Contacts of the strand formed by residues 340 - 356 (chain B) in PDB entry 2PY5
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 340 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292B PHE* 3.6 24.2 - + + -
293B GLU 3.4 4.3 - - - +
294B LEU* 3.5 33.0 - - + -
295B LYS* 3.4 10.6 - - - -
300B PRO* 3.4 2.1 - - - +
301B THR* 3.0 42.7 + - - -
302B ILE* 3.1 21.5 + - + +
316B LEU 2.7 30.0 + - - -
336B MET* 2.9 29.0 + - + +
337B LYS 3.3 16.3 - - - +
338B GLU 3.6 0.4 - - - -
339B HIS* 1.3 89.3 - - + +
341B ASP* 1.3 62.7 + - - +
342B LEU* 3.7 20.5 + - + +
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Residues in contact with ASP 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PHE* 3.2 5.5 - - - +
293B GLU* 2.8 43.3 + - + +
294B LEU 5.0 1.2 - - - +
295B LYS* 3.6 31.7 - - - +
340B TYR* 1.3 71.8 - - - +
342B LEU* 1.3 62.0 + - - +
343B TYR* 3.8 22.2 + - + +
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 5.6 2.7 - - + -
290B CYS* 4.2 9.0 - - - -
291B GLU 3.5 2.0 - - - +
292B PHE* 3.5 24.5 - - + -
333B LEU* 5.5 3.1 - - + -
336B MET* 4.2 23.6 - - + -
337B LYS* 4.0 34.1 - - + -
340B TYR* 3.7 17.4 + - + +
341B ASP* 1.3 78.6 - - - +
343B TYR* 1.3 65.9 + - - +
345B VAL* 3.6 28.2 - - + +
347B TYR* 5.7 0.7 - - - +
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Residues in contact with TYR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B CYS* 3.5 2.4 - - - +
291B GLU* 2.8 51.6 + - + +
292B PHE* 4.2 1.6 - - - -
293B GLU* 4.0 26.8 - - + +
341B ASP* 3.8 31.3 + - + +
342B LEU* 1.3 78.3 - - - +
344B ASN* 1.3 79.1 + - - +
345B VAL* 3.1 3.4 + - - -
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Residues in contact with ASN 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B ARG 3.4 7.4 - - - +
290B CYS* 3.9 2.9 - - - -
291B GLU* 3.9 20.6 + - - +
323B ILE* 5.2 10.3 - - + +
343B TYR* 1.3 82.6 - - - +
345B VAL* 1.3 63.8 + - - +
346B GLU* 3.4 6.1 + - - +
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 5.1 7.6 - - + -
289B ARG 3.5 7.6 - - - +
290B CYS* 4.1 9.6 - - + -
342B LEU* 3.6 40.4 - - + +
343B TYR 4.0 4.3 - - - +
344B ASN* 1.3 74.4 - - - +
346B GLU* 1.3 64.1 + - - +
347B TYR* 3.4 45.2 + - + +
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Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B ILE* 3.2 6.4 - - - +
289B ARG* 2.8 79.9 + - + +
344B ASN 3.4 3.8 + - - +
345B VAL* 1.3 73.9 - - - +
347B TYR* 1.3 64.2 + - - +
348B ILE* 3.4 13.0 + - + +
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Residues in contact with TYR 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B GLY* 3.3 13.2 - - - -
274B LYS* 3.5 55.6 - - + +
286B GLN* 3.6 17.7 - - + +
287B HIS 4.0 1.8 - - - -
288B ILE* 3.5 24.9 - - + -
333B LEU* 4.6 9.6 - - + -
337B LYS* 2.8 33.9 + - - -
342B LEU* 5.7 0.9 - - - +
345B VAL* 3.4 27.5 - - + +
346B GLU* 1.3 73.4 - - - +
348B ILE* 1.3 63.8 + - - +
349B SER 3.9 0.4 - - - -
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Residues in contact with ILE 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B GLU* 4.0 5.7 - - - +
273B GLY* 2.9 17.6 + - - -
287B HIS* 3.0 50.1 + - + +
288B ILE 4.1 0.2 - - - -
289B ARG* 3.3 58.3 - - + +
346B GLU* 3.8 19.5 - - + +
347B TYR* 1.3 72.2 - - - +
349B SER* 1.3 67.1 + - - +
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Residues in contact with SER 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 5.4 3.9 - - - +
271B PHE* 3.3 17.0 - - - -
272B GLU* 3.9 13.7 - - - -
273B GLY 3.6 6.9 + - - +
286B GLN* 3.0 11.2 + - - -
287B HIS* 2.8 28.5 + - - +
327B TRP* 4.2 17.2 - - - -
348B ILE* 1.3 87.8 - - - +
350B GLY* 1.3 60.9 + - - +
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Residues in contact with GLY 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B VAL* 3.5 8.1 - - - +
271B PHE* 2.9 41.1 + - - +
285B ILE 3.1 13.9 - - - -
287B HIS 4.4 1.8 - - - -
327B TRP* 4.6 6.7 - - - -
349B SER* 1.3 81.3 + - - +
351B LEU* 1.3 67.1 + - - +
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B LEU* 3.7 25.1 - - + +
221B GLU* 4.3 17.5 - - + +
222B VAL* 3.7 32.1 - - + +
268B PRO* 4.1 14.8 - - + -
269B ILE 3.5 2.0 - - - -
270B VAL* 3.6 27.6 - - + -
271B PHE* 3.4 3.1 - - - -
284B HIS* 3.2 3.5 - - - +
285B ILE* 2.8 38.0 + - + +
327B TRP* 4.7 7.6 - - + -
350B GLY* 1.3 83.3 - - - +
352B LYS* 1.3 59.2 + - - +
353B PHE* 3.8 15.5 - - + -
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Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B PRO* 3.2 7.1 - - - +
269B ILE* 2.9 64.7 + - + +
271B PHE* 3.8 15.3 - - + +
275B TYR* 3.8 28.3 - - + -
276B VAL 5.0 3.0 + - - +
278B ASP* 2.8 29.6 + - - +
281B TYR* 3.6 23.8 - - + -
283B LEU 3.4 10.1 - - - +
351B LEU* 1.3 75.1 - - - +
353B PHE* 1.3 61.8 + - - +
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Residues in contact with PHE 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B VAL* 4.3 5.8 - - + -
264B PRO* 3.8 14.4 - - + -
265B TYR 4.5 1.6 - - - +
266B GLY 4.4 2.5 - - - -
268B PRO* 3.6 33.2 - - + -
281B TYR* 3.2 22.6 - - - -
282B PRO* 3.3 7.6 - - - +
283B LEU* 2.8 23.6 + - + +
284B HIS* 4.4 3.6 - - - -
285B ILE* 3.8 25.1 - - + -
351B LEU* 3.8 25.6 - - + -
352B LYS* 1.3 75.7 - - - +
354B LYS* 1.3 71.4 + - - +
426B TYR* 3.6 18.2 - - - -
428B PRO* 3.4 34.8 - - + -
432B PHE* 4.6 8.1 - + - -
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Residues in contact with LYS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B PRO* 3.3 5.5 - - - +
265B TYR* 3.0 69.7 + - + +
266B GLY* 4.1 17.7 - - - -
267B GLU 4.8 5.5 + - - +
280B ASP 3.7 18.2 - - - +
281B TYR* 3.4 33.0 - - + +
353B PHE* 1.3 77.1 - - - +
355B ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LEU* 3.5 20.9 - - + +
263B LEU 3.1 13.0 - - - +
265B TYR* 3.6 9.6 + - - -
280B ASP 4.8 0.4 + - - -
282B PRO* 3.9 14.7 - - + +
283B LEU* 3.5 28.0 - - + -
353B PHE 3.8 0.4 + - - -
354B LYS* 1.3 78.7 - - - +
356B THR* 1.3 63.7 + - - +
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Residues in contact with THR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B ARG 3.8 0.7 - - - +
262B LEU* 3.8 9.9 - - - -
263B LEU* 2.9 30.0 + - - +
265B TYR* 4.0 15.7 - - + -
355B ALA* 1.3 76.6 - - - +
357B THR* 1.3 77.6 + - - +
359B LEU* 3.5 39.7 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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