Contacts of the helix formed by residues 245 - 252 (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 ALA 245 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PRO* 3.5 26.6 - - + +
5B VAL* 4.2 19.1 - - + -
7B LEU* 3.7 5.7 - - + +
244B THR* 1.3 71.2 - - - +
246B GLY* 1.3 58.3 + - - +
247B GLY 2.7 12.7 + - - -
248B VAL* 2.8 29.0 + - + +
249B ALA 4.5 0.3 + - - -
259B VAL* 5.7 1.5 - - + +
262B VAL* 4.2 17.9 - - + -
322B ASN* 3.1 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLY 3.2 22.5 - - - +
249A ALA* 3.7 27.4 - - - -
250A THR* 3.7 12.2 + - - -
256A PRO* 3.9 11.6 - - - +
244B THR* 3.3 10.0 + - - -
245B ALA* 1.3 76.2 - - - +
247B GLY* 1.3 57.5 + - - +
248B VAL 3.2 2.0 + - - -
249B ALA* 4.0 7.4 + - - +
250B THR* 4.1 1.6 + - - -
321B LEU 4.9 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A THR* 4.1 6.3 + - - -
33B TYR* 3.2 20.3 - - - +
34B GLN* 5.5 0.2 - - - +
242B ASN* 4.7 15.0 - - - +
244B THR* 3.5 10.7 + - - -
245B ALA 2.7 4.8 + - - -
246B GLY* 1.3 73.9 - - - +
248B VAL* 1.3 58.4 + - - +
249B ALA 3.5 0.4 - - - -
250B THR* 3.9 10.2 - - - +
251B GLY* 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.9 22.2 - - + -
33B TYR* 3.6 32.8 - - + -
220B PHE* 3.8 42.4 - - + -
245B ALA* 2.8 21.7 + - + +
247B GLY* 1.3 76.0 - - - +
249B ALA* 1.3 68.0 + - - +
250B THR 3.1 1.6 + - - -
252B SER* 2.4 30.2 + - - -
254B LEU* 5.4 3.1 - - + +
259B VAL* 4.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A HIS* 4.2 1.4 + - - -
244A THR* 5.5 1.3 + - - -
246A GLY* 3.6 28.5 - - - +
321A LEU 5.3 3.0 - - - +
245B ALA 4.5 0.4 + - - -
246B GLY 4.0 3.4 + - - +
248B VAL* 1.3 81.6 - - - +
250B THR* 1.3 57.8 + - - +
253B GLY* 2.9 29.6 + - - -
254B LEU 3.1 25.0 + - - +
255B GLY* 4.5 0.2 - - - -
256B PRO* 3.8 20.9 - - + -
259B VAL* 6.0 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASP* 4.2 13.3 - - - +
232A HIS* 2.9 25.9 + - - -
242A ASN* 4.5 18.8 + - - +
244A THR* 5.0 4.5 + - - -
246A GLY* 3.3 26.6 + - - -
247A GLY* 4.1 3.3 + - - -
250A THR* 5.1 3.3 + - - +
70B ASN* 3.1 8.0 + - - -
242B ASN* 6.1 1.3 - - - +
246B GLY 4.1 0.6 + - - -
247B GLY* 3.9 16.8 - - - +
248B VAL 3.1 0.2 - - - -
249B ALA* 1.3 76.5 - - - +
251B GLY* 1.3 60.5 + - - +
252B SER 3.1 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 3.4 33.4 - - - +
69B GLY* 3.5 4.0 - - - -
70B ASN* 3.0 16.2 + - - +
71B GLY* 3.2 24.8 + - - -
247B GLY 2.9 14.5 + - - -
250B THR* 1.3 75.6 - - - +
252B SER* 1.3 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A HIS* 4.1 1.4 - - - -
31B VAL* 4.6 3.7 - - - +
33B TYR* 3.8 8.3 - - - +
69B GLY* 4.8 1.8 - - - -
70B ASN* 3.1 13.9 + - - +
204B VAL* 3.5 26.6 - - - +
205B SER* 4.3 5.4 + - - -
208B LEU* 4.1 20.5 - - - +
220B PHE* 3.7 16.8 - - - -
248B VAL 2.4 24.7 + - - -
250B THR 3.1 0.6 - - - -
251B GLY* 1.3 79.7 + - - +
253B GLY* 1.3 61.0 + - - +
254B LEU* 3.9 8.1 - - - -
----------------------------------------------------------
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