Contacts of the strand formed by residues 256 - 263 (chain D) in PDB entry 3DV0
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 256 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D ILE* 4.1 1.7 - - - +
205D THR* 3.1 23.6 - - + +
207D ILE* 4.9 2.7 - - + -
250D VAL* 4.1 22.0 - - + -
255D ARG* 1.3 78.9 - - - +
257D ILE* 1.3 72.5 + - - +
276D ILE* 4.6 5.6 - - + -
284D LEU* 4.9 3.6 - - - +
286D ALA 5.4 0.2 + - - -
287D PRO 3.9 4.9 + - - +
288D VAL* 3.5 34.4 - - + -
289D LEU 3.5 0.7 + - - -
321D VAL* 4.4 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D ILE* 3.9 8.3 - - + -
205D THR 2.9 5.6 + - - +
206D ILE* 3.5 24.4 - - + +
207D ILE* 3.0 23.3 + - - +
256D ALA* 1.3 83.1 - - - +
258D VAL* 1.3 64.8 + - - +
259D VAL* 4.0 6.9 + - + -
288D VAL* 4.5 0.7 - - - -
289D LEU* 3.1 16.8 - - + +
291D VAL* 4.5 6.7 - - + -
314D VAL* 3.9 39.3 - - + +
317D THR* 4.3 6.7 - - + +
318D ALA* 4.1 11.2 - - + +
321D VAL* 3.4 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D ILE* 3.4 20.0 - - + +
209D TYR* 5.6 2.2 - - + -
235D LEU* 5.8 0.4 - - + -
257D ILE* 1.3 74.4 - - - +
259D VAL* 1.3 67.2 + - - +
268D ILE* 5.3 3.4 - - + -
269D ALA* 3.7 28.3 - - + +
272D VAL* 3.4 39.7 - - + -
273D VAL* 4.1 15.5 - - + -
288D VAL* 4.2 7.4 - - + -
289D LEU 3.0 6.1 + - - -
290D ARG* 3.4 14.8 - - + +
291D VAL* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ILE* 3.9 27.1 - - + -
207D ILE 2.7 12.6 + - - +
208D ALA* 3.6 20.7 - - + +
209D TYR* 4.1 8.5 + - - -
212D MET* 4.0 26.6 - - + +
216D SER* 4.1 7.9 - - - +
257D ILE* 4.3 4.0 - - + -
258D VAL* 1.3 82.5 - - - +
260D GLN* 1.3 66.3 + - - +
291D VAL* 3.5 35.0 - - + +
314D VAL* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D TYR* 3.3 20.7 + - + +
212D MET* 3.7 9.0 - - - -
259D VAL* 1.3 76.7 - - - +
261D GLU* 1.3 60.3 + - - +
262D ALA* 3.6 11.1 + - - +
263D GLN 2.9 29.5 + - - -
264D ARG* 4.3 3.0 + - - +
266D ALA 3.0 15.4 + - - -
267D GLY* 3.7 6.0 - - - -
268D ILE 3.1 9.2 + - - -
269D ALA* 2.8 42.4 + - + +
291D VAL 2.9 17.5 + - - +
292D ALA* 3.5 21.4 - - + +
309D PRO* 3.7 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D PHE* 5.9 1.3 - - + -
119D GLY* 3.5 2.8 - - - -
120D GLY* 2.6 35.1 + - - +
129D SER 4.6 2.8 - - - +
131D SER* 4.3 14.6 + - - +
172D HIS* 2.9 26.9 + - - -
209D TYR* 5.2 3.4 + - - +
211D ALA* 3.8 12.5 + - - +
212D MET* 3.5 25.4 - - + +
260D GLN* 1.3 70.4 - - - +
262D ALA* 1.3 68.9 + - - +
293D ALA* 3.4 16.3 - - - +
298D TYR* 4.8 2.0 - - + -
307D TRP* 4.2 6.1 - - + -
308D LEU* 3.8 22.7 - - + +
309D PRO* 4.1 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D SER* 3.7 32.0 + - - +
133D GLU* 3.8 4.7 + - - +
260D GLN* 3.3 10.8 + - - +
261D GLU* 1.3 86.6 - - - +
263D GLN* 1.3 67.4 + - - +
266D ALA* 4.3 1.1 - - + -
267D GLY* 3.6 35.4 - - - +
292D ALA* 3.6 2.1 - - - +
293D ALA* 3.1 14.3 + - - -
307D TRP* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLN* 5.8 0.2 - - - +
140B PRO* 3.9 21.1 - - + +
130D ASP* 5.4 2.8 + - - +
131D SER* 4.7 8.3 + - - +
260D GLN* 2.9 11.8 + - - -
262D ALA* 1.3 77.9 - - - +
264D ARG* 1.3 57.3 + - - +
265D GLN* 4.2 2.2 - - + +
266D ALA* 2.7 38.0 + - + +
293D ALA* 3.4 7.4 - - - -
294D PRO 3.2 22.7 - - - +
295D ASP* 3.8 9.4 - - - +
296D THR 2.9 22.5 + - - +
297D VAL* 4.2 0.8 - - - +
298D TYR* 3.6 20.3 - - - +
307D TRP* 3.7 16.9 - - + -
----------------------------------------------------------
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