Contacts of the helix formed by residues 133 - 138 (chain B) in PDB entry 2QVS
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 ILE 133 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 4.1 5.2 - - - +
130B CYS* 3.2 28.3 + - + +
132B ASP* 1.3 73.5 - - + +
134B LEU* 1.3 61.9 - - + +
135B LEU* 4.2 5.8 - - + +
136B PHE* 2.9 29.0 + - + -
137B LYS* 2.6 34.2 + - - +
172B PHE* 4.1 16.4 - - + -
201B SER* 3.9 21.1 - - - +
204B GLU* 4.2 31.9 - - + -
248E GLU* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ASP 3.1 5.7 + - - -
133B ILE* 1.3 77.1 - - + +
135B LEU* 1.3 77.1 + - + +
136B PHE 3.4 0.7 + - - -
137B LYS* 3.7 24.9 + - + +
138B ASN* 4.4 3.5 + - - +
204B GLU* 5.7 5.6 - - + +
208B MET* 5.8 2.0 - - - -
210E ILE* 4.4 14.6 - - + -
211E LEU* 4.2 11.3 - - + +
244E ILE* 4.4 13.5 - - + -
247E TYR* 4.0 30.5 - - + +
248E GLU* 3.8 38.7 + - + +
251E VAL* 4.5 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ILE* 3.1 4.0 + - + +
134B LEU* 1.3 90.9 - - + +
136B PHE* 1.3 71.7 + - + +
138B ASN 5.2 0.2 + - - -
139B LEU* 3.4 23.6 + - - +
204B GLU* 4.3 9.2 - - + +
207B LEU* 3.9 25.8 - - + +
208B MET* 3.9 32.5 - - + -
233B PHE* 4.0 21.2 - - + -
210E ILE* 3.6 25.8 - - + +
211E LEU* 3.9 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B CYS* 3.6 46.2 - - + +
133B ILE* 2.9 23.4 + - + +
135B LEU* 1.3 85.0 - - + +
137B LYS* 1.3 65.2 - - - +
138B ASN 2.9 5.3 + - - -
139B LEU* 3.0 29.8 + - + +
144B LEU* 4.2 19.7 - - + +
147B VAL* 3.8 20.6 - - + -
148B LEU* 5.3 0.7 - - + -
151B MET* 5.2 4.3 - - - -
172B PHE* 4.2 14.1 - + - -
207B LEU* 3.6 23.8 - - + -
228B LEU* 3.9 23.6 - - + -
233B PHE* 4.2 9.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS 3.4 19.2 + - - +
132B ASP* 2.8 42.3 + - - +
133B ILE 2.6 19.4 + - - +
134B LEU* 3.7 19.7 - - + +
136B PHE* 1.3 71.8 - - - +
138B ASN* 1.3 81.9 + - - +
139B LEU 4.0 1.2 + - - +
248E GLU* 5.9 1.1 - - - -
251E VAL* 6.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU 4.4 4.4 + - - +
135B LEU 5.2 0.6 + - - -
136B PHE 2.9 2.0 + - - -
137B LYS* 1.3 106.1 - - - +
139B LEU* 1.3 63.4 - - - +
140B ASP 4.0 0.9 + - - -
211E LEU* 6.5 1.1 - - + -
213E LYS* 4.2 17.3 + - - +
251E VAL* 5.9 4.6 - - - +
----------------------------------------------------------
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