Contacts of the helix formed by residues 333 - 342 (chain B) in PDB entry 3V4V
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 ALA 333 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ASP 4.1 5.2 - - - +
271B ASP* 3.7 38.1 - - - +
272B THR* 4.0 5.8 - - - +
329B VAL* 4.5 2.0 - - + -
332B ALA* 1.3 74.9 - - + +
334B LEU* 1.3 60.4 + - - +
335B PRO* 3.4 7.7 - - - +
336B VAL* 3.4 19.2 + - - +
337B TYR* 3.0 27.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B VAL* 3.6 17.7 - - + -
330B THR 3.2 9.4 + - - +
331B SER 3.2 19.7 - - - +
332B ALA 2.7 8.9 + - - -
333B ALA* 1.3 71.7 - - - +
335B PRO* 1.4 67.2 - - + +
337B TYR* 3.1 2.6 + - - -
338B GLN* 3.0 41.6 + - - +
349B VAL* 3.4 33.2 - - + -
350B GLY 3.9 8.7 - - - +
351B GLU* 3.7 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B SER 3.9 6.5 - - - +
332B ALA* 4.3 1.6 - - - -
333B ALA* 3.5 10.5 - - - +
334B LEU* 1.4 93.9 - - + +
336B VAL* 1.3 64.5 + - + +
338B GLN* 3.3 20.6 - - - +
339B GLU* 3.2 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLU* 5.3 4.9 - - - +
244A GLN* 3.6 36.1 - - + +
269A LEU* 4.1 6.8 - - + +
272B THR* 4.1 10.8 - - - +
273B PHE* 3.6 26.5 - - + -
333B ALA* 3.4 18.4 + - - +
334B LEU 3.2 0.6 - - - -
335B PRO* 1.3 79.0 - - + +
337B TYR* 1.3 63.4 + - + +
339B GLU* 3.3 12.5 + - - +
340B LEU* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PHE* 5.9 1.6 - + - -
267B PHE* 3.4 37.3 - + - -
269B SER* 4.0 2.1 - - - -
271B ASP 3.0 28.3 + - - -
272B THR* 3.8 8.1 + - - -
273B PHE* 3.7 32.3 - + - +
327B PHE* 3.8 34.9 - + + -
329B VAL* 3.5 29.6 - - + -
333B ALA* 3.0 26.9 - - + -
334B LEU 3.1 6.5 + - - +
336B VAL* 1.3 75.2 - - + +
338B GLN* 1.3 58.6 + - - +
340B LEU* 3.5 11.8 + - + +
341B SER* 3.0 20.6 + - - -
349B VAL* 3.4 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 3.0 38.8 + - - +
335B PRO* 3.3 19.9 - - - +
336B VAL 3.1 0.4 - - - -
337B TYR* 1.3 74.2 - - - +
339B GLU* 1.3 59.3 + - + +
340B LEU 3.0 4.0 - - - -
341B SER* 2.9 19.9 + - - -
342B LYS* 3.2 25.8 + - - +
349B VAL* 4.1 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLU 4.9 2.3 - - - +
245A ILE* 4.5 13.1 - - - +
269A LEU* 3.8 28.4 - - + +
335B PRO* 3.2 20.8 + - - +
336B VAL* 3.3 9.4 + - - +
338B GLN* 1.3 75.7 - - + +
340B LEU* 1.3 59.7 + - - +
341B SER 3.4 0.2 - - - -
342B LYS* 3.8 34.2 + - + +
343B LEU* 3.4 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 3.7 13.0 - - + -
243B PHE* 4.1 18.6 - - + -
273B PHE* 3.9 24.0 - - + -
311B VAL* 3.9 29.4 - - + +
314B VAL* 6.1 3.1 - - + -
315B ALA* 6.2 0.4 - - + -
327B PHE* 4.0 29.6 - - + -
336B VAL 3.1 15.9 + - - +
337B TYR* 3.6 11.7 - - + +
338B GLN 3.0 0.4 - - - -
339B GLU* 1.3 77.3 - - - +
341B SER* 1.3 63.3 + - - +
342B LYS 3.2 0.7 - - - -
343B LEU* 3.2 18.3 + - + +
344B ILE* 3.6 19.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B PHE* 4.4 6.3 - - - -
337B TYR 3.0 4.2 + - - -
338B GLN* 2.9 8.6 + - - -
340B LEU* 1.3 72.4 - - - +
342B LYS* 1.3 57.7 + - - +
343B LEU 3.0 5.4 - - - -
344B ILE* 2.8 28.3 + - - +
347B SER* 2.6 43.1 + - - +
348B ALA 4.4 0.2 - - - -
349B VAL* 3.5 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLN* 3.2 24.6 + - - +
339B GLU* 3.8 34.1 - - + +
340B LEU 3.2 0.6 - - - -
341B SER* 1.3 76.4 - - - +
343B LEU* 1.3 65.9 + - + +
344B ILE 3.4 1.2 - - - -
406B ARG* 5.9 0.7 + - - -
----------------------------------------------------------
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