Contacts of the helix formed by residues 323 - 334 (chain A) in PDB entry 2VMX
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 323 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 3.6 6.6 - - - +
322A LEU* 1.3 78.0 - - - +
324A GLY* 1.3 63.7 + - - +
325A LYS* 3.6 5.7 + - - +
326A THR* 3.0 31.2 + - - +
327A ALA* 3.2 16.5 + - - +
348A GLU* 4.2 14.4 - - - +
352A VAL* 3.5 25.6 - - + +
353A THR 3.3 13.0 - - - +
354A SER* 4.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 3.8 8.3 - - - -
323A THR* 1.3 71.5 - - - +
325A LYS* 1.3 51.2 + - - +
327A ALA* 3.3 1.7 + - - +
328A GLU* 2.8 36.9 + - - +
340A LYS* 3.5 7.6 - - - +
353A THR* 2.9 20.0 + - - -
355A GLY 3.1 30.7 - - - +
356A ILE* 3.7 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A THR* 3.8 6.7 - - - +
324A GLY* 1.3 77.1 - - - +
326A THR* 1.3 62.8 + - - +
328A GLU* 3.5 5.3 + - - +
329A LYS* 3.0 36.2 + - + +
340A LYS* 3.7 23.3 - - + +
351A GLY 4.0 14.4 - - - +
352A VAL* 3.1 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LEU* 3.8 24.2 - - + -
323A THR* 3.0 27.7 + - - +
325A LYS* 1.3 76.9 - - - +
327A ALA* 1.3 59.7 + - - +
329A LYS* 3.3 8.3 + - - +
330A VAL* 3.0 29.5 + - + +
387A VAL* 4.6 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 3.5 31.9 - - + -
322A LEU* 5.1 3.1 - - + +
323A THR 3.2 3.6 + - - +
324A GLY 3.3 4.2 + - - +
326A THR* 1.3 77.9 - - - +
328A GLU* 1.3 59.8 + - - +
330A VAL* 3.3 3.0 - - - +
331A LEU* 2.9 36.9 + - - +
356A ILE* 3.8 9.4 - - + -
384A LEU* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLY 2.8 19.4 + - - +
325A LYS* 3.7 6.9 - - - +
327A ALA* 1.3 72.0 - - - +
329A LYS* 1.3 57.9 + - - +
331A LEU* 3.9 1.6 - - - +
332A ASP* 3.0 30.5 + - + +
336A ILE 4.9 0.7 - - - +
338A VAL* 3.7 28.8 + - + +
339A ASN* 3.4 11.4 - - - +
340A LYS* 2.8 61.7 + - - +
356A ILE* 4.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS* 3.0 29.3 + - + +
326A THR* 3.6 7.9 - - - +
328A GLU* 1.3 78.3 - - - +
330A VAL* 1.3 62.7 + - - +
332A ASP* 3.3 10.5 + - - +
333A GLU* 3.2 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A THR* 3.0 17.6 + - + +
327A ALA* 3.3 10.8 - - - +
329A LYS* 1.3 74.1 - - - +
331A LEU* 1.3 68.1 + - - +
333A GLU* 3.1 27.9 + - - +
334A VAL* 3.6 8.3 + - - +
383A VAL* 3.8 8.3 - - + -
384A LEU* 3.7 22.2 - - + -
387A VAL* 4.0 30.7 - - + -
393A LEU* 3.8 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA 2.9 21.5 + - - +
328A GLU 4.0 3.1 - - - +
330A VAL* 1.3 73.3 - - - +
332A ASP* 1.3 65.6 + - - +
334A VAL* 3.1 12.6 + - + +
335A GLY 3.2 0.2 + - - -
336A ILE* 3.0 50.9 + - + +
338A VAL* 3.9 27.8 - - + -
356A ILE* 3.9 19.7 - - + -
380A ILE* 4.1 24.9 - - + -
383A VAL* 3.9 24.7 - - + -
384A LEU* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 4.7 8.0 + - - -
328A GLU* 3.0 15.4 + - + +
329A LYS* 3.3 13.7 - - - +
330A VAL 3.3 0.2 - - - -
331A LEU* 1.3 76.7 - - - +
333A GLU* 1.3 64.9 + - - +
334A VAL 3.2 0.9 + - - -
335A GLY* 3.3 11.2 + - - +
336A ILE 3.5 9.0 + - - +
337A THR* 5.8 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A LYS* 3.2 40.0 + - + +
330A VAL* 3.1 19.9 + - + +
332A ASP* 1.3 79.2 - - - +
334A VAL* 1.3 59.7 + - + +
335A GLY 3.6 0.2 - - - -
390A GLU* 4.6 6.9 - - - +
393A LEU* 3.9 18.7 - - + +
397A ARG* 3.0 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A VAL 3.9 7.9 - - - +
331A LEU* 3.1 21.4 + - - +
333A GLU* 1.3 81.5 - - + +
335A GLY* 1.3 56.6 + - - +
336A ILE* 4.2 19.3 - - + -
383A VAL* 4.0 21.8 - - + -
393A LEU* 3.4 37.5 - - + +
396A ALA* 3.9 17.0 - - + -
397A ARG* 3.8 20.3 - - - +
400A VAL* 3.4 22.2 - - + +
----------------------------------------------------------
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