Contacts of the helix formed by residues 231 - 238 (chain B) in PDB entry 3VBB
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 231 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B MET 3.6 0.8 + - - -
230B ARG* 1.3 71.1 - - - +
232B GLU* 1.3 63.0 + - + +
234B MET* 4.0 1.8 - - - +
235B GLN* 3.3 38.4 + - - +
265B GLU* 3.1 35.7 + - + +
267B TYR* 3.5 32.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ARG* 3.0 48.9 + - - +
231B LYS* 1.3 81.8 + - + +
233B VAL* 1.3 65.5 + - + +
235B GLN* 4.0 12.9 + - - +
236B GLU* 3.8 17.8 + - - +
265B GLU 5.3 2.9 + - - +
281B ARG* 4.6 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL* 3.8 27.8 - - + +
188A VAL* 4.5 7.6 - - + +
229B MET* 4.0 7.9 - - + -
230B ARG* 3.1 17.1 + - + +
232B GLU* 1.3 78.9 - - - +
234B MET* 1.3 65.3 + - - +
236B GLU* 3.4 8.0 + - - +
237B VAL* 3.1 17.9 - - + +
278B ALA* 3.2 34.5 - - + +
281B ARG* 3.9 37.7 - - - +
406B LEU* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B MET* 3.6 41.6 - - + +
230B ARG 2.9 17.8 + - - +
231B LYS* 4.1 8.3 - - - +
233B VAL* 1.3 76.1 - - - +
235B GLN* 1.3 65.2 + - - +
237B VAL* 3.0 14.2 + - - -
238B ALA* 3.0 18.4 + - - +
243B PHE* 3.6 22.2 - - + -
247B LEU* 4.3 11.7 - - + -
267B TYR* 4.0 27.8 - - + +
269B ILE* 4.4 6.3 - - - -
274B GLN* 4.0 34.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG* 4.0 10.9 + - - +
231B LYS* 3.3 27.1 + - - +
232B GLU* 4.2 10.3 - - - +
233B VAL 3.4 0.6 - - - -
234B MET* 1.3 75.5 - - - +
236B GLU* 1.3 58.8 + - + +
238B ALA 3.3 17.1 - - - +
243B PHE* 3.4 28.9 - - + -
267B TYR* 5.3 4.2 + - - -
405B ARG* 3.4 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLU 3.8 13.0 - - - +
233B VAL 3.4 8.0 + - - +
234B MET 3.1 0.8 - - - -
235B GLN* 1.3 81.7 - - + +
237B VAL* 1.3 59.3 + - - +
238B ALA 3.5 1.8 + - - +
281B ARG* 2.5 35.4 + - - +
402B GLN* 4.9 7.6 - - - +
405B ARG* 3.7 58.7 + - + +
406B LEU* 3.6 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B MET* 4.2 5.4 - - + -
233B VAL 3.1 18.8 - - - +
234B MET* 3.0 4.1 + - - +
236B GLU* 1.3 77.2 - - - +
238B ALA* 1.3 59.4 + - - +
273B GLU* 3.7 14.0 - - - +
274B GLN* 3.7 32.4 - - + +
277B ALA* 3.4 30.5 - - + -
278B ALA* 4.1 15.0 - - + -
402B GLN* 3.6 23.0 - - - +
406B LEU* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG* 4.3 4.0 + - - -
234B MET* 3.0 18.8 + - - +
235B GLN 3.3 17.0 - - - +
236B GLU 4.5 1.7 - - - +
237B VAL* 1.3 79.8 - - - +
239B GLN* 1.3 62.7 + - - +
242B GLN* 3.9 18.4 - - + -
243B PHE* 4.2 10.3 - - + -
247B LEU* 5.1 1.6 - - + -
274B GLN* 4.0 15.3 - - - +
405B ARG* 4.8 3.5 + - - -
----------------------------------------------------------
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