Contacts of the helix formed by residues 204 - 213 (chain B) in PDB entry 1ADI
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 VAL 204 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 5.7 1.1 - - + -
67B ILE* 3.5 32.8 - - + -
68B ILE 4.6 0.4 - - - +
69B GLY* 4.9 5.6 - - - -
70B ASN 5.6 0.2 - - - +
98B LEU* 6.0 0.7 - - + -
99B LEU 4.4 4.5 - - - +
100B SER* 3.9 32.7 - - - +
202B VAL* 3.2 10.2 + - + +
203B ASP* 1.3 72.1 + - - +
205B SER* 1.4 62.5 + - - +
207B LEU* 3.8 7.4 - - + +
208B LEU* 2.9 41.9 + - + +
252B SER* 3.5 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A HIS* 4.7 3.8 + - - -
317A ARG* 3.4 23.6 + - - -
320A GLN* 3.7 12.9 - - - +
321A LEU* 3.9 14.7 - - - +
203B ASP* 3.2 1.6 + - - -
204B VAL* 1.4 76.7 - - - +
206B ASP* 1.3 58.5 + - - +
208B LEU* 3.9 3.3 - - - +
209B ASP* 2.9 30.5 + - - +
252B SER 4.3 5.2 + - - -
253B GLY* 3.5 30.3 + - - +
254B LEU* 4.9 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG* 4.9 1.5 + - - +
320A GLN* 3.6 24.1 + - - +
357A THR* 3.0 35.0 - - - +
203B ASP* 3.1 25.3 + - + +
205B SER* 1.3 75.7 - - - +
207B LEU* 1.3 69.1 + - - +
209B ASP* 3.1 2.3 + - - +
210B GLN* 2.8 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 3.8 30.5 - - + +
67B ILE* 4.2 27.8 - - + -
98B LEU* 4.2 16.2 - - + -
202B VAL* 4.1 22.7 - - + -
203B ASP 2.8 21.6 + - - +
204B VAL* 3.8 7.9 - - + +
206B ASP* 1.3 76.3 - - - +
208B LEU* 1.3 64.3 + - + +
210B GLN* 3.1 8.0 + - + +
211B ALA* 3.0 18.0 + - - +
214B ARG* 4.7 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 4.9 4.0 - - + -
31B VAL* 3.8 25.4 - - + -
67B ILE* 4.0 16.2 - - + -
204B VAL* 2.9 40.6 + - + +
205B SER* 4.1 1.3 - - - +
207B LEU* 1.3 73.8 - - + +
209B ASP* 1.3 58.2 + - - +
211B ALA* 3.1 7.3 + - - +
212B ARG* 2.9 29.6 + - - +
218B VAL* 4.0 20.4 - - + +
220B PHE* 3.9 27.6 - - + -
252B SER* 4.1 6.7 - - - +
254B LEU* 4.0 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLN* 2.8 39.5 + - + +
205B SER 2.9 19.8 + - - +
206B ASP 3.1 3.8 + - - +
208B LEU* 1.3 75.5 - - - +
210B GLN* 1.3 69.6 + - - +
212B ARG* 3.2 29.0 + - - +
213B GLN* 2.9 47.5 + - - +
254B LEU* 4.2 9.9 - - + +
258B TYR* 5.0 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLN* 5.6 0.2 - - - +
206B ASP* 2.8 37.2 + - - +
207B LEU* 3.4 9.2 - - + +
209B ASP* 1.3 84.6 + - - +
211B ALA* 1.3 56.4 + - - +
213B GLN* 3.0 34.1 + - - +
214B ARG* 2.9 52.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 3.7 35.0 - - + -
207B LEU 3.0 11.9 + - - +
208B LEU* 3.1 11.4 + - - +
210B GLN* 1.3 75.5 - - - +
212B ARG* 1.3 52.8 + - - +
214B ARG* 3.1 5.0 + - - +
215B GLY 2.7 30.1 + - - -
216B ASP* 2.9 25.4 + - + +
218B VAL* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASN* 5.1 3.8 - - - +
3B ASN* 4.3 23.3 - - - +
208B LEU 2.9 15.9 + - - +
209B ASP* 3.2 22.1 + - - +
211B ALA* 1.3 75.6 - - - +
213B GLN* 1.3 89.3 + - - +
215B GLY* 2.9 20.8 + - - -
216B ASP 5.1 1.8 - - - +
218B VAL* 5.3 0.4 - - - +
254B LEU* 4.6 7.2 - - + -
258B TYR* 3.6 59.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ASP* 2.9 36.8 + - - +
210B GLN* 3.0 30.3 + - - +
212B ARG* 1.3 106.7 - - - +
214B ARG* 1.3 59.2 + - - +
215B GLY 3.3 0.4 + - - -
----------------------------------------------------------
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