Contacts of the strand formed by residues 215 - 231 (chain B) in PDB entry 3C0M
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 215 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLN* 4.9 15.5 - - + -
213B SER* 3.4 13.3 - - - +
214B GLY* 1.3 85.3 - - - +
216B ASP* 1.3 61.2 + - - +
282B ARG* 4.1 6.2 - - - +
283B PRO* 3.7 22.7 - - - +
441B LEU* 4.4 23.6 - - + +
464B VAL* 4.6 11.7 - - + -
465B THR* 3.2 11.9 - - - +
466B PRO* 3.2 43.9 - - + +
467B ALA* 3.4 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B TYR* 1.3 74.8 - - - +
217B VAL* 1.3 65.2 + - - +
218B THR* 3.7 8.3 + - - -
280B SER* 4.9 7.9 + - - -
281B VAL 2.9 23.1 - - - +
282B ARG* 4.1 17.8 + - - +
463B SER 4.0 0.9 - - - +
464B VAL* 4.9 1.3 - - - -
465B THR* 2.8 43.5 + - - +
466B PRO 3.8 1.3 - - - +
467B ALA* 3.7 15.6 + - - -
468B ALA 5.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ALA* 5.1 2.5 - - + -
216B ASP* 1.3 74.0 - - - +
218B THR* 1.3 64.1 + - - +
280B SER* 3.1 23.4 - - - -
281B VAL* 3.2 19.2 + - + -
283B PRO* 4.0 23.5 - - + +
293B VAL* 6.0 7.9 - - + -
414B ILE* 4.1 11.9 - - + +
416B ILE* 6.5 0.2 - - + -
441B LEU* 4.8 8.1 - - + -
443B LEU* 3.7 43.7 - - + -
462B LEU* 4.4 13.0 - - + -
463B SER 3.7 5.2 - - - +
464B VAL* 4.7 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ASP* 4.5 7.1 + - - -
217B VAL* 1.3 73.9 + - - +
219B LEU* 1.3 67.6 + - - +
220B ARG* 3.5 40.3 + - - +
278B SER* 5.3 3.1 - - - -
279B GLN 3.4 9.0 - - - +
280B SER* 2.9 25.5 - - - +
414B ILE* 4.3 0.2 - - - -
461B SER 3.7 0.7 - - - +
462B LEU* 3.4 7.8 - - - -
463B SER* 3.0 38.4 + - - -
465B THR* 6.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B THR* 1.3 76.2 - - - +
220B ARG* 1.3 75.4 + - - +
277B LEU* 5.3 9.4 - - + +
278B SER* 3.2 22.9 - - - -
279B GLN* 3.3 17.0 + - + +
295B ILE* 3.6 36.8 - - + -
297B LEU* 5.1 4.7 - - + -
411B ALA* 4.0 17.7 - - + -
414B ILE* 3.8 13.3 - - + +
447B LEU* 6.0 0.9 - - + -
460B VAL* 3.8 24.7 - - + -
461B SER 3.4 11.0 - - - +
462B LEU* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B THR* 3.5 30.1 - - - +
219B LEU* 1.3 82.3 - - - +
221B GLY* 1.3 58.7 + - - +
276B SER* 5.6 1.3 - - - +
277B LEU 3.0 11.4 - - - +
278B SER* 4.8 11.0 - - - -
459B ASN 3.1 3.5 - - - +
460B VAL* 3.0 2.2 - - - -
461B SER* 2.7 57.3 + - - +
463B SER* 3.6 22.7 + - - -
465B THR* 6.0 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG* 1.3 76.3 - - - +
222B ASP* 1.3 69.0 + - - +
276B SER* 3.4 3.2 + - - -
277B LEU* 3.0 41.5 + - - +
458B ASN 3.4 4.5 - - - -
459B ASN 3.2 16.6 - - - -
460B VAL* 3.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLY* 1.3 81.9 - - - +
223B THR* 1.3 65.6 + - - +
274B THR* 5.2 9.9 - - - -
275B THR 3.5 6.4 - - - +
276B SER* 4.0 13.9 + - - -
277B LEU* 4.1 2.9 - - - +
457B PHE* 3.6 2.1 - - - -
458B ASN* 2.8 46.4 + - + +
459B ASN* 2.7 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASP* 1.3 78.3 - - - +
224B ALA* 1.3 55.8 + - - +
274B THR* 4.4 3.4 - - - -
275B THR* 2.7 50.9 + - + +
277B LEU* 4.1 19.3 - - + -
409B GLN* 3.0 61.7 + - + +
456B GLY 3.0 10.5 + - - -
457B PHE* 4.4 5.1 - - + -
458B ASN* 5.0 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B THR* 1.3 79.2 + - - +
225B THR* 1.3 64.7 + - - +
226B ASN* 4.2 9.0 + - - +
272B SER* 4.1 16.4 - - - +
273B THR 4.0 3.6 - - - -
274B THR* 4.1 16.2 - - + +
275B THR* 4.1 0.7 - - - -
407B GLU 4.2 0.5 - - - +
408B SER* 3.8 14.2 - - - -
409B GLN* 3.8 10.1 + - - +
456B GLY 4.6 1.8 + - - -
458B ASN* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA* 1.3 73.8 - - - +
226B ASN* 1.3 69.4 + - - +
227B TRP* 3.9 2.7 + - + +
255B LEU* 4.4 11.8 - - + -
256B SER 4.5 9.3 + - - +
257B ILE* 4.3 26.0 - - + -
271B GLY 3.9 1.2 - - - +
272B SER* 3.4 3.5 - - - -
273B THR* 3.1 40.3 + - - +
275B THR* 3.1 20.5 - - - +
406B ALA* 5.0 0.7 - - + -
407B GLU 3.4 9.4 - - - +
408B SER* 3.5 20.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ALA* 4.7 8.7 + - - +
225B THR* 1.3 75.2 - - - +
227B TRP* 1.3 59.4 + - - +
271B GLY 3.9 4.3 - - - +
272B SER* 2.8 31.0 + - - -
405B SER 4.1 0.5 - - - +
406B ALA* 3.5 1.7 - - - -
407B GLU* 2.8 59.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR* 4.6 7.0 - - + -
226B ASN* 1.3 75.5 - - - +
228B SER* 1.3 70.0 + - - +
229B LYS* 4.0 26.5 - - + -
247B TRP* 5.1 3.4 - + - -
257B ILE* 3.5 51.7 - - + +
258B GLU 5.5 2.0 - - - -
259B ILE* 4.0 20.4 - - + -
268B GLN* 3.5 24.2 - - + -
270B GLY* 3.2 23.3 + - - -
271B GLY* 3.0 46.0 + - - +
273B THR* 4.3 16.4 - - + +
404B PHE* 3.8 19.3 - + + -
405B SER 3.3 10.3 - - - +
406B ALA* 4.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B TRP* 1.3 81.4 - - - +
229B LYS* 1.3 68.5 + - - +
230B THR* 5.5 2.3 - - - +
269B ASN 3.5 11.4 + - - -
270B GLY* 4.1 1.3 - - - -
404B PHE* 3.6 2.3 - - - -
405B SER* 2.9 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B TRP* 4.0 20.0 - - + -
228B SER* 1.3 81.3 + - - +
230B THR* 1.3 61.9 + - - +
231B ASN* 3.1 17.7 - - - +
247B TRP* 4.4 8.5 - - + -
259B ILE* 5.1 2.5 - - - -
265B TRP* 2.9 51.5 + - + +
268B GLN* 3.1 15.9 + - - -
269B ASN* 2.9 45.3 + - - +
306B TYR* 3.9 20.2 - - + +
403B ASP 3.0 17.3 - - - +
404B PHE* 4.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B SER* 5.5 2.5 - - - +
229B LYS* 1.3 76.4 - - - +
231B ASN* 1.3 71.7 + - - +
232B THR* 3.9 1.5 + - - -
269B ASN* 5.8 0.2 - - - -
306B TYR* 3.3 4.2 + - - -
402B GLY* 3.2 21.5 - - - -
403B ASP* 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LYS* 3.1 17.5 + - - +
230B THR* 1.3 73.7 + - - +
232B THR* 1.3 67.5 + - - +
233B TYR 3.1 7.8 + - - +
236B SER* 3.8 17.0 - - - +
265B TRP* 3.2 11.4 - - - +
266B ALA* 3.1 24.8 - - + +
269B ASN* 3.1 23.2 + - - +
306B TYR* 2.7 29.3 + - - -
400B ILE* 5.4 0.2 - - - +
401B THR 3.8 4.4 + - - -
----------------------------------------------------------
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