Contacts of the strand formed by residues 202 - 206 (chain A) in PDB entry 2DH3
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 ARG 202 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TRP* 3.4 60.9 - - + +
156A LYS 3.0 15.2 + - - +
157A GLY* 3.2 2.9 - - - -
158A LEU* 3.1 24.3 + - - +
197A LYS* 5.8 7.7 - - - +
200A SER* 5.5 9.6 - - - +
201A ILE* 1.3 83.4 - - - +
203A VAL* 1.3 60.7 + - - +
204A ILE 4.2 0.2 - - - -
242A ASP* 3.3 30.9 + - + +
272A ASP* 3.6 22.8 + - - -
273A ARG* 5.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 3.8 17.0 - - + -
160A LEU* 4.0 33.9 - - + -
189A PHE* 5.0 6.3 - - + -
192A LEU* 5.4 9.4 - - + -
193A LEU* 3.8 32.3 - - + -
196A ALA* 4.2 21.1 - - + -
201A ILE 4.3 0.7 - - - +
202A ARG* 1.3 77.9 - - - +
204A ILE* 1.3 66.6 + - - +
205A LEU* 5.0 0.9 - - - +
241A VAL* 3.8 7.0 - - + +
242A ASP* 3.1 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TRP* 3.5 31.6 - - + -
123A LEU* 4.1 12.8 - - + -
157A GLY* 5.4 0.4 - - - -
158A LEU 3.0 11.9 + - - +
159A VAL* 3.5 18.8 - - + -
160A LEU* 2.7 34.5 + - - +
202A ARG 5.6 0.2 - - - -
203A VAL* 1.3 78.6 - - - +
205A LEU* 1.3 60.1 + - - +
243A GLY* 3.6 13.9 - - - -
244A PHE 3.5 32.8 - - - +
245A GLN 3.8 2.7 - - - +
274A LEU* 3.9 11.0 - - + -
276A ILE* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 5.5 0.2 - - - -
160A LEU* 3.5 24.0 - - + +
163A ILE* 3.8 34.1 - - + -
189A PHE* 4.3 8.1 - - + -
203A VAL* 4.1 2.0 + - + -
204A ILE* 1.3 73.2 - - - +
206A ASP* 1.3 67.8 + - - +
207A LEU* 3.9 12.3 - - + -
236A TRP* 3.9 49.1 - - + -
241A VAL* 4.7 9.2 - - + +
243A GLY 3.2 11.8 + - - +
244A PHE* 3.2 17.0 - - + +
245A GLN 2.9 20.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 5.0 2.9 - - + +
160A LEU 2.8 18.6 + - - +
161A GLY 3.7 4.1 - - - +
162A PRO* 3.4 39.7 - - - +
163A ILE 4.6 0.5 + - - -
164A HIS* 4.5 1.7 + - - -
204A ILE 4.0 0.2 + - - -
205A LEU* 1.3 75.3 - - - +
207A LEU* 1.3 65.6 + - - +
208A THR* 2.6 42.4 + - - -
245A GLN* 2.7 41.0 + - + +
247A ARG* 3.3 18.4 + - - -
----------------------------------------------------------
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