Contacts of the helix formed by residues 331 - 345 (chain D) in PDB entry 1VLP
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 ASN 331 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D SER 3.9 1.0 + - - -
330D LEU* 1.3 77.2 - - - +
332D VAL* 1.3 65.3 + - - +
333D GLU* 3.1 10.5 + - - +
334D LYS* 2.9 41.4 + - - +
335D ALA* 2.9 23.3 + - - +
353D ILE* 4.8 7.0 - - - -
356D ASN* 3.7 27.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D LYS* 3.7 44.6 - - + +
166D THR* 3.6 31.4 - - + -
167D LEU* 4.1 21.5 - - + -
331D ASN* 1.3 75.8 - - - +
333D GLU* 1.3 57.9 + - - +
335D ALA* 3.2 7.2 + - - +
336D ILE* 3.0 37.6 + - + +
353D ILE* 5.3 2.2 - - + -
356D ASN* 4.7 2.3 + - - +
357D PHE* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D ASN* 3.1 10.4 + - - +
332D VAL* 1.3 79.9 - - - +
334D LYS* 1.3 62.8 + - + +
336D ILE* 3.4 9.9 + - - +
337D THR* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 334 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D ASP 4.1 4.0 + - - +
329D SER* 2.8 39.4 + - - +
330D LEU* 3.7 16.6 - - + -
331D ASN* 2.9 29.7 + - - +
333D GLU* 1.3 74.7 - - + +
335D ALA* 1.3 60.8 + - - +
337D THR* 3.2 5.7 + - - -
338D TYR* 2.8 60.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D LEU* 3.7 23.3 - - + -
172D ILE* 3.9 4.7 - - + -
330D LEU* 3.8 2.6 - - + +
331D ASN 2.9 18.1 + - - +
332D VAL 3.2 5.4 + - - +
334D LYS* 1.3 76.0 - - - +
336D ILE* 1.3 55.7 + - - +
339D SER* 3.0 31.0 + - - -
351D PHE* 3.2 38.5 - - + -
353D ILE* 4.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D THR* 4.3 5.4 - - + +
170D ASN* 3.6 33.2 - - + +
172D ILE* 3.7 22.0 - - + -
332D VAL* 3.0 30.9 + - + +
333D GLU* 3.7 10.8 - - - +
334D LYS 3.3 0.2 - - - -
335D ALA* 1.3 74.7 - - - +
337D THR* 1.3 63.9 + - - +
339D SER* 3.5 1.8 + - - -
340D HIS* 3.2 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D VAL* 5.7 5.6 - - + -
333D GLU* 2.9 20.6 + - - +
334D LYS* 3.6 8.9 - - - -
336D ILE* 1.3 77.8 - - - +
338D TYR* 1.3 71.5 + - + +
340D HIS* 3.3 12.5 + - + +
341D ALA* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D GLN* 5.1 0.7 - - - -
300D PRO* 3.4 37.8 - - + +
301D VAL* 4.9 12.6 - - + -
326D TYR* 3.9 32.8 + + + -
328D ASP 5.4 2.4 + - - -
330D LEU* 3.9 30.3 - - + -
334D LYS* 2.8 50.3 + - + +
337D THR* 1.3 86.4 - - + +
339D SER* 1.3 60.4 + - - +
341D ALA* 3.2 7.2 + - + +
342D ALA* 2.9 29.5 + - - +
351D PHE* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 339 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D ASN 5.3 1.9 + - - -
172D ILE* 4.2 18.6 - - - +
335D ALA 3.0 20.1 + - - -
336D ILE* 3.6 5.4 - - - -
337D THR 3.3 0.2 - - - -
338D TYR* 1.3 76.9 - - - +
340D HIS* 1.3 64.9 + - - +
342D ALA 3.4 0.7 + - - -
343D LYS* 2.7 58.8 + - - +
349D ALA* 4.5 3.6 - - - -
351D PHE* 3.7 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D ASN* 5.1 4.0 + - - -
336D ILE* 3.2 38.1 + - + +
337D THR* 3.5 10.3 - - + +
338D TYR 3.3 0.2 - - - -
339D SER* 1.3 76.7 - - - +
341D ALA* 1.3 60.2 + - - +
343D LYS* 3.3 12.3 + - + +
344D GLU* 2.9 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 341 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D PRO 6.0 0.2 - - - -
301D VAL* 4.1 33.4 - - + -
304D THR* 4.3 10.5 - - + +
326D TYR* 5.0 0.7 - - + +
337D THR 3.0 13.4 + - - +
338D TYR* 3.2 12.1 + - - +
340D HIS* 1.3 75.4 - - - +
342D ALA* 1.3 62.5 + - - +
344D GLU* 3.3 8.4 + - - +
345D ASN* 2.8 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D THR* 4.0 10.8 - - - -
326D TYR* 3.6 13.4 + - + +
338D TYR 2.9 16.3 + - - +
339D SER 3.7 5.2 - - - +
340D HIS 3.2 0.2 - - - -
341D ALA* 1.3 77.8 - - - +
343D LYS* 1.3 62.2 + - - +
345D ASN 3.1 7.8 + - - -
347D MSE 3.0 45.3 + - + +
348D LEU 4.5 0.2 - - - +
349D ALA* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D ASN 6.1 0.4 - - - -
320D PHE* 3.6 26.0 - - + -
339D SER* 2.7 54.5 + - - +
340D HIS* 3.3 14.6 + - + +
342D ALA* 1.3 78.5 - - - +
344D GLU* 1.3 62.4 + - + +
345D ASN 3.2 0.9 + - - -
346D GLY 3.5 7.1 + - - -
347D MSE 4.3 3.4 + - - +
348D LEU* 5.6 0.6 - - - +
349D ALA* 4.1 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D HIS* 2.9 36.2 + - - +
341D ALA* 3.7 8.7 - - - +
342D ALA 3.3 0.2 - - - -
343D LYS* 1.3 76.3 - - + +
345D ASN* 1.3 66.6 + - - +
346D GLY 3.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D THR* 3.9 18.8 - - + +
305D LYS* 3.4 47.3 + - - +
308D SER* 2.6 38.6 + - - -
319D LYS* 5.4 2.7 - - - -
341D ALA* 2.8 31.4 + - - +
342D ALA 3.1 0.6 + - - -
344D GLU* 1.3 87.7 + - - +
346D GLY* 1.3 57.0 + - - +
347D MSE 3.4 3.3 + - - +
----------------------------------------------------------
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