Contacts of the helix formed by residues 357 - 371 (chain C) in PDB entry 5ZR1
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 CYS 357 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ILE 4.7 0.2 + - - -
354C LEU 3.2 17.5 + - - +
355C SER 3.2 2.0 - - - -
356C ARG* 1.3 78.5 - - - +
358C PRO* 1.3 67.7 - - - +
359C THR* 3.3 15.7 - - - -
360C PHE* 3.1 24.6 + - + +
361C MET* 3.3 12.0 + - - +
462C PHE* 3.9 11.2 - - + -
464C GLU* 3.2 30.7 - - - -
465C LEU* 3.7 25.8 - - + -
412F LEU* 4.6 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C ARG 3.5 4.7 - - - +
357C CYS* 1.3 91.3 - - - +
359C THR* 1.3 62.9 + - - +
361C MET* 3.7 21.9 + - + +
362C PHE* 3.4 18.4 + - - +
464C GLU* 3.7 19.7 - - + +
411F ILE* 3.6 25.4 - - + +
412F LEU* 4.3 4.5 - - - -
413F VAL* 5.4 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C CYS* 3.3 15.8 - - - -
358C PRO* 1.3 78.0 - - - +
360C PHE* 1.3 59.7 + - - +
362C PHE* 3.2 11.3 + - - +
363C PHE* 3.0 23.0 + - - +
459C ASP* 5.2 7.9 - - + -
460C THR 4.3 13.5 - - - +
461C ILE* 3.3 16.1 - - - +
462C PHE 3.3 16.1 + - - -
463C GLN* 5.0 5.6 - - + +
464C GLU* 3.3 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C LEU 4.7 0.2 - - - +
355C SER* 3.2 36.8 - - - +
357C CYS* 3.1 21.7 + - + +
359C THR* 1.3 82.5 + - - +
361C MET* 1.3 62.4 + - + +
363C PHE* 3.3 5.7 + + + +
364C VAL* 3.1 33.6 + - + +
380C LEU* 4.0 23.3 - - + -
381C LEU* 4.3 13.2 - - + -
388C LEU* 3.8 20.4 - - + -
391C PHE* 3.8 29.4 - + - -
461C ILE* 3.9 10.1 - - + -
462C PHE* 3.5 28.5 - + + -
418F TYR* 4.9 2.2 - + - -
421F TRP* 5.7 1.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C SER 4.4 3.1 - - - +
356C ARG 5.2 0.2 - - - -
357C CYS 3.3 7.2 + - - +
358C PRO* 3.9 23.8 - - + +
359C THR 3.3 0.2 - - - -
360C PHE* 1.3 76.9 - - + +
362C PHE* 1.3 59.0 + - - +
364C VAL 3.4 0.5 + - - -
365C GLU* 2.8 31.2 + - - +
413F VAL* 3.7 44.0 - - + -
417F GLN 5.5 0.2 - - - +
418F TYR* 4.0 13.7 - - + -
421F TRP* 3.6 60.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C PRO 3.4 11.7 + - - +
359C THR* 3.2 14.0 + - - +
361C MET* 1.3 78.5 - - - +
363C PHE* 1.3 58.0 + - - +
365C GLU* 3.8 24.1 - - + +
366C GLY* 3.1 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C THR 3.0 11.8 + - - +
360C PHE* 3.6 10.3 - + - +
361C MET 3.2 0.2 - - - -
362C PHE* 1.3 78.5 - - - +
364C VAL* 1.3 59.5 + - + +
366C GLY* 3.3 2.7 + - - -
367C LEU* 3.1 56.1 + - + +
380C LEU* 4.0 17.0 - - + -
391C PHE* 3.5 35.9 - + - -
395C PHE* 5.6 5.2 - + - -
461C ILE* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C PHE* 3.1 31.4 + - + +
361C MET 3.4 0.4 + - - +
363C PHE* 1.3 72.4 - - - +
365C GLU* 1.3 61.1 + - - +
367C LEU* 3.2 8.0 + - - +
368C ILE* 2.9 27.4 + - - +
377C ILE* 3.8 23.6 - - + -
380C LEU* 3.8 24.7 - - + -
381C LEU* 4.4 10.5 - - + -
421F TRP* 3.6 30.3 - - + -
425F ILE* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C MET 2.8 17.8 + - - +
362C PHE* 3.8 29.9 - - + +
364C VAL* 1.3 76.4 - - - +
366C GLY* 1.3 59.3 + - - +
368C ILE* 3.4 9.8 + - + +
369C LYS* 3.2 25.5 + - + +
421F TRP* 4.6 10.1 + - + +
424F ARG* 6.2 2.5 - - - +
425F ILE* 5.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C PHE* 3.1 16.7 + - - -
363C PHE* 3.3 5.5 + - - -
364C VAL 3.2 0.2 - - - -
365C GLU* 1.3 77.0 - - - +
367C LEU* 1.3 60.4 + - - +
369C LYS* 4.2 9.3 - - - -
370C GLN* 3.3 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C PHE* 3.1 51.8 + - + +
364C VAL* 3.2 7.1 + - - +
366C GLY* 1.3 77.0 - - - +
368C ILE* 1.3 61.9 + - - +
370C GLN* 4.1 1.3 - - + +
371C HIS* 2.9 47.0 + - + +
376C GLU* 5.4 3.1 - - + +
377C ILE* 3.4 26.6 - - + +
380C LEU* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C VAL* 2.9 19.2 + - + +
365C GLU* 3.6 11.2 - - + +
367C LEU* 1.3 78.8 - - - +
369C LYS* 1.3 65.7 + - + +
370C GLN 3.4 0.7 + - - -
371C HIS 3.5 11.6 + - - +
372C ALA* 4.5 6.0 + - - +
377C ILE* 3.7 18.6 - - + -
425F ILE* 3.9 24.9 - - + +
428F ASP* 3.4 31.0 - - + +
429F LEU* 3.7 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 369 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C GLU* 3.2 16.0 + - + +
366C GLY* 3.7 7.9 + - - +
367C LEU 3.4 0.2 - - - -
368C ILE* 1.3 81.9 - - + +
370C GLN* 1.3 90.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C GLY 3.3 19.2 + - - +
367C LEU* 5.0 0.7 - - + -
368C ILE 4.3 0.2 - - - -
369C LYS* 1.3 111.3 - - - +
371C HIS* 1.3 79.2 + - + +
372C ALA 3.8 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C LEU* 2.9 41.9 + - + +
368C ILE* 3.5 8.3 - - - +
370C GLN* 1.3 92.0 - - + +
372C ALA* 1.3 65.0 + - - +
373C PRO* 3.5 17.2 - - + +
376C GLU* 6.0 1.3 - - + +
377C ILE* 4.4 1.7 - - + +
----------------------------------------------------------
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