Contacts of the strand formed by residues 326 - 341 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A ASP* 3.8 13.8 - - - +
318A LYS 3.3 12.8 - - - +
319A HIS* 3.9 26.5 + - + +
324A HIS 4.1 1.2 - - - -
325A TYR* 1.3 80.0 - - - +
327A ARG* 1.3 66.4 + - - +
328A LYS* 3.6 31.4 + - - +
356A ASP 4.9 2.4 - - - +
357A PRO* 3.2 5.4 - - - +
358A LYS* 3.0 47.3 + - + +
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Residues in contact with ARG 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ASN* 4.5 4.6 - - - +
202A THR 4.0 5.8 + - - -
203A ASP* 3.7 8.8 + - - -
237A LEU* 3.4 24.7 - - - +
316A GLN* 3.6 4.7 - - - +
318A LYS* 3.0 53.2 + - + +
325A TYR* 2.4 50.9 + - + +
326A GLU* 1.3 77.3 - - - +
328A LYS* 1.4 64.6 + - - +
329A THR* 3.8 27.0 + - + +
355A ASN* 4.7 6.1 - - - -
356A ASP 3.7 16.8 - - - +
357A PRO* 4.2 6.3 - - + -
1819A PO4 3.0 41.0 + - - -
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Residues in contact with LYS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A TYR* 3.2 34.3 - - + +
316A GLN 3.3 6.5 - - - +
317A ASP* 4.0 18.3 + - - +
326A GLU* 3.6 27.8 + - - +
327A ARG* 1.4 69.6 - - - +
329A THR* 1.3 61.4 + - - +
330A SER* 5.3 1.3 + - - +
354A ASP 3.3 3.3 - - - +
356A ASP* 3.2 46.6 + - + +
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Residues in contact with THR 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A LEU 6.0 0.2 - - - +
239A ASP* 4.1 13.9 + - - -
314A ALA 4.1 0.7 - - - +
315A TYR* 3.4 7.6 - - - -
316A GLN* 2.7 52.0 + - + +
318A LYS* 6.1 1.6 - - - -
327A ARG* 3.8 32.1 - - + +
328A LYS* 1.3 77.0 - - - +
330A SER* 1.3 62.1 + - - +
331A VAL* 4.7 4.3 - - - +
353A GLN* 4.8 6.3 + - - +
354A ASP 3.1 8.7 - - - -
355A ASN* 4.0 17.5 - - - +
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Residues in contact with SER 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ALA 3.5 6.5 - - - -
315A TYR* 3.8 16.5 - - - -
328A LYS* 5.3 0.9 + - - +
329A THR* 1.3 75.7 + - - +
331A VAL* 1.3 65.2 + - - +
332A TYR* 4.2 24.2 + - - -
352A TYR* 3.6 8.5 - - - +
353A GLN* 3.1 5.4 - - - +
354A ASP* 2.9 38.0 + - - +
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASP* 3.6 34.8 - - + +
241A ALA* 4.8 2.7 - - + -
242A ILE* 3.7 30.1 - - + -
312A VAL* 4.8 3.8 - - + -
313A ALA* 3.2 4.5 - - - -
314A ALA* 2.9 47.6 + - + +
329A THR* 4.7 3.1 - - - +
330A SER* 1.3 82.6 - - - +
332A TYR* 1.3 72.5 + - - +
352A TYR 3.1 11.7 - - - +
353A GLN* 4.3 12.3 - - + +
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Residues in contact with TYR 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 5.3 0.3 - - - +
312A VAL 3.2 7.2 - - - +
313A ALA* 4.0 18.4 - - + -
314A ALA 5.6 0.7 - - - -
330A SER* 4.2 16.8 + - - -
331A VAL* 1.3 83.8 - - - +
333A TYR* 1.3 63.4 + - - +
351A ASP* 3.3 3.7 - - - +
352A TYR* 2.9 67.4 + + + +
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Residues in contact with TYR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.6 35.4 - - + -
270A ARG* 3.4 34.5 - - + +
271A LYS* 2.8 32.1 + - + -
310A ARG* 4.9 4.0 - - + -
311A ALA* 3.3 7.4 - - - +
312A VAL* 2.8 53.3 + - + +
332A TYR* 1.3 77.4 - - - +
334A GLY* 1.3 67.1 + - - +
335A ILE* 3.5 34.7 - - + +
350A ALA 3.3 17.7 - - - -
351A ASP* 3.7 11.2 - - + -
399A PHE* 4.4 7.2 - + - -
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Residues in contact with GLY 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ARG 3.5 7.0 - - - -
311A ALA* 5.1 0.2 - - - -
333A TYR* 1.3 78.5 - - - +
335A ILE* 1.3 59.8 + - - +
349A GLY* 3.2 1.9 - - - -
350A ALA 2.7 36.8 + - - +
1816A N8E 3.7 30.7 - - - +
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Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ASP* 6.1 0.7 - - - +
270A ARG* 5.9 0.9 - - + -
271A LYS 4.1 3.1 - - - +
272A LYS* 5.0 7.9 - - + -
273A PRO* 4.1 23.6 - - + -
309A GLY* 3.4 2.6 - - - -
310A ARG* 3.1 49.5 + - + +
333A TYR* 3.5 33.4 - - + +
334A GLY* 1.3 73.6 - - - +
336A LEU* 1.3 68.7 + - - +
347A THR* 3.6 30.7 - - + -
348A VAL 3.4 9.9 - - - +
349A GLY* 4.5 1.1 - - - -
399A PHE* 4.1 13.9 - - + -
1816A N8E 4.1 2.4 - - - +
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Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A PRO* 5.2 0.2 - - - -
301A LEU* 3.5 31.4 - - + -
307A VAL* 5.1 4.3 - - + -
308A ARG 3.3 7.9 - - - +
309A GLY* 4.5 0.2 - - - -
335A ILE* 1.3 73.1 - - - +
337A GLU* 1.3 62.5 + - - +
338A PHE* 3.8 30.2 - - + -
346A LEU 4.1 0.3 - - - +
347A THR* 3.5 4.3 - - - +
348A VAL* 3.0 40.3 + - + +
1816A N8E 3.9 43.1 - - + +
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Residues in contact with GLU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS* 3.5 23.8 + - - +
273A PRO* 3.1 33.9 - - + +
306A ASN 3.6 0.9 - - - +
307A VAL* 3.2 9.5 - - - +
308A ARG* 2.7 74.1 + - + +
335A ILE* 5.1 0.2 - - + -
336A LEU* 1.3 73.6 - - - +
338A PHE* 1.3 62.9 + - - +
339A ASP 4.3 0.2 - - - -
345A MET* 3.4 32.5 - - + +
346A LEU 3.5 1.8 - - - -
347A THR* 3.9 17.8 - - + +
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Residues in contact with PHE 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ASN 3.6 4.9 - - - +
307A VAL* 4.1 27.1 - - + -
336A LEU* 3.8 42.6 - - + -
337A GLU* 1.3 74.9 - - - +
339A ASP* 1.3 62.7 - - - +
340A LEU* 3.5 11.7 + - + -
345A MET* 3.3 4.0 - - - +
346A LEU* 2.6 68.8 + - + +
348A VAL* 4.6 14.8 - - + -
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Residues in contact with ASP 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 4.3 13.2 + - - -
275A HIS* 4.9 2.3 + - - -
305A GLY 4.6 0.7 - - - +
306A ASN* 3.1 36.1 + - + +
308A ARG* 2.7 34.7 + - - -
338A PHE* 1.3 69.2 - - - +
340A LEU* 1.3 67.3 + - - +
341A ASN* 3.1 12.9 - - - +
342A PRO* 5.6 2.0 - - + -
344A THR 3.8 4.7 - - - -
345A MET* 3.4 18.9 - - - +
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Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A PHE* 3.5 10.5 + - + -
339A ASP* 1.3 74.8 - - - +
341A ASN* 1.3 67.6 + - - +
344A THR* 2.9 25.0 + - + +
346A LEU* 4.4 26.5 - - + -
402A LEU* 4.1 26.0 - - + -
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Residues in contact with ASN 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 4.5 0.9 + - - -
339A ASP* 3.1 10.7 - - - +
340A LEU* 1.3 82.7 + - - +
342A PRO* 1.4 78.5 - - + +
343A ASP* 2.7 20.7 + - - +
344A THR* 2.9 42.9 + - - +
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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