Contacts of the helix formed by residues 508 - 518 (chain A) in PDB entry 3VRY
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 THR 508 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 3.5 21.1 - - - +
442A LYS* 3.8 16.2 - - - +
445A VAL* 5.0 0.7 - - - -
507A PRO* 1.3 74.6 - - + +
509A PHE* 1.3 58.7 + - - +
510A GLU* 3.8 8.1 + - - +
511A TYR* 2.8 27.9 + - - +
512A ILE* 2.7 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ALA* 4.0 11.2 - - + +
374A MET* 3.3 47.3 - - + -
375A ALA* 3.6 21.7 - - - +
378A GLU* 2.9 17.7 + - - +
387A LEU* 4.8 0.4 - - + -
441A ILE* 3.7 36.1 - - + -
444A ASP* 3.7 7.2 - - + -
445A VAL* 3.5 28.2 - - + +
448A PHE* 3.7 28.0 - + + -
507A PRO 4.2 0.6 + - - -
508A THR* 1.3 68.5 - - - +
510A GLU* 1.3 57.1 + - - +
512A ILE* 3.7 13.3 - - + +
513A GLN* 2.6 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ALA* 3.6 14.6 - - + +
378A GLU* 3.3 16.2 + - - +
379A GLN* 5.5 3.8 - - - +
508A THR* 3.8 9.1 + - - +
509A PHE* 1.3 77.1 - - - +
511A TYR* 1.3 62.1 + - - +
513A GLN* 3.5 5.1 + - - +
514A SER* 3.2 22.3 + - - -
497B ARG* 4.7 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A ILE* 5.5 6.7 - - + -
497A ARG* 3.8 30.7 + - - -
507A PRO* 3.9 18.8 - - + -
508A THR* 2.8 27.2 + - - +
510A GLU* 1.3 71.2 - - - +
512A ILE* 1.3 71.4 + - + +
514A SER* 3.0 19.9 + - - -
515A VAL* 3.1 35.3 + - + +
511B TYR* 3.7 37.5 - + + -
514B SER* 4.2 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ALA* 3.9 4.9 - - + -
445A VAL* 4.3 10.1 - - + -
448A PHE* 3.6 33.0 - - + -
494A ILE* 4.5 15.0 - - + -
498A CYS* 3.8 28.3 - - - -
507A PRO* 4.2 20.0 - - + -
508A THR 2.7 24.9 + - - +
509A PHE* 3.7 15.7 - - + +
511A TYR* 1.3 75.5 - - + +
513A GLN* 1.3 65.0 + - - +
515A VAL* 3.2 5.4 + - - +
516A LEU* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ALA 4.5 1.1 - - - +
371A ALA* 4.0 17.2 - - - +
372A GLU* 3.6 36.8 + - + +
375A ALA* 3.4 21.3 - - - +
509A PHE 2.6 19.4 + - - +
510A GLU* 3.7 5.3 - - - +
512A ILE* 1.3 74.8 - - - +
514A SER* 1.3 55.0 + - - +
516A LEU* 3.9 2.0 - - - +
517A ASP* 2.7 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A GLU 3.2 11.1 + - - -
511A TYR* 3.0 19.6 + - - -
513A GLN* 1.3 81.4 - - - +
515A VAL* 1.3 63.7 + - - +
517A ASP* 4.0 5.7 - - - +
518A ASP* 3.6 23.5 + - - +
511B TYR* 4.1 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A ILE* 3.6 28.3 - - + -
511A TYR* 3.1 48.7 + - + +
512A ILE* 3.7 7.0 - - - +
514A SER* 1.3 76.9 - - - +
516A LEU* 1.3 68.5 + - + +
518A ASP* 3.1 5.2 + - - +
519A PHE* 3.0 26.8 + - + -
523B THR* 4.1 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LYS* 5.1 1.4 + - - -
364A ILE* 4.0 19.5 - - + +
367A SER* 3.6 34.3 - - - +
368A ALA* 3.6 22.1 - - + +
371A ALA* 4.2 1.3 - - + -
448A PHE* 3.7 12.1 - - + -
452A LEU* 4.3 1.6 - - + -
491A LEU* 4.3 24.0 - - + -
494A ILE* 4.9 8.1 - - + -
512A ILE* 2.9 39.1 + - + +
513A GLN* 3.9 1.6 - - - +
515A VAL* 1.3 79.7 - - + +
517A ASP* 1.3 63.2 + - - +
518A ASP 3.2 0.3 + - - -
519A PHE* 3.4 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LYS* 2.8 63.5 + - + +
161A ARG* 3.9 4.0 + - - -
368A ALA* 3.5 21.4 - - - +
372A GLU* 5.3 3.2 - - - +
513A GLN* 2.7 51.8 + - - +
514A SER* 4.0 7.2 - - - +
515A VAL 3.2 0.2 - - - -
516A LEU* 1.3 74.0 - - - +
518A ASP* 1.3 66.2 + - - +
519A PHE 3.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 2.8 34.6 + - - -
157A LYS* 5.4 1.9 + - - +
160A GLU* 5.7 0.3 - - - +
514A SER* 3.6 15.0 + - - +
515A VAL 3.1 5.5 + - - +
517A ASP* 1.3 85.7 - - - +
519A PHE* 1.3 65.0 + - - +
520A TYR 3.0 4.5 + - - -
521A THR* 3.0 37.1 + - - +
526A GLN* 3.1 30.1 + - - +
523B THR* 4.7 5.2 + - - -
----------------------------------------------------------
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