Contacts of the helix formed by residues 202 - 208 (chain B) in PDB entry 1A4I
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 202 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 4.1 8.5 - - + -
195B CYS* 3.6 37.7 - - + -
199B THR* 3.9 18.8 + - + +
200B ALA 3.2 5.1 + - - -
201B HIS* 1.3 75.8 - - - +
203B ASP* 1.4 63.1 + - - +
205B GLU* 3.1 1.7 + - - +
206B VAL* 2.9 32.9 + - + +
221B MET* 3.7 31.4 - - + -
222B VAL* 5.3 0.2 - - + -
226B TRP* 3.8 19.7 - - + -
302B NDP 3.8 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B HIS* 3.6 15.4 - - - +
202B LEU* 1.4 74.3 - - - +
204B GLU* 1.3 74.4 + - - +
206B VAL* 3.3 1.7 + - - +
207B ASN* 3.0 29.7 + - - +
226B TRP* 3.5 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B HIS* 3.0 36.6 + - + +
203B ASP* 1.3 89.6 - - - +
205B GLU* 1.3 63.9 + - + +
207B ASN* 3.5 9.1 + - - +
208B LYS* 2.9 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A HIS* 2.7 44.4 + - - +
191A THR* 3.9 9.3 - - - +
208A LYS* 5.5 1.9 - - - -
169B VAL* 3.4 17.2 - - - +
193B THR* 4.0 7.0 - - + +
195B CYS* 3.8 19.5 - - - -
199B THR* 3.9 18.8 - - + +
200B ALA 4.1 5.2 - - - +
201B HIS* 3.2 13.3 + - + +
202B LEU 3.1 6.6 + - - +
204B GLU* 1.3 75.9 - - + +
206B VAL* 1.3 64.5 + - - +
208B LYS* 3.1 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 4.3 8.2 - - + +
171B VAL* 3.9 27.8 - - + -
202B LEU* 2.9 28.7 + - + +
203B ASP 3.8 3.4 - - - +
205B GLU* 1.3 75.5 - - - +
207B ASN* 1.3 59.5 + - - +
208B LYS 3.1 0.2 - - - -
209B GLY* 3.0 23.9 + - - +
212B LEU* 3.8 29.9 - - + +
222B VAL* 4.2 9.4 - - + -
226B TRP* 3.7 37.4 - - + +
227B ILE* 4.5 1.3 - - + -
228B LYS 4.5 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ASP 3.0 15.7 + - - +
204B GLU* 3.7 9.4 - - - +
205B GLU 3.2 0.4 - - - -
206B VAL* 1.3 78.3 - - - +
208B LYS* 1.4 66.9 + - - +
209B GLY 3.4 0.4 - - - -
225B GLU 4.1 2.8 + - - -
226B TRP* 3.0 28.5 + - - +
227B ILE 3.4 17.6 + - - -
228B LYS* 3.2 27.5 - - - +
229B PRO* 4.6 2.8 - - - +
264B ARG* 3.9 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LYS* 4.3 31.9 - - - +
167B HIS* 3.7 20.2 - - + +
169B VAL* 4.3 4.9 - - + -
204B GLU* 2.9 39.7 + - - +
205B GLU* 3.5 15.3 - - - +
206B VAL 3.0 1.0 + - - -
207B ASN* 1.4 90.2 + - - +
209B GLY* 1.3 60.9 + - - +
210B ASP* 3.3 5.4 + - - -
228B LYS* 4.2 10.7 + - - +
----------------------------------------------------------
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