Contacts of the helix formed by residues 430 - 451 (chain F) in PDB entry 3FZ7
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 GLU 430 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E LEU 4.3 3.1 - - - +
15E ASP* 3.3 35.7 - - - +
16E SER* 2.4 44.5 + - - -
17E ARG* 3.4 24.8 + - - +
345F ALA* 4.4 3.3 - - - +
349F VAL* 3.9 4.6 - - - +
428F GLY* 2.8 25.2 + - - +
429F PHE* 1.3 77.8 + - - +
431F MET* 1.3 71.9 + - - +
432F ASP* 3.2 4.7 - - + +
433F PHE* 2.8 27.8 + - + -
434F ALA* 3.0 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 431 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E LEU* 3.9 31.6 - - + -
14E LEU 5.7 4.5 - - - +
22E SER* 4.9 12.6 - - - +
24E SER* 6.2 2.5 - - - -
348F GLN* 3.7 39.0 - - + +
349F VAL* 3.5 17.9 - - + +
352F TYR* 3.6 36.5 - - + -
430F GLU* 1.3 76.6 + - - +
432F ASP* 1.3 58.4 + - - +
434F ALA* 3.1 5.9 + - - +
435F GLU* 2.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 432 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ILE 4.3 2.4 - - - +
24E SER* 2.6 32.5 + - - -
25E THR* 2.7 36.6 + - - +
26E ILE* 3.7 29.2 - - + +
49E GLU* 4.4 5.5 - - - +
430F GLU* 3.2 3.6 - - + +
431F MET* 1.3 77.4 - - - +
433F PHE* 1.3 72.1 + - + +
435F GLU* 3.4 7.3 + - - +
436F LEU* 3.2 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 433 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ARG* 4.3 15.3 - - - -
48E ASP* 3.7 35.7 - - + -
49E GLU* 4.0 13.7 - - + -
52E LEU* 3.6 41.1 - - + -
57F ARG* 6.0 4.7 - - + -
404F TRP* 3.6 12.6 - + + -
428F GLY 3.9 12.8 - - - -
429F PHE* 3.8 21.5 - + + -
430F GLU* 2.8 33.5 + - + +
432F ASP* 1.3 76.4 - - + +
434F ALA* 1.3 66.1 + - - +
436F LEU* 3.2 7.8 + - - +
437F LEU* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 434 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349F VAL* 3.9 28.0 - - + -
352F TYR* 4.6 8.7 - - + -
353F LEU* 3.9 19.2 - - + +
429F PHE* 3.7 14.2 - - + -
430F GLU 3.0 6.7 + - - +
431F MET* 3.5 9.4 - - - +
433F PHE* 1.3 72.7 - - - +
435F GLU* 1.3 68.2 + - - +
436F LEU 3.2 0.2 + - - -
437F LEU* 3.2 4.7 + - - +
438F LEU* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 435 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E ILE* 4.1 26.9 - - + +
352F TYR* 2.2 42.4 + - + -
431F MET* 2.9 16.1 + - + +
432F ASP* 3.6 10.8 - - - +
434F ALA* 1.3 76.8 - - - +
436F LEU* 1.3 61.4 + - - +
438F LEU* 3.3 11.6 + - - +
439F GLU* 3.1 34.2 + - - +
442F LYS* 5.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLN* 4.5 7.6 - - - +
26E ILE* 5.2 3.3 - - + +
52E LEU* 3.4 34.5 - - + -
58F GLN* 5.2 2.0 - - - +
404F TRP* 3.9 17.3 - - + -
432F ASP 3.2 9.8 + - - +
433F PHE* 3.2 10.0 + - + +
434F ALA 3.1 0.4 - - - -
435F GLU* 1.3 75.5 - - - +
437F LEU* 1.3 65.4 + - - +
439F GLU* 3.1 23.8 + - + +
440F ASP* 2.9 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 437 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F LEU* 3.8 26.5 - - + -
353F LEU* 3.8 31.9 - - + -
357F ILE* 5.1 3.8 - - + -
399F LEU* 4.2 14.6 - - + -
404F TRP* 3.5 40.1 - - + +
406F VAL* 4.4 7.4 - - + -
423F ILE* 4.4 15.0 - - + -
429F PHE* 4.3 2.0 - - + -
433F PHE 3.1 12.3 + - - +
434F ALA* 3.3 10.3 - - - +
436F LEU* 1.3 73.7 - - - +
438F LEU* 1.3 57.3 + - - +
440F ASP* 2.9 4.7 + - - +
441F TYR* 2.8 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352F TYR* 3.7 26.9 - - + +
353F LEU* 3.8 14.8 - - + -
356F GLU* 3.6 37.7 - - + +
357F ILE* 3.9 23.8 - - + -
360F LEU* 4.3 13.9 - - + -
434F ALA 3.0 15.0 + - - +
435F GLU* 3.5 16.4 - - - +
437F LEU* 1.3 74.1 - - + +
439F GLU* 1.3 59.3 + - - +
441F TYR* 3.0 6.7 + - + +
442F LYS* 2.8 49.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 439 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E ILE* 6.0 2.1 - - - +
402F ARG* 5.4 0.7 - - - -
435F GLU* 3.1 24.4 + - - +
436F LEU* 3.1 23.8 + - + +
438F LEU* 1.3 76.1 - - - +
440F ASP* 1.3 61.1 + - - +
442F LYS* 3.3 13.7 + - + +
443F ALA* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 440 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F GLN* 5.0 0.3 + - - -
399F LEU* 4.0 4.7 - - + -
402F ARG* 3.0 47.3 + - + +
404F TRP* 2.7 36.7 + - + +
436F LEU* 2.9 29.5 + - - +
437F LEU 2.9 7.8 + - - +
439F GLU* 1.3 80.9 - - - +
441F TYR* 1.3 50.9 + - - +
443F ALA* 3.4 3.2 + - - +
444F SER* 2.7 37.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 441 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357F ILE* 4.0 28.9 - - + -
360F LEU* 3.8 24.7 - - + -
363F TYR* 2.9 30.4 + - - -
380F PHE* 3.3 22.7 - + - -
395F LEU* 3.3 29.1 - - + +
399F LEU* 3.9 24.0 - - + +
406F VAL* 6.2 0.2 - - + -
421F MET* 4.4 7.4 - - - -
423F ILE* 5.3 2.0 - - + -
437F LEU* 2.8 22.9 + - + +
438F LEU* 3.3 12.1 - - - +
440F ASP* 1.3 69.9 - - - +
442F LYS* 1.3 65.5 + - - +
444F SER* 3.1 5.8 + - - -
445F LEU* 2.9 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 442 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356F GLU* 5.1 9.3 + - - -
360F LEU* 4.2 33.9 - - + -
435F GLU* 5.9 1.0 + - - -
438F LEU* 2.8 37.5 + - - +
439F GLU* 3.7 10.9 - - + +
441F TYR* 1.3 73.0 - - - +
443F ALA* 1.3 60.5 + - - +
445F LEU* 3.1 10.1 + - - +
446F LYS* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 443 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402F ARG* 3.8 37.0 - - - +
439F GLU 3.0 16.8 + - - +
440F ASP 3.8 2.5 - - - +
441F TYR 3.3 0.2 - - - -
442F LYS* 1.3 73.3 - - - +
444F SER* 1.3 57.5 + - - +
446F LYS* 3.4 8.0 + - - +
447F TYR* 2.8 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 444 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395F LEU* 3.7 17.3 - - - -
398F ARG* 3.5 32.1 - - - +
399F LEU* 3.8 12.8 + - - +
402F ARG* 4.9 5.2 - - - +
440F ASP 2.7 21.5 + - - -
441F TYR* 3.5 5.2 - - - -
443F ALA* 1.3 77.9 - - - +
445F LEU* 1.3 55.9 + - - +
447F TYR* 3.4 5.0 + - - +
448F LEU* 2.9 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360F LEU* 3.4 45.1 - - + +
363F TYR* 4.2 3.8 - - - +
390F TYR* 3.4 43.5 - - + +
395F LEU* 4.2 14.4 - - + -
441F TYR* 2.9 26.1 + - + +
442F LYS* 3.1 9.6 + - + +
444F SER* 1.3 72.1 - - - +
446F LYS* 1.3 61.4 + - - +
448F LEU* 3.3 5.0 + - + +
449F SER* 2.7 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 446 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442F LYS 3.0 12.4 + - - +
443F ALA* 3.7 9.9 - - - +
445F LEU* 1.3 71.9 - - - +
447F TYR* 1.3 68.4 + - - +
449F SER* 3.0 7.7 + - - +
450F ASP* 2.8 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 447 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397E GLU* 4.7 3.8 + - - -
457E ILE* 3.9 16.3 + - + +
458E ALA* 4.1 12.0 - - - +
459E GLN* 4.9 1.9 + - - +
398F ARG* 3.7 30.7 - - + -
443F ALA 2.8 18.7 + - - +
444F SER* 3.7 7.4 - - - +
446F LYS* 1.3 76.0 - - - +
448F LEU* 1.3 61.9 + - - +
450F ASP* 3.0 9.3 + - - -
451F HIS* 3.0 63.8 + + - +
454F LEU* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389F GLY 4.6 7.3 - - - +
390F TYR* 3.9 37.7 - - + -
394F ASP* 4.1 18.6 - - + -
395F LEU* 4.2 21.3 - - + -
398F ARG* 3.9 22.0 - - + -
444F SER 2.9 26.9 + - - +
445F LEU* 3.7 6.7 - - + +
447F TYR* 1.3 74.4 - - - +
449F SER* 1.3 63.2 + - - +
451F HIS 3.2 19.6 + - - +
452F PRO* 3.7 6.2 - - - +
454F LEU* 3.7 31.9 - - + -
455F GLN 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 449 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390F TYR* 6.1 0.4 - - - -
445F LEU 2.7 21.5 + - - -
446F LYS* 3.7 7.5 - - - +
448F LEU* 1.3 73.5 - - - +
450F ASP* 1.3 67.3 + - - +
451F HIS 3.6 0.3 + - - -
452F PRO* 4.5 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 450 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446F LYS* 2.8 48.5 + - - +
447F TYR* 3.6 2.1 - - - +
449F SER* 1.3 84.0 + - - +
451F HIS* 1.3 86.2 + - + +
452F PRO* 3.8 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 451 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457E ILE* 3.6 36.1 + - + -
459E GLN* 4.5 13.3 + - - +
447F TYR* 3.0 59.8 + + - +
448F LEU* 3.2 7.3 + - - +
450F ASP* 1.3 99.9 + - + +
452F PRO* 1.3 69.5 - - - +
453F LYS* 3.0 4.8 + - - -
454F LEU* 3.0 32.8 + - + +
----------------------------------------------------------
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