Contacts of the helix formed by residues 517 - 526 (chain B) in PDB entry 2VJD
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 ARG 517 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B TYR* 4.5 1.6 - - - -
393B ASP* 4.0 25.9 + - - +
397B ASP* 2.8 43.0 + - - -
401B ILE* 3.9 23.3 - - + +
422B PHE* 5.3 5.6 - - + -
515B ARG 3.0 3.2 + - - -
516B LEU* 1.3 86.4 - - + +
518B VAL* 1.3 64.9 + - - +
519B GLN 3.3 3.0 + - - -
520B MET* 3.4 23.3 + - + +
521B CYS* 3.0 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 518 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A TRP* 3.6 31.9 - - + +
379A MET* 3.9 16.6 - - + -
500B GLN* 4.5 6.3 - - - +
515B ARG* 3.1 51.4 - - + +
516B LEU 3.1 4.8 + - - +
517B ARG* 1.3 75.0 - - - +
519B GLN* 1.3 65.1 + - - +
521B CYS* 3.7 4.0 - - - +
522B VAL* 2.9 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 3.6 31.9 + - - +
376A THR 3.0 19.7 + - - +
377A ASP* 3.7 6.0 - - - +
378A TRP* 2.8 35.5 + - - +
379A MET* 4.5 3.8 + - + +
374B GLN* 5.1 2.0 + - - +
517B ARG 3.3 1.0 - - - -
518B VAL* 1.3 85.5 - - + +
520B MET* 1.3 82.8 + - + +
522B VAL* 3.3 9.8 + - - +
523B PHE* 3.4 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B GLN* 3.1 41.5 - - + +
375B TYR* 3.5 31.9 - - - +
397B ASP* 3.8 15.5 - - - +
402B CYS* 4.6 1.1 - - - -
517B ARG* 3.4 35.2 + - + +
518B VAL 3.3 0.4 - - - -
519B GLN* 1.3 95.1 - - + +
521B CYS* 1.3 62.4 + - - +
523B PHE* 3.0 5.5 + - - +
524B TRP* 2.9 34.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ILE* 4.4 6.7 - - - -
402B CYS* 2.0 56.1 - - - -
405B MET* 4.1 16.2 - - + -
516B LEU 5.0 0.4 - - - +
517B ARG* 3.0 24.3 + - - +
518B VAL* 4.1 2.7 - - - +
520B MET* 1.3 72.9 - - - +
522B VAL* 1.3 57.7 + - - +
524B TRP 4.3 0.2 - - - +
525B ASN* 2.7 50.2 + - - +
1542B CL 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 4.0 21.1 - - + -
378A TRP* 3.9 37.5 - - + +
518B VAL* 2.9 28.9 + - + +
519B GLN 3.6 5.6 - - - +
521B CYS* 1.3 76.5 - - - +
523B PHE* 1.3 59.1 + - - +
526B GLN* 2.9 57.0 + - + +
527B PHE* 3.1 7.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 4.0 13.9 - - + +
370B ALA* 3.6 40.6 - - + -
371B VAL* 3.8 16.6 - - + -
374B GLN* 3.6 42.4 - - + +
375B TYR* 4.8 1.1 - + - -
519B GLN 3.4 3.4 + - - +
520B MET* 3.0 10.9 + - - +
522B VAL* 1.3 82.3 - - - +
524B TRP* 1.3 97.8 + + - +
527B PHE* 3.4 28.2 + + - -
528B LEU* 2.8 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B VAL* 4.0 20.4 - - + -
371B VAL* 4.1 14.4 - - + -
375B TYR* 2.6 44.2 + + - -
394B ILE* 4.0 12.1 - - + -
397B ASP* 3.5 6.9 - - + +
398B HIS* 3.5 50.0 - + + +
402B CYS* 3.7 31.6 - - + -
520B MET 2.9 26.2 + - - +
523B PHE* 1.3 90.5 - + - +
525B ASN* 1.3 59.6 + - - +
528B LEU* 3.5 31.1 - - + +
529B PRO* 3.3 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B CYS* 3.3 33.7 + - - +
403B PRO* 4.4 2.8 - - - +
406B HIS* 3.9 31.2 + - - +
521B CYS* 2.7 33.0 + - - +
522B VAL* 5.1 0.2 - - - -
524B TRP* 1.3 77.1 - - - +
526B GLN* 1.3 66.6 + - + +
529B PRO* 3.8 11.3 - - - +
1542B CL 3.3 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B VAL* 2.9 41.2 + - + +
524B TRP 3.6 0.2 - - - -
525B ASN* 1.3 88.1 - - + +
527B PHE* 1.3 66.2 + - - +
528B LEU 3.7 0.4 - - - -
529B PRO* 3.6 7.7 - - - +
530B LYS* 3.4 24.5 + - + +
----------------------------------------------------------
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