Contacts of the helix formed by residues 411 - 430 (chain F) in PDB entry 4U0Z
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 VAL 411 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354F LEU* 3.9 26.7 - - + -
357F TYR* 3.9 25.6 - - + -
406F ALA* 3.7 28.3 - - + +
409F GLY 4.1 3.0 + - - +
410F ASP* 1.3 72.1 + - - +
412F ARG* 1.4 68.2 + - + +
413F PRO 3.6 0.9 - - - -
414F PHE* 3.3 9.9 + - + +
415F ILE* 3.2 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 412 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F ASP* 2.8 30.8 + - - -
161F TYR* 4.7 2.2 - - - +
164F THR* 3.3 25.7 + - - +
180F ARG* 3.7 11.5 - - - +
187F VAL* 3.6 16.8 - - - +
188F GLU* 5.9 2.2 - - - +
191F ASP* 4.6 6.7 - - - +
410F ASP* 3.0 32.0 + - - +
411F VAL* 1.4 78.7 - - + +
413F PRO* 1.4 65.7 - - + +
415F ILE* 3.0 25.8 + - + +
416F ARG* 3.0 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 413 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F TYR* 4.2 24.0 - - + -
401F HIS* 6.5 0.2 - - + -
402F VAL* 3.9 21.9 - - + +
405F ALA* 4.4 9.4 - - + -
410F ASP* 3.4 23.8 - - - +
411F VAL 3.8 0.4 - - - -
412F ARG* 1.4 91.0 - - + +
414F PHE* 1.4 56.3 + - - +
416F ARG* 3.4 22.1 + - + +
417F PHE* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 414 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353F ALA* 3.2 30.7 - - + -
356F HIS* 3.7 27.1 - + - -
357F TYR* 3.9 24.9 - + + -
399F TYR* 3.7 24.2 - + - -
402F VAL* 3.7 38.0 + - + +
403F LEU* 3.8 15.3 - - + -
406F ALA* 5.0 5.2 - - + -
411F VAL* 3.3 13.0 + - + +
412F ARG 3.2 1.2 - - - -
413F PRO* 1.4 75.1 - - - +
415F ILE* 1.4 60.2 + - + +
417F PHE* 3.2 3.8 + + - +
418F ILE* 3.0 53.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 415 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F PHE* 3.9 25.6 - - + -
349F VAL* 4.3 1.7 - - - +
350F GLU* 3.7 42.2 - - + +
353F ALA* 4.0 20.0 - - + -
354F LEU* 4.3 11.0 - - + +
411F VAL* 3.2 35.1 + - + +
412F ARG* 3.0 16.6 + - + +
414F PHE* 1.4 75.9 - - + +
416F ARG* 1.4 57.1 + - + +
418F ILE* 3.6 2.1 + - - +
419F ALA* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 416 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157F ILE* 3.5 41.2 + - - +
160F ASP* 4.9 1.0 + - - -
161F TYR* 5.8 3.6 - - - +
187F VAL* 4.0 12.3 - - - +
191F ASP* 3.0 40.3 + - - +
194F TYR* 4.8 4.4 - - + -
195F PHE* 6.2 0.2 - - - -
410F ASP* 5.5 0.8 + - - -
412F ARG* 3.0 42.1 + - - +
413F PRO* 3.4 39.8 - - + +
415F ILE* 1.4 73.8 - - + +
417F PHE* 1.3 54.5 + - - +
419F ALA* 3.2 8.9 + - - +
420F LYS* 2.8 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 417 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391F ILE* 4.0 8.7 - - + -
395F GLN* 3.3 32.1 - - + -
398F ASP* 3.8 26.7 - - + -
399F TYR* 3.7 39.7 - + + -
402F VAL* 3.9 26.0 - - + -
413F PRO 2.9 14.7 + - - +
414F PHE* 3.2 9.8 + + - +
416F ARG* 1.3 74.8 - - - +
418F ILE* 1.4 69.7 + - + +
420F LYS* 3.1 11.1 + - + +
421F CYS* 3.0 42.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 418 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349F VAL* 4.2 14.4 - - + +
352F ALA* 5.3 2.0 - - + -
353F ALA* 3.8 26.5 - - + +
377F MET* 3.9 27.4 - - + -
381F LEU* 5.8 0.7 - - + -
389F ILE* 5.4 1.6 - - + -
391F ILE* 3.8 31.4 - - + -
414F PHE* 3.0 48.5 + - + +
415F ILE 3.9 0.9 - - - +
417F PHE* 1.4 79.8 - - + +
419F ALA* 1.4 57.2 + - - +
421F CYS* 3.4 7.1 + - + +
422F THR* 2.9 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 419 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F TYR* 3.7 19.7 - - + -
195F PHE* 3.9 11.4 - - + -
198F ILE* 3.6 13.6 - - + +
349F VAL* 3.7 14.6 - - + +
415F ILE 3.0 19.8 + - - +
416F ARG* 3.5 7.4 - - - +
418F ILE* 1.4 74.4 - - - +
420F LYS* 1.4 58.4 + - - +
422F THR* 3.1 11.2 + - - -
423F GLU* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 420 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F TYR* 3.4 16.9 + - + +
416F ARG 2.8 16.9 + - - +
417F PHE* 3.1 13.7 + - + +
419F ALA* 1.4 70.6 - - - +
421F CYS* 1.4 51.4 + - - +
423F GLU* 3.4 3.5 + - - +
424F THR* 2.7 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 421 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389F ILE* 4.1 17.9 - - + -
390F THR 4.6 5.6 - - - +
391F ILE* 4.1 15.5 - - + -
395F GLN* 3.3 32.1 - - - +
417F PHE* 3.0 32.8 + - - -
418F ILE* 3.4 11.4 - - - +
419F ALA 3.3 0.2 - - - -
420F LYS* 1.4 74.5 - - - +
422F THR* 1.3 64.7 + - - +
424F THR* 3.3 8.6 + - - -
425F THR* 3.0 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 422 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F ILE* 3.6 19.7 - - - +
349F VAL* 3.7 25.1 - - + +
381F LEU* 4.3 13.5 - - + -
386F TYR* 5.4 3.6 - - - -
389F ILE* 3.6 33.2 - - + +
418F ILE* 2.9 27.2 + - + +
419F ALA* 3.1 13.0 + - - -
421F CYS* 1.3 74.7 - - - +
423F GLU* 1.4 54.9 + - - +
425F THR* 3.3 2.9 + - - -
426F LEU* 3.0 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 423 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194F TYR* 2.8 43.6 + - + +
197F ILE* 3.9 13.8 - - + +
198F ILE* 4.3 12.1 - - + -
201F LYS* 3.4 28.2 + - + +
419F ALA 3.0 9.0 + - - +
420F LYS 3.4 3.4 + - - +
422F THR* 1.4 76.1 + - - +
424F THR* 1.4 54.7 + - + +
426F LEU* 3.0 8.2 + - - -
427F ASP* 2.8 54.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 424 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395F GLN* 5.3 5.2 + - - -
420F LYS* 2.7 24.5 + - + +
421F CYS* 3.3 13.5 + - - -
423F GLU* 1.4 78.6 - - + +
425F THR* 1.3 54.9 + - - +
427F ASP* 4.0 11.6 - - + +
428F THR* 2.8 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 425 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F PRO* 4.4 11.2 - - + -
388F PRO 3.4 25.8 - - - +
389F ILE* 3.7 19.0 - - + +
390F THR* 4.0 17.1 + - - +
421F CYS 3.0 17.2 + - - -
422F THR 3.7 3.8 - - - -
424F THR* 1.3 74.1 - - - +
426F LEU* 1.4 63.9 + - - +
428F THR* 3.6 5.8 + - - -
429F LEU* 3.3 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 426 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F ILE* 3.5 42.6 - - + +
201F LYS* 4.0 15.9 - - + +
202F VAL* 3.8 27.1 - - + +
205F VAL* 3.9 20.3 - - + +
386F TYR* 5.0 3.6 - - + -
387F PRO* 3.8 25.4 - - + -
389F ILE* 5.9 0.2 - - + -
422F THR* 3.0 23.9 + - - +
423F GLU* 3.6 6.5 - - - +
425F THR* 1.4 76.0 - - - +
427F ASP* 1.4 60.2 + - - +
429F LEU* 3.6 6.3 + - - +
430F LEU* 3.3 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 427 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F LYS* 2.5 42.4 + - - +
423F GLU* 2.8 31.9 + - - +
424F THR* 4.0 13.0 - - + +
426F LEU* 1.4 70.6 - - - +
428F THR* 1.4 65.4 + - - +
430F LEU* 3.3 16.2 + - - +
431F PHE* 3.5 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 428 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F VAL* 5.8 2.8 - - - +
222F THR* 5.5 11.7 - - + -
424F THR 2.8 22.1 + - - -
425F THR* 3.9 6.3 - - - -
426F LEU 3.5 0.2 - - - -
427F ASP* 1.4 76.5 - - - +
429F LEU* 1.4 62.2 + - + +
431F PHE* 3.5 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205F VAL* 3.8 31.4 - - + -
215F LEU* 5.8 2.1 - - - +
218F VAL* 5.0 16.6 - - + -
219F MET* 4.2 25.8 - - - -
222F THR* 5.5 8.5 - - + +
387F PRO* 3.8 31.9 - - + -
425F THR* 3.3 20.4 + - + +
426F LEU* 3.8 6.3 - - - +
427F ASP 3.3 0.4 - - - -
428F THR* 1.4 78.5 - - + +
430F LEU* 1.3 57.7 + - - +
431F PHE 3.2 6.1 + - - -
432F ALA* 3.7 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F LYS* 3.9 36.8 - - + +
204F LYS* 3.7 39.9 - - + +
205F VAL* 3.7 14.4 - - + -
426F LEU 3.3 18.3 + - - +
427F ASP* 3.3 10.9 + - - +
429F LEU* 1.3 74.0 - - - +
431F PHE* 1.3 60.9 + - - +
432F ALA 3.3 11.2 + - - +
433F THR* 5.2 4.5 - - - -
----------------------------------------------------------
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