Contacts of the helix formed by residues 4327 - 4333 (chain B) in PDB entry 6W75
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 CYS4327 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4323B GLY 3.3 4.0 + - - +
4324B ALA 3.2 10.4 + - - +
4325B SER 3.4 0.6 - - - -
4326B CYS* 1.3 77.8 - - - +
4328B LEU* 1.3 61.7 + - - +
4329B TYR* 3.5 12.8 - - - -
4330B CYS* 3.4 10.3 - - + -
4331B ARG* 2.9 32.4 + - - +
4336B HIS* 3.5 8.5 - - - -
4343B CYS* 3.7 7.2 - - - -
4344B ASP* 6.0 0.2 - - - -
4345B LEU* 3.8 20.2 - - + -
4361B VAL* 4.5 0.7 - - - -
4364B THR* 5.0 0.4 - - - -
4401B ZN 2.3 36.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4276B ALA* 3.7 41.7 - - + +
4277B ALA* 3.7 4.5 - - - +
4280B TYR* 4.1 8.7 - - + -
4291B ILE* 3.8 17.7 - - + -
4326B CYS 3.8 0.6 + - - -
4327B CYS* 1.3 72.0 - - - +
4329B TYR* 1.3 61.5 + - + +
4331B ARG* 4.6 2.9 - - - -
4332B CYS* 2.8 63.7 + - + +
4361B VAL* 3.7 23.7 - - + +
4364B THR* 5.3 1.0 + - - -
4365B LEU* 3.6 32.0 - - + +
4272D PHE* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR4329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4276B ALA* 4.3 20.0 - - + -
4277B ALA* 3.7 22.9 + - - +
4327B CYS* 3.2 11.6 - - - -
4328B LEU* 1.3 77.1 - - + +
4330B CYS* 1.3 65.1 + - - +
4333B HIS* 3.0 4.2 + - - -
4334B ILE* 2.9 52.1 + - + +
4335B ASP 3.4 16.4 - - - -
4336B HIS* 3.5 22.4 - + + +
4337B PRO* 3.4 41.3 - - + +
4365B LEU* 4.0 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS4330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6902A VAL* 3.1 26.8 - - + +
4324B ALA* 3.4 25.1 - - - +
4327B CYS* 3.3 8.6 + - - +
4329B TYR* 1.3 77.8 - - - +
4331B ARG* 1.3 60.2 + - - +
4333B HIS* 3.3 14.9 + - - -
4336B HIS* 3.6 9.6 - - - -
4343B CYS* 3.9 6.1 - - - -
4346B LYS* 4.3 19.7 - - - -
4401B ZN 2.3 34.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6874A LYS 4.3 14.1 + - - -
6875A GLY 5.1 1.2 + - - -
6876A VAL* 3.8 18.9 - - - +
6902A VAL* 4.1 11.5 - - - +
4291B ILE* 3.6 32.2 - - + +
4292B THR* 2.9 29.5 + - - +
4293B ASN* 3.8 15.2 + - - +
4294B CYS* 4.0 1.2 - - - +
4324B ALA 4.0 2.2 - - - +
4325B SER* 3.0 45.8 + - - +
4327B CYS 2.9 25.1 + - - +
4328B LEU* 4.0 3.8 - - - +
4330B CYS* 1.3 71.7 - - - +
4332B CYS* 1.3 58.6 + - - +
4333B HIS* 3.2 18.4 + - - -
4361B VAL* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS4332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4291B ILE* 4.5 6.1 - - - -
4328B LEU* 2.8 47.9 + - - +
4331B ARG* 1.3 73.0 - - - +
4333B HIS* 1.3 72.7 + - - +
4334B ILE* 3.5 27.9 - - + +
4272D PHE* 3.6 25.4 - - - -
4273D ALA* 6.1 0.4 - - - -
4274D VAL* 5.0 1.8 - - + -
4335D ASP* 3.9 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS4333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6875A GLY 5.5 0.8 + - - -
6900A ASP* 3.7 29.5 + - - -
6901A PHE* 4.8 5.1 - - - -
6902A VAL* 3.7 25.8 - - + +
4329B TYR 3.0 7.1 + - - -
4330B CYS 3.3 4.6 + - - -
4331B ARG 3.2 26.8 + - - -
4332B CYS* 1.3 81.0 - - - +
4334B ILE* 1.3 59.5 + - - +
4333D HIS 3.9 12.0 - - - +
4334D ILE* 4.4 3.8 - - - -
4335D ASP* 3.8 30.0 - - - +
----------------------------------------------------------
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