Contacts of the helix formed by residues 323 - 328 (chain B) in PDB entry 6WCZ
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 323 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 1.3 81.7 - - - +
324B GLY* 1.3 63.0 + - - +
325B VAL* 2.9 30.6 + - - +
326B VAL* 4.0 12.7 - - + +
327B ARG* 3.3 12.1 + - - +
740B ALA* 3.4 27.8 + - - +
741B ARG* 2.8 12.0 + - - +
742B VAL 4.0 6.5 - - - +
743B SER* 3.6 9.9 - - - -
753B THR* 3.9 19.8 + - + -
756B LEU* 5.2 5.2 - - + +
757B ALA* 3.4 31.1 - - - +
760B TYR* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 3.3 8.2 + - - -
323B ASN* 1.3 73.6 + - - +
325B VAL* 1.3 62.0 + - - +
327B ARG* 3.7 13.2 - - - -
328B LEU* 2.9 37.2 + - - +
753B THR* 5.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ASN* 2.9 21.3 + - - +
324B GLY* 1.3 77.8 - - - +
326B VAL* 1.3 55.2 - - - +
328B LEU* 2.7 25.9 + - - +
329B LEU* 2.9 26.2 + - + +
750B ILE* 5.3 9.4 - - + -
753B THR* 4.1 23.1 - - - +
754B ALA* 4.7 6.3 - - + -
757B ALA* 4.5 3.4 - - + -
781B ILE* 4.0 24.5 - - + -
784B ALA* 5.7 1.8 - - + -
785B VAL* 5.4 6.3 - - + -
872B VAL* 4.9 18.6 - - + -
876B ILE* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ASN* 4.0 15.5 - - - +
325B VAL* 1.3 76.0 - - - +
327B ARG* 1.3 57.3 + - - +
329B LEU* 3.5 10.0 - - - +
330B SER* 2.7 36.5 + - - -
737B ILE* 6.0 2.0 - - + +
740B ALA* 4.6 20.0 - - + +
741B ARG* 4.2 8.7 - - - +
757B ALA* 5.6 0.7 - - + -
764B TRP* 6.1 0.2 - - + -
777B MET* 4.8 14.4 - - + -
781B ILE* 5.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 4.3 24.7 - - - +
323B ASN 3.3 18.8 + - - +
324B GLY* 3.3 10.5 - - - +
326B VAL* 1.3 79.9 - - - +
328B LEU* 1.3 73.2 + - + +
329B LEU 3.3 2.8 + - - -
330B SER 3.5 15.4 - - - +
334B ASP* 4.3 27.7 + - - +
741B ARG* 3.8 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLY* 2.9 24.7 + - - +
325B VAL* 2.7 15.1 + - - +
327B ARG* 1.3 92.1 - - + +
329B LEU* 1.3 62.5 + - + +
868B THR* 4.0 18.7 - - - +
871B MET* 5.8 9.1 - - + +
872B VAL* 5.9 6.5 - - + -
875B ILE* 5.2 16.4 - - + -
----------------------------------------------------------
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