Contacts of the strand formed by residues 257 - 265 (chain D) in PDB entry 2J2M
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 GLU 257 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D ARG 5.3 1.6 + - - +
219D PRO* 3.7 1.9 - - - +
220D LYS* 3.1 64.3 + - + +
221D GLU* 4.8 4.4 + - - +
255D PHE* 3.2 16.1 + - - +
256D PRO* 1.3 74.3 - - - +
258D TRP* 1.3 72.4 + - - +
296D THR* 5.2 8.8 + - - -
297D MET 3.1 5.4 - - - +
298D THR* 3.7 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D PHE* 3.6 24.2 - + - -
113D PHE* 3.5 24.2 - + - -
190D TYR 3.2 24.7 - - - -
191D ARG* 3.7 13.7 - - - -
193D MET 2.8 22.3 + - - -
217D TRP* 3.6 26.1 - - + -
218D VAL 3.1 8.3 - - - +
219D PRO* 3.4 25.5 - - + +
220D LYS 4.5 0.7 - - - +
246D THR* 5.6 0.2 - - + -
256D PRO* 3.5 37.7 - - + -
257D GLU* 1.3 95.5 - - - +
259D ASP* 1.3 63.9 + - - +
260D LEU 3.9 0.2 + - - -
296D THR* 3.3 3.5 - - - -
297D MET* 2.8 49.5 + - + +
299D LEU* 3.7 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D ARG 3.4 1.4 - - - +
217D TRP* 3.3 6.9 - - - -
218D VAL* 2.8 41.6 + - + +
220D LYS* 5.2 10.7 + - - +
258D TRP* 1.3 74.5 - - - +
260D LEU* 1.3 59.8 + - - +
261D PHE* 3.7 24.9 - - + -
293D HIS* 3.2 14.6 + - - +
295D GLY 3.5 2.0 - - - -
296D THR* 2.6 31.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D PHE* 3.7 25.4 - - + -
80D PHE* 6.4 0.7 - - + -
81D LEU* 6.1 0.9 - - + -
117D PHE* 5.1 0.7 - - + -
124D TRP* 5.0 14.8 - - + -
126D PHE* 5.7 0.2 - - + -
203D TRP* 6.2 1.6 - - + -
215D LEU* 3.9 21.3 - - + -
216D ARG 3.4 26.7 - - - +
217D TRP* 3.8 40.6 - - + +
258D TRP 3.9 1.4 + - - -
259D ASP* 1.3 73.4 - - - +
261D PHE* 1.3 58.4 + - - +
293D HIS* 3.8 5.7 - - - -
294D VAL* 2.8 46.9 + - + -
295D GLY 2.7 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D LEU* 3.6 6.3 - - - +
216D ARG* 2.7 40.5 + - + +
218D VAL* 3.7 31.6 - - + -
259D ASP* 3.7 25.1 - - + -
260D LEU* 1.3 74.6 - - - +
262D VAL* 1.3 60.4 + - - +
291D PHE* 3.7 38.8 - + + -
292D GLN 3.2 7.6 - - - +
293D HIS* 3.6 46.7 - + + -
294D VAL* 4.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D MET* 3.8 28.3 - - - -
75D TYR* 5.0 0.2 - - + -
203D TRP* 3.8 17.9 - - + -
213D ILE* 3.9 18.2 - - + -
214D LYS 3.4 11.0 - - - +
215D LEU* 3.7 16.8 - - + -
261D PHE* 1.3 73.9 - - - +
263D GLN* 1.3 65.0 + - - +
264D VAL* 4.3 11.0 - - + -
291D PHE* 4.5 0.2 - - - -
292D GLN* 2.7 58.6 + - + +
294D VAL* 3.8 6.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
213D ILE* 3.2 7.8 - - - +
214D LYS* 2.9 40.7 + - + +
216D ARG* 2.6 35.6 + - + -
261D PHE 4.3 0.4 + - - -
262D VAL* 1.3 71.7 - - - +
264D VAL* 1.3 61.2 + - - +
284D TRP* 2.8 47.4 + - + +
285D PHE 3.7 1.0 + - - -
289D ILE* 2.6 32.6 + - + +
290D PRO 3.8 6.7 - - - +
291D PHE* 3.5 28.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D TYR* 3.7 36.3 - - + +
211D VAL* 3.6 31.4 - - + -
212D TYR 3.6 1.6 - - - -
213D ILE* 4.4 5.2 - - + -
262D VAL* 4.1 15.9 + - + -
263D GLN* 1.3 78.1 - - - +
265D LEU* 1.3 65.9 + - - +
266D ASP 5.0 0.7 - - - +
289D ILE* 3.2 22.6 - - - +
290D PRO 4.5 0.8 + - - -
292D GLN* 3.6 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D VAL* 3.6 5.0 - - - -
212D TYR* 2.7 45.1 + - + +
264D VAL* 1.3 76.9 - - - +
266D ASP* 1.3 78.5 + - - +
269D ASP* 3.9 14.6 - - + +
270D VAL* 4.5 7.9 - - + -
273D PHE* 3.8 31.0 - - + -
277D PRO* 3.9 26.0 - - + -
284D TRP* 3.8 37.7 - - + +
289D ILE* 4.3 9.4 - - + -
----------------------------------------------------------
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