Contacts of the helix formed by residues 429 - 436 (chain G) in PDB entry 6O0T
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 TYR 429 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421G LEU* 4.6 1.1 - - + -
426G PHE* 3.0 33.3 + + + +
428G LYS* 1.3 115.0 + - + +
430G CYS* 1.3 63.4 + - - +
431G GLU 3.5 1.8 - - - -
432G SER* 3.6 10.5 + - - -
433G PHE* 3.0 40.0 + + + -
455G LEU 3.8 15.5 - - - -
456G GLY 3.9 10.5 + - - -
457G MSE 3.7 51.7 - - + +
458G LYS 4.6 1.2 + - - -
459G SER* 5.5 1.4 + - - -
462G THR* 4.1 17.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 430 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418G GLN* 2.8 48.9 + - - +
421G LEU* 4.2 15.0 - - - -
422G GLN* 3.7 30.7 - - - -
426G PHE 3.7 0.4 + - - -
427G SER* 3.0 32.8 + - - +
428G LYS 3.5 0.8 - - - -
429G TYR* 1.3 76.3 - - - +
431G GLU* 1.3 64.1 + - - +
433G PHE 3.1 2.9 + - - -
434G ARG 3.1 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 431 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418G GLN* 5.0 0.2 - - - -
427G SER 4.9 0.2 + - - -
428G LYS 5.2 1.0 + - - -
429G TYR 3.5 0.2 - - - -
430G CYS* 1.3 78.8 - - - +
432G SER* 1.3 58.8 + - - +
434G ARG* 3.1 31.1 + - - +
435G GLU* 2.8 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 432 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428G LYS 5.4 0.9 + - - -
429G TYR* 3.6 17.8 + - - -
430G CYS 3.2 0.6 - - - -
431G GLU* 1.3 78.3 - - - +
433G PHE* 1.3 63.1 + - - +
435G GLU* 3.1 33.9 + - - +
436G GLN* 3.1 14.7 + - - +
455G LEU* 3.7 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 433 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414G GLU* 5.9 0.2 - - - +
417G VAL* 4.1 6.3 - - + -
418G GLN* 3.5 17.6 + - - +
421G LEU* 3.4 26.0 - - + -
429G TYR* 3.0 34.1 - - + -
430G CYS 3.1 2.7 + - - +
432G SER* 1.3 77.7 - - - +
434G ARG* 1.3 57.2 + - - +
437G GLN 3.2 3.5 + - - -
438G VAL* 3.0 52.7 + - + +
443G LEU* 4.2 5.6 - - + -
446G MSE 3.7 20.2 - - + -
451G LEU* 4.1 3.6 - - + -
455G LEU* 3.6 32.5 - - + -
457G MSE 4.4 8.7 - - + -
466G PHE* 3.6 32.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 434 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414G GLU* 4.0 18.5 - - + +
418G GLN* 3.6 25.3 + - + +
430G CYS 3.1 7.5 + - - +
431G GLU* 3.1 33.2 + - - +
433G PHE* 1.3 76.1 - - - +
435G GLU* 1.3 62.4 + - - +
436G GLN 3.1 1.8 - - - -
437G GLN* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 435 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431G GLU* 2.8 25.9 + - + +
432G SER* 3.1 32.3 + - - +
434G ARG* 1.3 76.6 - - - +
436G GLN* 1.3 79.1 + - - +
437G GLN* 3.5 7.6 + - - +
454G ASP 4.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 436 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432G SER 3.1 17.9 + - - +
435G GLU* 1.3 94.6 + - + +
437G GLN* 1.3 71.7 + - - +
438G VAL* 3.5 15.4 + - + -
454G ASP* 3.7 19.5 + - - +
455G LEU* 3.6 16.4 - - + -
459H SER* 2.5 36.9 + - - -
461H ILE* 3.7 25.4 - - + +
462H THR* 4.0 7.8 + - - -
465H ARG* 3.8 6.9 + - - -
----------------------------------------------------------
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