Contacts of the helix formed by residues 482 - 493 (chain C) in PDB entry 3GZN
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 LYS 482 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C PRO* 4.1 23.9 + - + +
427C ASP* 2.9 41.4 + - - -
431C VAL* 5.3 0.6 - - - +
480C MET* 4.1 20.5 + - + -
481C VAL* 1.3 76.9 - - - +
483C ASP* 1.3 58.8 + - - +
484C ASP* 3.0 18.4 - - + +
485C TYR* 2.9 41.8 + - + +
486C VAL* 4.0 1.6 + - - +
51D PHE* 6.2 1.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 483 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C LYS* 5.7 4.2 - - - +
480C MET* 5.8 0.2 - - - +
481C VAL 3.3 8.4 + - - +
482C LYS* 1.3 71.6 - - - +
484C ASP* 1.3 63.7 + - - +
485C TYR 3.1 0.5 + - - -
486C VAL* 3.2 15.9 + - + +
487C HIS* 3.1 33.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 484 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C LYS* 4.6 16.9 - - + +
483C ASP* 1.3 80.5 - - - +
485C TYR* 1.3 55.8 + - - +
487C HIS* 4.2 5.0 - - - -
488C GLU* 3.0 27.7 + - - +
50D PRO* 3.4 35.3 - - + +
51D PHE* 3.6 18.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 485 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C PRO 4.1 11.0 - - - -
427C ASP* 2.8 42.3 + - - +
431C VAL* 4.0 21.7 - - + +
432C LEU* 3.8 30.0 - - + +
435C MET* 4.0 17.7 - - + -
481C VAL* 4.2 5.4 - - + -
482C LYS* 2.9 31.9 + - + +
484C ASP* 1.3 76.4 - - - +
486C VAL* 1.3 65.8 + - - +
488C GLU* 2.9 2.8 + - + -
489C PHE* 2.9 36.5 + + - -
532C MET* 4.8 12.5 - - + +
51D PHE* 4.0 27.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 486 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C MET* 3.7 15.7 - - + +
461C ILE* 3.3 37.5 - - + +
464C LEU* 3.8 11.2 - - + +
465C LYS* 4.0 23.8 - - + +
468C LEU* 3.8 28.7 - - + -
481C VAL 6.0 0.2 - - - +
482C LYS 5.1 1.8 - - - +
483C ASP* 3.2 19.7 + - + +
485C TYR* 1.3 75.3 - - - +
487C HIS* 1.3 62.4 + - + +
489C PHE 3.5 0.3 + - - -
490C CYS* 3.3 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 487 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LYS* 4.0 24.0 - - + +
307A GLN* 3.0 31.4 + - + -
377A GLN* 6.2 0.4 - - - -
461C ILE* 3.6 34.9 - - + +
483C ASP* 3.1 32.2 + - + +
484C ASP* 3.5 12.6 - - - +
486C VAL* 1.3 77.6 - - + +
488C GLU* 1.3 57.1 + - - +
490C CYS* 3.4 5.0 + - - +
491C ARG* 3.1 24.8 + - - +
50D PRO* 3.7 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 488 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C ASP 3.0 17.8 + - - +
485C TYR* 2.9 7.2 + - + +
487C HIS* 1.3 76.7 - - - +
489C PHE* 1.3 62.0 + - + +
491C ARG* 3.1 20.0 + - - +
492C TYR* 3.1 49.6 + - + +
532C MET* 4.5 1.6 - - - -
49D GLY* 4.1 0.3 - - - -
50D PRO* 3.4 18.8 - - - +
51D PHE* 3.5 26.6 + - + -
336D TYR* 2.5 43.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C TYR* 3.8 42.2 + + - -
166C VAL* 3.5 25.8 - - + -
432C LEU* 3.9 24.0 - - + -
435C MET* 3.5 48.2 - - + -
436C LEU* 4.2 14.8 - - + -
439C VAL* 4.0 10.5 - - + -
450C PRO* 4.3 3.0 - - - +
464C LEU* 4.1 9.9 - - + -
485C TYR* 2.9 25.5 + + - +
488C GLU* 1.3 77.3 - - + +
490C CYS* 1.3 65.6 + - - +
492C TYR* 3.6 28.2 - + - +
493C GLY 3.8 3.1 + - - -
532C MET* 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C PRO* 3.9 16.9 - - - +
451C GLY* 3.7 8.0 - - - +
457C VAL* 4.7 13.5 - - + +
460C ASP* 3.9 8.1 - - - -
461C ILE* 3.8 40.4 - - + -
464C LEU* 3.9 15.7 - - - -
486C VAL 3.3 17.4 + - - -
487C HIS 3.6 8.5 - - - +
488C GLU 3.2 0.4 - - - -
489C PHE* 1.3 75.8 - - - +
491C ARG* 1.3 68.0 + - - +
493C GLY* 2.9 14.7 + - - -
47D ARG* 3.4 9.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 491 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C VAL* 5.5 3.7 - - - +
487C HIS 3.1 13.7 + - - +
488C GLU* 3.2 26.5 + - - +
490C CYS* 1.3 74.9 - - - +
492C TYR* 1.3 61.7 + - + +
43D LYS* 3.7 16.5 + - - +
44D PHE* 3.1 36.5 + - + +
47D ARG* 2.8 59.2 + - + +
48D SER 3.2 20.7 + - - +
49D GLY* 3.7 3.6 - - - -
52D THR* 3.5 23.9 - - - +
56D PHE* 3.8 4.2 - - - -
335D ALA 3.9 5.3 + - - -
336D TYR* 2.8 44.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 492 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C TYR* 4.0 14.8 - + + -
164C GLY* 3.4 26.0 - - - +
165C LEU* 3.5 30.5 - - + +
166C VAL* 4.3 6.8 - - + +
488C GLU* 3.1 37.1 + - + +
489C PHE* 3.6 38.7 - + - +
490C CYS 3.1 0.4 + - - -
491C ARG* 1.3 79.4 - - + +
493C GLY* 1.3 64.1 + - - +
494C ALA 3.2 5.8 - - - +
495C ALA* 3.0 22.9 + - - +
532C MET* 3.6 17.2 - - - +
43D LYS* 3.6 7.3 - - - +
44D PHE* 3.6 17.0 - + - -
336D TYR* 3.4 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 493 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C PRO 3.5 10.1 - - - -
451C GLY 3.3 26.5 - - - -
452C VAL* 4.0 13.9 - - - +
489C PHE 3.8 1.8 + - - -
490C CYS 2.9 15.3 + - - -
491C ARG 3.0 0.2 + - - -
492C TYR* 1.3 71.7 - - - +
494C ALA* 1.3 68.2 + - - +
43D LYS* 3.1 16.7 + - - -
47D ARG* 3.9 3.1 - - - -
----------------------------------------------------------
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