Contacts of the strand formed by residues 261 - 268 (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 TYR 261 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GLY* 4.4 4.9 - - - -
3B ASN 3.3 6.6 + - - +
4B VAL* 3.5 9.6 - - + -
5B VAL* 3.2 22.2 + - - +
259B VAL* 4.2 0.5 - - - +
260B ASP* 1.3 76.9 - - - +
262B VAL* 1.3 89.9 + - - +
263B LEU* 3.5 34.5 - - + +
325B SER* 3.7 15.9 - - - -
326B GLY* 3.4 12.2 - - - -
411B ASP* 2.5 40.7 + - - +
426B ARG* 4.8 6.1 - - + -
428B PRO* 3.7 46.7 - - + +
431B ALA* 4.1 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PRO* 5.3 0.4 - - + -
257A ARG* 4.0 16.4 - - + -
5B VAL* 3.5 15.7 - - + +
7B LEU* 4.6 8.5 - - + -
245B ALA* 4.2 18.8 - - + -
259B VAL* 3.7 22.0 - - + -
261B TYR* 1.3 81.4 - - - +
263B LEU* 1.3 60.7 + - - +
322B ASN* 3.6 29.2 - - + +
323B SER* 4.0 5.6 - - - +
324B LEU* 2.9 28.6 - - + +
325B SER* 2.9 18.9 + - - -
326B GLY 3.4 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 5.0 2.7 - - + -
5B VAL 2.7 16.5 + - - +
6B VAL* 3.7 19.3 - - + -
7B LEU* 3.4 24.6 + - - -
19B ILE* 4.0 26.2 - - + -
23B LEU* 4.2 8.7 - - + -
261B TYR* 3.5 34.5 - - + +
262B VAL* 1.3 71.4 - - - +
264B GLY* 1.3 61.7 + - - +
265B ILE* 3.4 3.9 + - + +
324B LEU* 3.9 1.6 - - - -
326B GLY 3.7 8.5 - - - +
327B PHE 4.2 16.8 - - - +
328B CYS* 4.2 14.4 - - + +
411B ASP* 5.0 0.4 - - + -
412B ILE* 4.3 8.3 - - + -
428B PRO* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.7 4.5 - - - -
9B THR* 3.5 25.4 - - - -
263B LEU* 1.3 70.5 - - - +
265B ILE* 1.3 61.0 + - - -
266B LEU 3.2 4.7 + - - -
324B LEU* 3.3 14.5 - - - +
326B GLY 2.9 13.9 + - - -
327B PHE* 3.4 7.4 - - - -
328B CYS 2.9 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 3.6 31.2 - - + -
7B LEU 2.7 26.2 + - - +
8B GLY* 4.2 2.9 - - - -
9B THR* 3.2 21.1 + - - -
14B GLU* 3.3 34.5 - - + +
15B GLY 4.0 2.0 - - - -
16B LYS* 3.8 24.2 - - + +
19B ILE* 3.8 36.1 - - + -
263B LEU* 4.2 6.3 - - + +
264B GLY* 1.3 66.7 - - - -
266B LEU* 1.3 60.8 + - - +
328B CYS* 3.8 11.7 - - + +
330B THR* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 3.6 11.7 - - - +
10B GLN* 3.4 31.2 - - + +
264B GLY 3.2 0.4 + - - -
265B ILE* 1.3 73.1 - - - +
267B LYS* 1.3 64.8 + - - +
310B LEU* 4.1 6.1 - - + -
315B VAL* 4.1 20.4 - - + -
327B PHE* 3.8 45.3 - - + -
328B CYS 2.8 14.8 + - - +
329B LEU* 3.3 16.4 - - + +
330B THR* 2.7 33.4 + - - -
402B ILE* 4.2 18.2 - - + -
410B ILE* 5.6 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLN* 2.7 19.2 + - - +
12B GLY 4.0 1.7 + - - -
13B ASP* 2.7 30.2 + - - +
14B GLU* 4.2 10.5 - - - +
265B ILE 4.2 0.8 + - - -
266B LEU* 1.3 75.6 - - - +
268B ALA* 1.3 68.9 + - - +
269B TYR* 3.0 47.1 + - + +
271B THR* 2.7 48.4 + - - +
296B GLU* 3.7 11.0 + - - +
310B LEU* 3.0 18.2 - - - +
329B LEU* 4.6 0.2 - - - -
330B THR* 3.4 14.8 + - - +
331B LYS* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU 3.7 0.6 + - - -
267B LYS* 1.3 71.9 - - - +
269B TYR* 1.3 61.4 + - + +
310B LEU* 3.1 12.1 - - - +
329B LEU* 4.1 12.1 - - + -
330B THR 2.8 21.9 + - - +
331B LYS 3.4 18.2 - - - +
332B LEU* 3.6 21.8 - - + -
335B LEU* 4.4 12.1 - - + +
398B TYR* 3.0 26.8 + - + -
----------------------------------------------------------
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