Contacts of the strand formed by residues 326 - 341 (chain B) in PDB entry 2W77
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 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ASP* 2.9 27.6 - - - +
318B LYS 3.1 13.2 - - - +
319B HIS* 3.1 31.7 - - + +
324B HIS 4.2 0.8 + - - -
325B TYR* 1.3 76.1 - - - +
327B ARG* 1.3 60.6 + - - +
328B LYS* 4.0 21.7 + - + -
356B ASP 4.9 0.2 - - - -
357B PRO* 3.1 3.6 - - - +
358B LYS* 2.8 46.2 + - + +
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Residues in contact with ARG 327 (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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184B ASN* 4.1 7.1 - - - +
202B THR 4.0 9.1 + - - -
203B ASP* 3.6 15.3 + - - -
237B LEU* 3.2 28.6 - - - +
316B GLN 3.7 1.2 - - - +
317B ASP* 3.6 2.4 - - - -
318B LYS* 2.9 57.2 + - + +
325B TYR* 3.1 32.4 + - + +
326B GLU* 1.3 75.9 - - - +
328B LYS* 1.3 63.8 + - - +
329B THR* 3.8 21.0 + - + +
355B ASN* 4.6 15.1 + - - -
356B ASP 3.8 8.7 - - - +
357B PRO* 3.7 14.1 - - + -
1817B PO4 2.9 36.1 + - - -
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Residues in contact with LYS 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B TYR* 3.8 19.9 + - + +
316B GLN 3.3 4.0 - - - -
317B ASP* 3.3 30.5 + - - +
326B GLU* 4.0 25.5 + - + +
327B ARG* 1.3 72.9 - - - +
329B THR* 1.3 60.5 + - - +
330B SER* 4.3 0.6 + - - -
354B ASP* 3.7 2.3 - - - +
356B ASP* 3.0 45.3 + - + +
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Residues in contact with THR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASP* 4.1 12.8 + - - -
314B ALA 4.1 0.2 - - - +
315B TYR* 3.4 6.0 - - - -
316B GLN* 2.7 60.7 + - + +
318B LYS* 6.0 2.2 - - + -
327B ARG* 4.1 31.2 - - + +
328B LYS* 1.3 75.8 - - - +
330B SER* 1.3 60.8 + - - +
331B VAL* 4.6 3.5 - - - +
353B GLN* 4.1 9.0 + - - -
354B ASP 3.3 9.1 + - - -
355B ASN* 3.6 16.6 + - - +
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Residues in contact with SER 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ALA 3.7 4.5 - - - -
315B TYR* 3.6 22.0 - - - -
328B LYS 4.3 0.7 + - - -
329B THR* 1.3 71.2 + - - +
331B VAL* 1.3 63.1 + - - +
332B TYR* 4.9 13.6 + - - -
352B TYR* 4.0 9.6 - - - +
353B GLN* 3.3 5.6 - - - +
354B ASP* 2.9 44.9 + - - -
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASP* 3.6 37.2 - - + +
241B ALA* 4.7 4.7 - - + -
242B ILE* 3.8 30.3 - - + -
312B VAL* 4.8 2.5 - - + +
313B ALA* 3.1 5.2 - - - +
314B ALA* 2.8 54.3 + - + +
329B THR* 4.6 3.8 - - - +
330B SER* 1.3 78.5 - - - +
332B TYR* 1.3 74.1 + - - +
352B TYR 3.5 9.9 - - - +
353B GLN* 4.2 10.3 - - + +
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Residues in contact with TYR 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B VAL 3.3 6.7 - - - +
313B ALA* 3.7 18.8 - - + -
314B ALA 5.6 1.3 - - - -
330B SER* 4.9 13.1 + - - -
331B VAL* 1.3 85.8 - - - +
333B TYR* 1.3 62.5 + - - +
351B ASP* 3.3 4.1 - - - +
352B TYR* 3.0 68.2 + + + +
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Residues in contact with TYR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 3.7 41.3 - - + -
270B ARG* 3.6 30.0 - - - +
271B LYS* 2.7 34.0 + - + -
310B ARG* 5.4 2.9 - - + -
311B ALA* 3.1 6.8 - - - +
312B VAL* 2.8 50.2 + - + +
332B TYR* 1.3 78.7 - - - +
334B GLY* 1.3 70.4 + - - +
335B ILE* 3.3 33.4 - - + +
350B ALA 3.0 25.8 - - - -
351B ASP* 3.7 10.5 - - + -
399B PHE* 4.4 7.6 - + - -
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Residues in contact with GLY 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ARG 3.4 6.7 - - - -
311B ALA* 4.4 3.8 - - - -
333B TYR* 1.3 77.1 - - - +
335B ILE* 1.3 62.3 + - - +
336B LEU* 6.0 0.2 - - - -
349B GLY* 3.2 3.1 - - - -
350B ALA* 2.9 35.7 + - - +
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Residues in contact with ILE 335 (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 ARG* 6.0 0.4 - - + -
271B LYS 4.2 6.1 - - - +
272B LYS* 4.8 9.4 - - + +
273B PRO* 3.9 21.3 - - + -
309B GLY* 3.0 5.9 - - - -
310B ARG* 2.8 63.4 + - + +
333B TYR* 3.3 34.8 - - + +
334B GLY* 1.3 75.0 - - - +
336B LEU* 1.3 70.2 + - - +
347B THR* 3.6 23.3 - - + -
348B VAL 3.3 14.8 - - - +
349B GLY* 4.4 0.9 - - - -
399B PHE* 4.1 13.9 - - + -
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LEU* 3.8 28.7 - - + -
307B VAL* 5.4 2.2 - - + -
308B ARG 3.2 6.3 - - - +
309B GLY* 4.7 1.3 - - - -
335B ILE* 1.3 79.5 - - - +
337B GLU* 1.3 61.7 + - - +
338B PHE* 3.8 32.5 - - + -
346B LEU 4.0 0.2 - - - +
347B THR* 3.2 10.2 - - - +
348B VAL* 2.9 52.8 + - + -
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LYS* 3.9 22.0 + - - +
273B PRO* 3.4 36.8 - - + +
306B ASN 3.7 1.2 - - - +
307B VAL* 3.4 5.0 - - - +
308B ARG* 2.7 82.2 + - + +
336B LEU* 1.3 73.2 - - - +
338B PHE* 1.3 62.5 + - - +
345B MET* 3.8 23.4 - - - +
346B LEU 3.7 3.1 - - - -
347B THR* 3.7 20.1 - - + +
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Residues in contact with PHE 338 (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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306B ASN 3.7 3.1 - - - -
307B VAL* 3.8 30.3 - - + -
336B LEU* 3.8 39.7 - - + -
337B GLU* 1.3 76.6 - - - +
339B ASP* 1.3 62.9 + - - +
340B LEU* 3.7 17.7 - - + -
345B MET* 3.3 7.4 - - - +
346B LEU* 3.0 53.5 + - + +
348B VAL* 4.7 9.4 - - + -
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Residues in contact with ASP 339 (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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275B HIS* 5.3 0.5 - - - -
306B ASN* 2.9 37.5 + - + +
307B VAL* 5.2 0.4 - - - +
308B ARG* 2.6 34.8 + - - -
338B PHE* 1.3 74.5 - - - +
340B LEU* 1.3 69.5 + - - +
341B ASN* 3.3 13.9 + - - +
344B THR 3.7 3.1 - - - -
345B MET* 3.6 16.8 - - - +
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Residues in contact with LEU 340 (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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338B PHE* 3.7 17.7 + - + -
339B ASP* 1.3 73.3 - - - +
341B ASN* 1.3 67.2 + - - +
344B THR* 2.8 24.6 + - + +
346B LEU* 4.1 25.8 - - + +
402B LEU* 4.0 25.1 - - + -
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Residues in contact with ASN 341 (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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339B ASP* 4.1 15.7 - - - +
340B LEU* 1.3 81.2 + - - +
342B PRO* 1.3 73.5 - - + +
343B ASP* 2.7 41.3 + - - +
344B THR* 2.8 39.2 + - - +
404B HIS* 4.9 1.7 - - - -
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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
------------------------------------------------------------
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