 - - - +
454F VAL* 2.9 18.4 + - + +
455F HIS* 3.2 8.3 + - - +
457F ILE* 1.3 78.9 - - + +
459F THR* 1.3 58.9 + - + +
461F ASN* 3.3 8.3 + - - +
462F LYS* 2.9 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 459 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455F HIS* 3.0 16.0 + - + +
456F MET* 2.9 36.5 + - - -
458F GLU* 1.3 78.4 - - + +
460F ILE* 1.3 57.2 + - - +
462F LYS* 3.4 5.6 + - + +
463F LEU* 2.9 29.4 + - - +
487F MET* 3.8 21.4 - - + +
497F VAL* 5.0 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 460 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448F ARG* 5.4 3.6 - - - +
452F ILE* 5.0 7.4 - - + -
456F MET 2.9 19.1 + - - +
457F ILE* 3.3 30.5 - - + +
459F THR* 1.3 75.2 + - - +
461F ASN* 1.3 62.7 + - - +
463F LEU* 3.6 21.5 - - + +
464F ASN* 2.9 45.8 + - - +
497F VAL* 3.4 46.7 - - + +
498F LEU* 4.6 4.3 - - + +
500F ILE 5.3 4.0 - - - +
501F ALA* 5.9 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 461 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252 A 5.5 10.7 + - - +
262 A 6.1 0.2 - - - +
443F ILE* 5.4 4.7 - - - +
457F ILE* 2.9 38.0 + - - +
458F GLU* 3.7 12.0 - - - +
459F THR 3.3 0.2 - - - -
460F ILE* 1.3 79.6 + - - +
462F LYS* 1.3 60.2 + - - +
464F ASN* 3.3 13.0 + - - +
465F ARG* 2.9 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 462 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262 A 3.3 25.6 + - + +
272 A 4.6 15.6 + - - +
458F GLU* 2.9 33.7 + - + +
459F THR* 3.7 7.2 - - + +
461F ASN* 1.3 75.7 - - - +
463F LEU* 1.3 57.7 + - - +
465F ARG* 3.2 29.4 + - - +
466F ILE* 2.9 38.1 + - + +
487F MET* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 463 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459F THR 2.9 17.5 + - - +
460F ILE* 3.6 18.8 - - + +
461F ASN 3.2 0.2 - - - -
462F LYS* 1.3 76.5 - - - +
464F ASN* 1.3 64.3 + - - +
466F ILE* 3.8 5.9 - - - +
467F SER* 2.9 32.2 + - - -
483F LEU* 4.2 26.0 - - + +
487F MET* 4.5 9.8 - - + +
494F ILE* 3.8 42.4 - - + +
497F VAL* 3.8 20.6 - - + -
498F LEU* 4.4 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 464 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460F ILE* 2.9 35.1 + - - +
461F ASN* 3.7 14.6 - - - +
463F LEU* 1.3 85.5 - - - +
465F ARG* 1.3 56.2 + - - +
467F SER* 2.7 23.0 + - - -
468F ARG* 2.9 36.4 + - - +
498F LEU* 5.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 465 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252 A 3.9 14.1 + - - -
262 A 2.8 45.0 + - - -
461F ASN* 2.9 14.9 + - - +
462F LYS* 3.2 40.8 + - - +
464F ASN* 1.3 77.3 - - - +
466F ILE* 1.3 66.2 + - + +
468F ARG* 3.3 10.9 + - + +
469F GLN* 2.9 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 466 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462F LYS* 2.9 24.4 + - + +
463F LEU* 3.9 5.6 - - - +
465F ARG* 1.3 86.4 - - + +
467F SER* 1.3 57.6 + - - +
469F GLN* 3.3 22.6 + - - +
470F MET* 2.9 30.5 + - + +
483F LEU* 3.8 24.2 - - + +
486F ARG* 4.1 38.8 - - + +
487F MET* 4.9 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 467 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463F LEU* 2.9 17.2 + - - -
464F ASN* 2.7 25.9 + - - +
466F ILE* 1.3 77.4 - - - +
468F ARG* 1.3 57.7 + - - +
470F MET* 3.5 1.8 + - - +
471F LEU* 2.9 36.8 + - - +
478F PRO* 4.1 16.3 - - - +
483F LEU* 3.8 26.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 468 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C ASN* 4.4 29.8 - - + +
495C ALA* 5.0 5.8 - - - +
496C LYS* 3.4 38.2 - - + +
497C PRO* 6.0 0.4 - - - +
464F ASN* 2.9 34.5 + - - +
465F ARG* 3.7 9.2 - - + +
466F ILE 3.3 0.2 - - - -
467F SER* 1.3 78.5 + - - +
469F GLN* 1.3 58.3 + - - +
471F LEU* 3.3 14.8 + - + +
472F GLN* 2.9 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 469 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C ASP* 5.5 13.7 - - + +
465F ARG* 2.9 18.1 + - + +
466F ILE* 3.3 27.9 + - - +
468F ARG* 1.3 77.7 - - - +
470F MET* 1.3 76.8 + - + +
472F GLN* 3.3 7.3 + - + +
473F GLU* 2.9 37.5 + - + +
486F ARG* 4.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 470 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466F ILE* 2.9 22.7 + - + +
467F SER 4.0 3.1 - - - +
469F GLN* 1.3 105.8 - - + +
471F LEU* 1.3 59.4 + - - +
473F GLU* 4.1 13.9 - - + +
474F MET* 2.9 36.4 + - - +
476F ARG 4.8 1.2 - - - +
478F PRO* 4.8 4.0 - - + -
482F GLU* 4.1 32.7 - - + +
483F LEU* 4.1 17.9 - - + -
486F ARG* 3.5 41.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 471 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C TYR* 3.2 40.6 - - + +
126C GLU* 5.1 1.6 - - - +
495C ALA* 4.5 15.3 - - + -
467F SER* 2.9 29.0 + - - +
468F ARG* 3.5 14.6 - - + +
469F GLN 3.3 0.2 - - - -
470F MET* 1.3 77.0 - - - +
472F GLN* 1.3 56.9 + - - +
475F GLY* 2.8 25.6 + - - +
476F ARG 3.3 27.8 - - - +
477F GLU* 4.4 3.8 - - + -
478F PRO* 3.8 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 472 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C VAL* 3.3 13.5 - - - +
123C TYR* 2.8 56.1 + - - +
490C GLN* 2.9 58.5 + - + +
491C ASP* 4.7 4.0 - - - +
493C ILE 3.2 20.0 + - - +
494C ASN* 5.4 1.3 - - - -
495C ALA* 3.4 20.4 - - - +
468F ARG* 2.9 21.4 + - + +
469F GLN* 3.3 7.4 + - + +
471F LEU* 1.3 76.4 - - - +
473F GLU* 1.3 60.1 + - + +
474F MET 5.1 0.3 - - - -
475F GLY 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 473 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLN* 4.5 4.4 + - - -
490C GLN* 3.0 25.6 + - - +
469F GLN* 2.9 33.0 + - + +
470F MET* 4.1 17.0 - - + +
471F LEU 3.3 0.2 - - - -
472F GLN* 1.3 78.8 - - + +
474F MET* 1.3 57.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 474 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ARG* 3.1 24.8 + - - -
123C TYR* 5.9 0.2 - - - -
470F MET* 2.9 18.3 + - - +
472F GLN 3.5 0.6 - - - -
473F GLU* 1.3 81.0 - - + +
475F GLY* 1.3 57.1 + - - +
476F ARG* 3.5 46.0 + - + +
477F GLU 4.9 1.1 - - - +
482F GLU* 3.4 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 475 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PRO* 3.8 27.3 - - - +
97C ARG* 4.2 1.8 - - - -
123C TYR* 4.0 18.3 - - - -
126C GLU* 3.0 21.8 - - - +
470F MET 4.0 0.2 + - - -
471F LEU* 2.8 24.7 + - - +
472F GLN 4.8 0.4 + - - -
474F MET* 1.3 71.4 - - - +
476F ARG* 1.3 61.8 + - - +
----------------------------------------------------------
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