Contacts of the strand formed by residues 254 - 264 (chain B) in PDB entry 3I5D
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 GLY 254 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B MET* 4.4 8.3 - - - +
253B GLY* 1.3 73.9 - - - -
255B VAL* 1.3 66.0 + - - +
281B ARG* 4.3 4.3 - - - -
283B ASP* 3.4 17.3 - - - -
295B TYR* 3.6 8.6 - - - +
319B GLY 3.1 6.4 + - - +
320B ILE* 3.1 9.9 - - - +
321B ARG 2.9 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B GLY* 1.3 79.4 - - - +
256B MET* 1.3 63.9 + - - +
281B ARG* 3.7 3.3 - - - +
282B LEU* 2.8 53.5 + - + +
283B ASP* 2.9 26.8 + - + +
295B TYR* 3.5 30.1 - - + -
321B ARG* 3.2 30.7 - - + +
323B ASP* 5.4 2.7 - - - +
66C SER* 5.2 3.8 - - - +
68C THR* 4.6 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ILE* 4.1 18.4 - - + +
239B VAL* 4.1 12.1 - - + -
242B ALA* 3.6 29.6 - - + -
249B MET* 4.0 20.0 - - - -
255B VAL* 1.3 73.4 - - - +
257B GLY* 1.3 63.7 + - - +
258B VAL 3.7 1.1 + - - -
279B PHE* 4.5 1.8 - - + -
280B ARG 3.8 16.4 - - - +
281B ARG* 3.7 17.9 - - - -
282B LEU* 4.1 2.0 - - - -
320B ILE* 3.7 19.9 - - + +
321B ARG 2.9 6.6 + - - +
322B PHE* 3.5 30.5 - - + +
323B ASP* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B MET* 1.3 72.8 - - - +
258B VAL* 1.3 62.1 + - - +
259B GLN* 3.5 5.5 + - - +
279B PHE* 3.4 7.4 - - - +
280B ARG* 3.0 37.7 + - - +
282B LEU* 3.5 10.4 - - - +
323B ASP 3.6 2.0 - - - -
325B MET* 3.3 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 5.9 0.7 - - + -
192B ILE* 4.3 21.5 - - + -
233B PHE* 5.6 1.1 - - + -
238B ILE* 4.2 23.3 - - + -
256B MET 4.6 1.3 - - - +
257B GLY* 1.3 71.4 - - - +
259B GLN* 1.3 61.2 + - - +
260B ILE* 3.6 13.7 + - + +
277B TYR* 5.2 5.8 - - + -
278B THR 3.8 4.7 - - - +
279B PHE* 4.2 22.7 - - + -
322B PHE* 4.3 21.1 - - + -
323B ASP 2.9 13.9 + - - +
324B VAL* 3.5 16.0 - - + +
325B MET 3.0 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLY 3.5 2.7 + - - +
258B VAL* 1.3 72.4 - - - +
260B ILE* 1.3 61.3 + - - +
261B ARG* 6.2 0.2 - - + -
276B ARG 3.5 1.6 - - - +
277B TYR* 3.4 5.7 - - - +
278B THR* 2.9 64.3 + - - +
280B ARG* 4.3 19.4 - - - +
282B LEU* 5.1 2.6 - - - +
325B MET* 3.3 38.5 - - + +
327B PHE* 4.3 15.4 - - + -
64C LEU* 4.6 11.0 - - + +
197C ARG* 3.7 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE* 4.4 11.2 - - + -
194B ASN* 3.8 23.3 - - + +
207B ASN* 5.7 0.7 - - + +
258B VAL* 4.4 9.6 - - + +
259B GLN* 1.3 75.5 - - - +
261B ARG* 1.3 60.8 + - - +
262B TRP* 3.3 29.2 - - + +
275B PRO* 3.9 19.7 - - + -
276B ARG 3.5 3.6 - - - +
277B TYR* 3.8 27.8 - - + -
324B VAL* 4.1 13.5 - - + -
325B MET 2.9 8.0 + - - +
326B VAL* 3.5 17.9 - - + +
327B PHE* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLN 4.1 0.4 - - - -
260B ILE* 1.3 73.3 - - - +
262B TRP* 1.3 62.9 + - - +
263B ASP* 2.7 41.2 + - - +
274B VAL 3.9 1.7 - - - +
275B PRO* 3.6 2.5 - - - +
276B ARG* 2.9 90.8 + - - +
278B THR* 5.0 9.0 + - - +
327B PHE* 3.1 42.4 - - + -
199C PRO* 5.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 4.0 9.4 - - + -
194B ASN* 3.0 36.1 + - - -
196B ILE* 3.4 39.7 - - + +
198B TYR* 2.8 32.5 + - + +
205B LYS* 4.5 11.4 - - + -
206B ARG* 3.8 7.0 - - - -
207B ASN* 3.7 19.7 - - + -
260B ILE* 3.3 11.1 - - + +
261B ARG* 1.3 69.0 - - - +
263B ASP* 1.3 61.8 + - - +
264B CYS* 3.8 1.8 - - - -
273B CYS* 4.1 21.8 - - - -
274B VAL* 4.2 5.4 - - - -
275B PRO* 3.2 45.8 - - + -
326B VAL* 3.8 20.9 - - + -
327B PHE 2.9 10.6 + - - -
328B GLY* 3.1 0.7 - - - -
329B GLN 3.0 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ARG* 2.7 46.9 + - - +
262B TRP* 1.3 77.4 - - - +
264B CYS* 1.3 64.1 + - - +
272B TRP 5.8 0.5 - - - +
273B CYS* 5.9 0.2 - - - -
274B VAL 4.6 6.3 + - - +
276B ARG* 5.8 3.6 + - - +
327B PHE* 5.5 0.5 - - - -
328B GLY* 3.6 5.2 - - - -
329B GLN* 3.3 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLN* 5.6 0.3 - - - +
198B TYR* 4.4 9.6 - - + +
262B TRP* 3.8 4.6 - - - -
263B ASP* 1.3 81.8 - - - +
265B ASP* 1.3 60.3 + - - +
266B LEU* 3.8 16.4 - - + -
272B TRP 5.8 1.3 - - - -
273B CYS* 2.0 62.6 - - + +
274B VAL 4.0 3.4 - - - -
329B GLN 3.2 6.5 + - - +
330B ALA* 3.2 29.3 - - + +
331B GLY 3.7 1.7 + - - -
----------------------------------------------------------
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