Contacts of the strand formed by residues 261 - 271 (chain A) in PDB entry 1B70
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 261 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLN* 5.5 0.7 - - - +
258A PHE* 3.1 40.9 + - + +
259A PRO 3.5 2.0 - - - -
260A PHE* 1.3 90.7 - - + +
262A GLU* 1.3 67.8 + - - +
263A PRO 3.7 1.3 - - - +
264A GLY* 3.8 13.4 + - - -
283A ALA 3.8 19.7 - - - +
284A GLY* 3.7 17.5 - - - +
285A MET 3.1 21.8 - - - +
286A VAL* 3.8 5.6 - - + +
287A HIS* 3.6 3.9 - - - +
314A ALA* 5.0 3.8 - - + +
352A PHE* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TYR* 4.6 9.2 - - + -
258A PHE 4.8 4.3 - - - +
261A VAL* 1.3 80.6 - - - +
263A PRO* 1.3 65.0 - - - +
264A GLY 5.2 0.2 - - - -
285A MET* 3.0 16.8 + - - +
286A VAL 4.8 2.8 - - - +
287A HIS* 4.2 19.6 + - + +
288A PRO* 5.2 1.3 - - + +
351A MG 2.9 13.0 - - - -
163B ASN* 4.3 9.4 + - - -
414B LEU* 4.9 1.2 - - - +
452B ASP* 5.0 1.2 - - - +
457B GLU* 4.1 26.9 - - + +
458B ASP* 3.1 37.6 - - - +
461B GLU* 2.6 40.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A MET* 4.2 13.4 - - - +
262A GLU* 1.3 83.8 + - - +
264A GLY* 1.3 60.2 + - - +
284A GLY* 3.1 5.2 - - - -
285A MET* 3.0 45.2 + - + -
414B LEU* 4.5 11.0 - - + -
415B LEU* 4.2 21.5 - - + -
457B GLU 4.9 1.3 - - - +
460B VAL* 4.6 0.9 - - + -
461B GLU* 3.2 35.4 - - + +
464B ALA* 4.9 1.1 - - + -
469B TYR* 3.4 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PRO* 3.6 0.2 - - - +
256A VAL* 3.1 26.5 + - - +
258A PHE* 4.9 1.6 - - - -
261A VAL* 3.8 19.1 + - - -
262A GLU* 3.8 0.4 - - - +
263A PRO* 1.3 74.6 - - - +
265A ALA* 1.3 63.0 + - - +
283A ALA 3.8 5.8 - - - -
461B GLU* 3.0 8.0 + - - +
469B TYR* 2.8 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A MET* 4.6 9.2 - - + -
253A PHE* 4.5 14.4 - - + -
254A GLN 3.0 17.7 - - - +
256A VAL* 3.2 19.1 - - - +
258A PHE* 4.0 0.2 - - - -
264A GLY* 1.3 75.3 - - - +
266A GLN* 1.3 61.2 + - - +
267A PHE* 5.4 0.7 - - - -
282A GLY* 3.4 1.9 - - - -
283A ALA* 3.0 36.5 + - + +
469B TYR* 3.4 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG 3.7 0.2 - - - +
253A PHE* 3.6 1.7 - - - -
254A GLN* 2.7 73.7 + - - +
255A PRO 5.0 1.8 - - - +
256A VAL* 3.5 25.6 - - + +
258A PHE* 5.6 0.7 - - + -
265A ALA* 1.3 76.8 - - - +
267A PHE* 1.3 60.2 + - - +
279A GLU* 3.3 25.1 + - + +
281A GLY 3.6 9.2 - - - +
282A GLY* 4.3 2.2 - - - -
31B GLU* 3.5 26.4 + - - +
159B GLU* 5.4 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 4.2 29.8 - - + -
240A LEU* 5.3 3.1 - - + -
252A ARG 2.9 12.3 - - - +
253A PHE* 3.8 26.5 - + + -
265A ALA 4.9 0.4 - - - -
266A GLN* 1.3 77.3 - - - +
268A ALA* 1.3 62.3 + - - +
269A VAL* 6.1 0.2 - - + -
279A GLU* 3.5 5.0 - - - +
280A LEU* 2.9 51.7 + - + -
281A GLY* 3.0 44.1 + - - +
282A GLY 3.5 16.2 - - - -
283A ALA* 3.9 19.3 - - + -
315A PHE* 4.2 5.8 - - + -
316A GLY 4.4 1.1 - - - -
317A LEU* 4.4 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 5.6 0.3 - - - +
251A VAL* 3.5 4.7 - - - +
252A ARG* 2.7 73.9 + - + +
267A PHE* 1.3 78.0 - - - +
269A VAL* 1.3 61.5 + - - +
277A TRP* 3.6 5.8 - - + -
278A LEU 2.8 13.9 - - - +
279A GLU* 3.6 11.2 + - - +
280A LEU 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 6.4 1.3 - - + -
241A ALA* 3.6 27.4 - - + -
245A PHE* 3.8 29.8 - - + -
250A LYS 3.5 9.9 - - - +
251A VAL* 4.8 1.8 - - + -
267A PHE* 6.1 0.2 - - + -
268A ALA* 1.3 76.0 - - - +
270A TRP* 1.3 67.9 + - - +
271A TRP 3.5 0.5 + - - -
276A LYS 3.6 0.5 - - - +
277A TRP* 3.2 6.6 - - - -
278A LEU* 2.6 46.9 + - + +
280A LEU* 3.2 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 3.8 5.9 - - - -
248A ASP 3.4 24.6 + - - -
249A SER* 2.9 31.3 - - - -
250A LYS* 2.7 48.1 + - + +
269A VAL* 1.3 72.3 - - - +
271A TRP* 1.3 63.5 + - - +
272A PRO* 3.1 16.5 - - + +
275A GLY* 3.0 34.8 - - - -
276A LYS* 3.2 31.0 - - - -
277A TRP* 3.1 33.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 3.9 25.7 - + + -
269A VAL 3.5 0.6 + - - -
270A TRP* 1.3 75.1 - - - +
272A PRO* 1.4 60.7 - - + +
273A GLU* 3.2 27.5 - - + +
274A GLY* 3.1 32.5 - - - -
275A GLY* 2.8 28.9 + - - -
276A LYS* 3.2 52.5 + - + +
278A LEU* 3.8 18.6 - - + -
325A LEU* 3.8 35.4 - - + +
----------------------------------------------------------
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