Contacts of the helix formed by residues 519 - 526 (chain A) in PDB entry 2VL7
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 ASP 519 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TYR* 3.4 10.6 - - - -
355A CYS 3.5 5.6 + - - -
358A VAL 3.4 7.2 - - - -
359A THR* 3.1 20.8 + - - -
360A SER* 3.0 20.4 + - - -
372A TYR* 4.2 0.2 - - - -
460A GLY* 3.5 2.8 - - - -
461A LEU* 3.1 7.7 + - + -
517A LEU 3.2 2.0 + - - +
518A CYS* 1.3 77.8 - - - +
520A SER* 1.3 67.2 + - - +
521A ARG* 2.9 51.7 + - - +
522A TYR* 3.0 34.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TYR* 2.6 28.1 + - - -
355A CYS 3.5 6.4 + - - -
356A PRO 3.3 23.6 - - - -
358A VAL 2.8 16.2 + - - -
359A THR* 4.0 9.5 + - - +
519A ASP* 1.3 75.0 + - - +
521A ARG* 1.3 67.1 + - - +
522A TYR 3.2 1.0 + - - -
523A ARG* 3.2 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A THR* 3.6 5.0 + - - +
360A SER* 3.3 8.5 + - - -
361A GLU* 3.2 49.3 - - - +
362A LEU 5.1 0.4 - - - +
365A ARG* 5.7 0.2 - - - +
461A LEU* 3.6 32.4 + - + +
463A TYR* 3.9 33.1 - - - +
519A ASP* 2.9 34.7 + - - +
520A SER* 1.3 81.3 + - - +
522A TYR* 1.3 60.0 + - - +
523A ARG* 3.0 8.9 + - - +
524A GLU* 3.1 35.4 + - - +
525A TYR* 3.4 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TYR* 4.3 4.7 - - + -
436A MET* 4.1 0.9 - - - +
458A LEU* 3.2 32.5 - - + +
460A GLY 2.8 29.1 + - - -
461A LEU* 3.6 13.0 - - + +
462A PRO* 3.5 12.0 - - - +
498A ILE* 3.6 32.5 - - + -
517A LEU* 3.7 33.4 - - + +
518A CYS 4.0 9.9 - - - -
519A ASP* 3.0 42.7 + - + +
521A ARG* 1.3 76.5 - - - +
523A ARG* 1.3 55.6 + - - +
524A GLU 3.2 0.4 - - - -
525A TYR* 2.9 25.7 + - + +
526A PHE* 3.3 19.1 + - + -
529A LEU* 5.0 1.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TYR* 3.7 17.4 - - + +
520A SER 3.2 17.9 + - - +
521A ARG* 3.0 4.4 - - - +
522A TYR* 1.3 77.7 - - - +
524A GLU* 1.3 97.5 + - - +
525A TYR 3.1 1.3 + - - -
526A PHE* 3.6 37.9 + - + +
527A ALA 5.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LEU* 6.3 0.2 - - - -
463A TYR* 6.1 1.2 - - - -
491A HIS* 3.0 26.9 + - + +
521A ARG* 3.1 36.7 + - - +
523A ARG* 1.3 111.7 + - - +
525A TYR* 1.3 76.6 + - + +
526A PHE 3.6 0.2 - - - -
527A ALA* 5.1 2.2 + - - +
528A ASP* 3.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A LEU* 3.8 26.8 - - + +
463A TYR* 4.8 5.7 - - - -
490A ILE 4.8 0.2 - - - -
491A HIS* 3.5 56.4 - + - -
494A THR* 3.3 24.3 + - + +
495A ALA* 3.9 15.3 - - + -
498A ILE* 3.6 23.3 - - + -
521A ARG 3.4 20.9 - - - -
522A TYR* 2.9 15.4 + - + +
524A GLU* 1.3 94.2 + - + +
526A PHE* 1.3 65.4 + - - +
527A ALA 3.2 2.9 - - - -
528A ASP* 3.2 11.9 + - + +
529A LEU* 3.1 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TYR* 3.7 40.4 - + + -
517A LEU* 4.1 16.4 - - + -
522A TYR 3.3 20.7 + - - -
523A ARG* 3.6 33.2 - - + +
524A GLU 3.6 1.8 - - - -
525A TYR* 1.3 76.1 - - - +
527A ALA* 1.3 62.1 + - - +
529A LEU* 3.1 10.2 + - + -
530A GLY 3.3 8.5 + - - -
531A ILE* 3.3 34.5 + - + +
533A GLU* 3.7 31.4 - - + +
536A ILE* 3.5 31.6 - - + -
----------------------------------------------------------
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