Contacts of the helix formed by residues 1621 - 1625 (chain B) in PDB entry 4BHW
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 CYS1621 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1326B VAL 3.1 27.1 - - - +
1327B HIS* 3.3 16.1 + - + +
1619B ILE* 3.5 3.3 + - + -
1620B PRO* 1.3 75.6 - - - +
1622B ASP* 1.3 62.3 + - - +
1623B LEU* 3.1 3.4 - - - -
1624B MET* 2.9 29.3 + - - -
1625B ASP 3.1 8.7 + - - -
1658B LEU* 3.7 27.4 - - - -
1661B GLN* 3.3 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1622 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1620B PRO 4.3 0.2 - - - -
1621B CYS* 1.3 72.6 + - - +
1623B LEU* 1.3 62.1 + - - +
1624B MET 3.3 0.3 + - - -
1625B ASP* 3.4 22.3 + - - +
1629B ALA* 3.7 11.3 - - - +
1661B GLN* 4.2 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1623 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1621B CYS* 3.1 4.7 + - - -
1622B ASP* 1.3 80.2 - - - +
1624B MET* 1.3 73.6 - - + +
1626B GLY 4.3 1.6 - - - +
1629B ALA* 3.2 41.0 - - + +
1630B PHE* 3.5 15.1 + - + -
1633B LEU* 4.1 21.1 - - + -
1654B MET* 5.0 1.8 - - - +
1657B GLU* 3.7 32.8 - - + -
1658B LEU* 4.1 18.4 - - + -
1661B GLN* 3.5 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1624 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1326B VAL* 3.6 17.9 - - + -
1327B HIS* 3.6 30.4 - - + +
1359B ALA* 3.8 4.0 - - + +
1361B PHE* 3.4 36.3 - - + -
1377B HIS* 3.5 15.6 + - - -
1621B CYS* 2.9 18.5 + - - +
1623B LEU* 1.3 87.6 - - + +
1625B ASP* 1.3 60.9 + - - +
1626B GLY 3.0 14.4 + - - +
1630B PHE* 3.9 24.5 - - + -
1654B MET* 3.7 22.2 - - + -
1658B LEU* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1625 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1327B HIS* 3.4 28.6 - - + -
1329B SER* 3.7 11.1 + - - -
1331B LYS* 2.9 31.5 + - - -
1357B THR* 5.7 0.7 - - - -
1621B CYS 3.1 5.4 + - - +
1622B ASP* 3.4 23.3 + - - +
1623B LEU 3.5 0.4 - - - -
1624B MET* 1.3 72.2 - - - +
1626B GLY* 1.3 62.3 + - - +
1628B ASP* 5.1 1.2 + - - +
1629B ALA* 5.0 5.4 + - - +
----------------------------------------------------------
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