Contacts of the helix formed by residues 327 - 340 (chain P) in PDB entry 3ZPV
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 SER 327 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797O TRP* 4.1 1.3 - - - -
798O CYS* 3.6 10.7 - - - +
800O ASP* 4.5 7.6 - - - -
803O VAL* 4.0 24.7 - - - -
325P VAL* 4.2 1.2 + - - +
326P PHE* 1.3 76.3 - - - +
328P THR* 1.3 65.7 + - - +
329P GLN* 3.6 10.7 + - - +
330P LEU* 3.2 25.9 + - - +
331P ALA* 2.9 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 328 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779O VAL* 3.2 30.9 + - - +
780O GLY* 3.6 10.3 - - - +
781O LEU* 3.7 16.7 - - + +
797O TRP* 3.1 29.7 + - - +
798O CYS 4.0 2.5 + - - -
800O ASP* 4.6 13.0 + - - -
327P SER* 1.3 72.5 - - - +
329P GLN* 1.3 64.5 + - - +
331P ALA* 3.3 1.4 + - - +
332P ASN* 2.9 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 329 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800O ASP* 5.3 3.0 + - - +
327P SER* 3.2 9.1 + - - +
328P THR* 1.3 81.2 - - - +
330P LEU* 1.3 60.3 + - - +
332P ASN* 3.3 8.0 + - - +
333P LYS* 3.0 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325P VAL 4.0 11.0 - - - +
326P PHE* 4.0 10.1 - - + -
327P SER* 3.2 20.5 + - - +
329P GLN* 1.3 82.5 - - - +
331P ALA* 1.3 58.6 + - - +
333P LYS* 3.4 6.1 + - + +
334P GLY* 2.9 26.9 + - - -
349P TYR* 3.9 29.2 - - + +
350P HIS* 3.8 31.4 - - + +
353P GLN* 4.5 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781O LEU* 3.9 9.4 - - + -
785O ALA* 3.5 7.0 - - + +
789O LEU* 3.9 32.5 - - + -
326P PHE* 3.9 17.4 - - + -
327P SER 2.9 17.9 + - - +
328P THR 3.7 3.4 - - - +
330P LEU* 1.3 76.7 - - - +
332P ASN* 1.3 58.0 + - - +
334P GLY* 3.8 0.7 - - - -
335P ALA* 3.0 30.5 + - - +
346P ILE* 4.7 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 332 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780O GLY 2.8 25.3 + - - -
781O LEU* 3.7 2.2 - - - -
782O THR* 2.9 45.1 + - + +
785O ALA* 3.3 9.5 - - - +
328P THR* 2.9 27.1 + - - +
329P GLN* 3.6 6.5 - - - +
331P ALA* 1.3 78.0 - - - +
333P LYS* 1.3 62.4 + - + +
335P ALA* 3.4 3.7 + - - +
336P GLU* 3.2 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 333 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329P GLN* 3.0 49.0 + - + +
330P LEU* 4.0 6.3 - - + +
332P ASN* 1.3 73.8 - - + +
334P GLY* 1.3 66.2 + - - +
336P GLU* 3.2 10.9 + - + +
337P SER* 3.0 23.4 + - - -
349P TYR* 3.4 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 334 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326P PHE* 5.5 0.2 - - - -
330P LEU 2.9 15.1 + - - -
331P ALA* 3.8 1.6 - - - -
333P LYS* 1.3 75.3 - - - +
335P ALA* 1.3 62.6 + - - +
337P SER* 3.1 17.8 - - - -
338P VAL* 3.1 12.5 + - - +
346P ILE* 3.7 14.1 - - - +
349P TYR* 3.5 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 335 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782O THR* 4.6 1.8 - - - +
784O ALA* 4.1 7.6 - - + -
785O ALA* 3.7 30.1 - - + +
788O MET* 3.8 21.2 - - - +
331P ALA 3.0 18.3 + - - +
332P ASN 3.8 4.7 - - - +
334P GLY* 1.3 75.1 - - - +
336P GLU* 1.3 61.3 + - - +
338P VAL* 3.2 2.9 + - - +
339P LEU* 3.0 30.1 + - + +
346P ILE* 3.8 2.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 336 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782C THR* 3.4 35.4 + - + +
783C GLU* 3.6 16.6 + - - +
784C ALA* 3.4 26.8 + - - +
335D ALA* 5.5 0.9 - - - +
336D GLU* 6.0 2.1 - - - +
339D LEU* 4.4 9.0 - - - +
332P ASN 3.2 15.5 + - - +
333P LYS* 3.2 14.5 + - + +
335P ALA* 1.3 76.5 - - - +
337P SER* 1.3 51.6 + - - +
339P LEU* 3.3 10.0 + - + +
340P SER* 2.8 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 337 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333P LYS 3.0 9.7 + - - -
334P GLY 3.1 11.4 - - - -
336P GLU* 1.3 76.6 - - - +
338P VAL* 1.3 59.0 + - - -
340P SER* 3.5 6.3 - - - -
341P GLY 3.5 1.6 + - - -
342P GLN* 3.1 45.4 + - - +
343P PHE* 3.3 23.5 + - - -
349P TYR* 3.2 28.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788O MET* 3.7 28.3 - - + -
334P GLY 3.1 13.5 + - - +
335P ALA 3.2 6.7 + - - +
336P GLU 3.2 0.4 - - - -
337P SER* 1.3 76.2 - - - +
339P LEU* 1.3 61.3 + - + +
341P GLY* 3.1 17.5 + - - -
343P PHE* 3.5 15.8 - - + +
344P GLN 3.7 16.6 - - - +
345P THR* 3.5 35.0 - - - +
346P ILE* 3.7 3.4 - - - +
349P TYR* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D GLU* 4.9 15.7 - - + +
339D LEU* 3.7 66.1 - - + +
340D SER* 4.6 7.2 - - - +
784O ALA* 3.9 24.2 - - + -
788O MET* 4.1 17.5 - - + -
335P ALA 3.0 22.2 + - - +
336P GLU* 3.8 4.9 - - + +
338P VAL* 1.3 78.0 - - + +
340P SER* 1.3 60.5 + - - +
341P GLY* 3.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 340 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784C ALA* 5.8 3.3 - - - +
339D LEU* 4.6 9.7 - - - +
336P GLU* 2.8 22.1 + - - +
337P SER* 3.5 9.4 - - - -
339P LEU* 1.3 75.7 - - - +
341P GLY* 1.3 57.1 + - - -
342P GLN* 3.3 26.1 + - - +
----------------------------------------------------------
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