Contacts of the helix formed by residues 462 - 474 (chain A) in PDB entry 3V9G
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 462 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A PRO* 2.8 32.4 + - + +
461A ASP* 1.3 79.3 - - + +
463A TYR* 1.3 60.5 + - - +
464A LYS 3.4 2.5 - - - -
465A GLU* 3.1 31.3 - - + +
466A THR* 2.8 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE* 4.2 9.4 - + + -
324A HIS* 4.4 20.4 - + + -
458A TYR* 3.4 33.7 - - + +
459A PRO 3.6 0.8 + - - -
460A ASP* 3.3 15.4 + - - +
461A ASP 3.5 3.6 + - - -
462A LYS* 1.3 75.8 - - - +
464A LYS* 1.3 93.9 + - + +
466A THR* 3.7 1.5 - - - -
467A LEU* 3.0 37.9 + - + +
489A VAL* 3.6 27.1 - - + +
492A GLU* 2.6 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ASP 5.2 0.2 + - - -
462A LYS 3.4 0.6 - - - -
463A TYR* 1.3 104.8 + - + +
465A GLU* 1.3 70.9 + - - +
467A LEU* 3.2 21.1 - - - +
468A GLN* 3.4 12.9 + - - +
492A GLU* 2.9 39.6 + - - +
496A VAL* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ASP 3.8 5.8 - - - +
462A LYS* 3.1 43.0 - - + +
464A LYS* 1.3 84.8 + - - +
466A THR* 1.3 58.2 + - - +
468A GLN* 3.3 13.6 + - - +
469A LEU* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE* 3.8 15.3 - - + -
355A TYR* 4.0 18.2 - - + -
456A TYR* 4.8 6.2 - - + -
458A TYR* 3.5 43.5 - - + +
459A PRO* 5.0 0.9 - - - +
462A LYS* 2.8 23.9 + - - +
463A TYR 3.7 4.9 - - - -
464A LYS 3.2 0.2 - - - -
465A GLU* 1.3 75.9 - - - +
467A LEU* 1.3 65.0 + - - +
469A LEU* 3.0 20.3 + - + +
470A VAL* 3.1 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE* 3.4 43.7 - - + -
463A TYR* 3.0 31.0 + - + +
464A LYS* 3.2 12.6 - - - +
466A THR* 1.3 74.8 - - - +
468A GLN* 1.3 61.7 + - - +
470A VAL* 3.2 15.2 + - - +
471A ASP* 3.3 9.4 + - - +
489A VAL* 5.3 1.1 - - + +
492A GLU* 4.4 13.9 - - + +
493A ALA* 3.9 36.6 - - + +
496A VAL* 4.1 20.4 - - + -
497A LEU* 3.8 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LYS 3.4 13.8 + - - +
465A GLU* 3.3 13.2 + - - +
466A THR 3.2 0.6 - - - -
467A LEU* 1.3 75.4 - - - +
469A LEU* 1.3 58.1 + - + +
471A ASP* 3.3 12.4 + - - +
472A SER* 2.9 33.0 + - - -
496A VAL* 3.9 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TYR* 4.6 8.3 - - + -
439A PRO* 3.6 38.8 - - + -
440A GLN* 3.5 26.2 - - - +
456A TYR* 4.7 10.1 - - + +
465A GLU 3.1 14.0 + - - +
466A THR* 3.0 17.3 + - + +
468A GLN* 1.3 71.9 - - + +
470A VAL* 1.3 66.6 + - - +
472A SER* 3.8 8.3 - - - +
473A THR* 2.7 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PHE* 3.5 33.2 - - + -
322A PHE* 3.9 19.5 - - + -
353A ARG* 3.0 39.2 + - - +
355A TYR* 3.6 33.2 - - + -
466A THR 3.1 14.8 + - - +
467A LEU* 3.2 8.7 + - + +
469A LEU* 1.3 77.1 - - - +
471A ASP* 1.3 63.9 + - - +
472A SER 3.4 0.2 + - - -
473A THR 3.8 4.5 + - - -
474A THR* 4.7 0.7 + - - -
497A LEU* 3.9 11.7 - - + -
500A ALA* 4.9 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A LEU 3.3 4.5 + - - +
468A GLN* 3.7 16.7 - - - +
469A LEU 3.3 0.4 - - - -
470A VAL* 1.3 82.3 - - - +
472A SER* 1.3 63.2 + - - +
474A THR 4.5 2.8 + - - +
496A VAL* 3.7 19.6 - - + +
497A LEU* 4.0 14.4 - - + -
499A ASN* 4.4 2.3 + - - +
500A ALA* 3.7 20.9 + - - +
524A ARG* 2.9 51.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A GLN* 4.7 3.6 + - - +
468A GLN* 2.9 19.6 + - - -
469A LEU* 3.2 17.2 + - - +
471A ASP* 1.3 81.6 - - - +
473A THR* 1.3 65.8 + - - +
474A THR 3.5 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TYR* 4.1 11.7 + - - +
439A PRO 3.6 22.5 + - - +
440A GLN* 3.7 25.1 + - - +
444A MET 4.1 5.8 - - - +
445A LYS* 3.1 40.5 + - + +
469A LEU* 2.7 28.8 + - - +
470A VAL 3.8 3.1 + - - -
471A ASP 3.6 1.2 - - - -
472A SER* 1.3 79.3 - - - +
474A THR* 1.3 67.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS* 3.9 9.8 + - + -
353A ARG* 2.7 37.1 + - - +
444A MET 3.6 22.0 - - - +
445A LYS* 3.9 21.3 - - - -
470A VAL 4.7 1.6 + - - -
471A ASP 4.5 0.9 + - - +
472A SER 4.2 5.7 - - - +
473A THR* 1.3 84.8 - - + +
475A SER* 1.3 63.5 + - - +
476A TYR* 3.3 21.7 + - - +
524A ARG* 4.5 13.7 + - - -
----------------------------------------------------------
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