Contacts of the helix formed by residues 100 - 106 (chain B) in PDB entry 2W9Z
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 LEU 100 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASP* 1.3 72.4 - - - +
101B ARG* 1.3 57.4 + - - +
103B TYR* 3.4 9.5 + - + +
104B LEU* 2.9 62.2 + - + +
120B LEU* 4.1 22.4 - - + -
143B PRO* 3.1 22.4 + - + +
146B ILE* 2.6 49.8 + - + +
148B VAL* 4.9 8.7 - - + -
154B VAL* 6.1 2.0 - - + -
203B ILE* 4.1 18.8 - - + -
207B MET* 5.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASP* 2.9 16.0 + - - +
100B LEU* 1.3 74.2 - - - +
102B THR* 1.3 53.9 + - - +
103B TYR 2.6 4.6 + - - -
104B LEU* 2.4 31.0 + - - +
105B ASP* 2.6 39.2 + - - +
143B PRO* 3.5 31.2 + - + +
144B GLU* 2.7 43.0 + - - +
179B TRP* 5.2 7.9 - - - -
180B TYR* 4.0 9.1 + - - -
206B GLU* 4.1 9.3 + - - -
211B LYS* 6.1 2.0 - - - +
212B PRO* 5.2 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLN* 3.5 30.7 - - + +
99B ASP* 3.2 25.0 + - - -
101B ARG* 1.3 83.8 - - - +
103B TYR* 1.3 55.3 + - - +
105B ASP* 4.0 9.6 - - - +
106B LYS* 2.8 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLN* 2.8 28.3 - - + +
99B ASP 3.1 14.0 + - - +
100B LEU* 3.5 14.6 - - + +
101B ARG 2.6 5.9 + - - -
102B THR* 1.3 74.3 - - - +
104B LEU* 1.3 79.8 + - + +
105B ASP 3.5 0.2 - - - -
106B LYS* 4.2 9.6 - - + +
107B ALA* 4.2 12.1 + - - +
116B THR* 3.7 23.9 - - + +
120B LEU* 4.3 21.3 - - + +
148B VAL* 4.6 21.3 - - + -
152B GLY* 5.6 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 2.9 36.9 + - + +
101B ARG* 2.4 18.6 + - - +
103B TYR* 1.3 99.4 - - + +
105B ASP* 1.3 60.5 + - - +
107B ALA* 3.1 21.9 - - + +
120B LEU* 5.1 4.0 - - + -
143B PRO* 6.3 1.1 - - + -
206B GLU* 4.6 11.7 - - + +
207B MET* 4.2 37.9 - - + +
210B ARG* 3.1 26.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 2.6 47.0 + - - +
102B THR* 4.3 6.6 + - - -
104B LEU* 1.3 72.1 - - - +
106B LYS* 1.3 53.2 + - - +
107B ALA 2.3 20.7 + - - +
210B ARG* 3.3 15.0 + - - +
211B LYS* 6.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLN* 3.5 27.2 - - - +
102B THR* 2.8 27.9 + - + +
103B TYR* 4.2 11.6 - - + +
105B ASP* 1.3 73.7 - - - +
107B ALA* 1.3 56.7 + - - +
108B PRO* 2.8 16.7 - - - +
----------------------------------------------------------
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