Contacts of the strand formed by residues 327 - 335 (chain A) in PDB entry 2AB5
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 ILE 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A LYS* 3.6 46.0 - - + -
320A LEU 3.5 5.8 - - - +
321A LYS* 4.5 27.8 - - + -
322A MSE 4.7 0.2 - - - -
325A GLY 4.9 4.7 - - - +
326A THR* 1.3 77.8 - - - +
328A LYS* 1.3 63.8 + - - +
329A GLU* 4.2 6.5 + - + +
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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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296A HIS* 4.6 12.4 - - - -
318A LYS 3.7 0.2 - - - +
319A LYS* 3.5 3.5 - - - -
320A LEU* 2.7 47.8 + - + +
322A MSE 3.6 32.1 - - + -
326A THR 3.9 1.2 + - - -
327A ILE* 1.3 73.4 - - - +
329A GLU* 1.3 69.3 + - - +
330A MSE 3.9 28.0 - - - -
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Residues in contact with GLU 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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296A HIS* 4.9 0.7 + - - -
297A ILE* 3.8 28.4 + - + +
317A ILE* 4.2 12.0 - - + +
318A LYS 3.4 9.4 - - - +
319A LYS* 3.8 32.0 + - + +
327A ILE* 4.2 6.7 + - + +
328A LYS* 1.3 83.8 - - - +
330A MSE 1.3 78.6 + - - +
603A SO4 4.8 5.0 + - - -
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Residues in contact with MSE 330 (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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294A GLU* 3.8 33.9 - - + +
295A MSE 3.3 36.8 - - - +
296A HIS* 3.3 36.3 - - + +
297A ILE* 3.9 8.3 - - - -
317A ILE* 3.6 6.2 - - - +
318A LYS* 2.8 33.6 + - + +
320A LEU* 4.3 20.2 - - + -
328A LYS* 3.9 12.1 - - - -
329A GLU* 1.3 85.1 - - - +
331A CYS* 1.3 61.4 + - - +
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Residues in contact with CYS 331 (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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294A GLU* 3.4 6.4 - - - +
295A MSE 2.9 35.8 + - - +
296A HIS 3.3 25.4 - - - -
297A ILE* 4.2 9.6 - - + +
299A ASP 4.2 0.9 - - - -
300A ILE* 3.7 36.6 - - + -
303A LEU* 3.4 22.1 - - + +
315A VAL* 5.2 0.4 - - + -
316A THR 3.3 11.0 - - - +
317A ILE* 4.7 0.9 - - + -
318A LYS* 5.3 0.9 - - - -
330A MSE 1.3 74.0 - - - +
332A LYS* 1.3 62.0 + - - +
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Residues in contact with LYS 332 (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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277A TRP* 3.8 24.6 - - + -
290A GLU* 4.0 5.5 + - - -
293A ILE 3.1 15.5 - - - +
294A GLU* 4.3 6.3 - - + +
303A LEU* 3.6 5.4 - - - -
314A LYS 3.6 0.7 - - - +
315A VAL* 3.2 5.7 - - - +
316A THR* 2.8 51.3 + - - +
318A LYS* 4.2 35.6 - - + +
331A CYS* 1.3 77.9 - - - +
333A PHE* 1.3 72.1 + - - +
334A ASN* 3.5 27.7 - - - +
336A ARG* 4.0 13.5 - - - +
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Residues in contact with PHE 333 (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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272A PHE* 3.7 29.4 - + - -
291A LEU* 5.2 1.8 - - + -
292A GLY* 3.3 1.7 - - - -
293A ILE* 2.9 40.8 + - + -
303A LEU* 4.1 18.4 - - + -
306A ILE* 3.9 13.0 - - + -
307A LYS* 3.7 20.4 - - + -
310A LEU* 4.1 14.4 - - + -
312A ILE 3.5 27.4 - - - -
313A GLY* 3.7 10.1 - - - -
314A LYS 3.3 14.1 - - - -
315A VAL* 4.0 13.9 - - + -
332A LYS* 1.3 78.7 - - - +
334A ASN* 1.3 63.3 + - - +
335A VAL* 3.9 25.1 - - + -
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Residues in contact with ASN 334 (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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290A GLU* 3.0 29.9 + - + +
291A LEU 3.1 12.1 - - - +
292A GLY* 4.1 2.5 - - - -
313A GLY* 3.3 4.7 - - - -
314A LYS* 3.1 38.8 + - - +
316A THR* 5.5 3.6 + - - +
332A LYS* 3.5 24.2 - - - +
333A PHE* 1.3 79.9 - - - +
335A VAL* 1.3 65.9 + - - +
336A ARG* 3.6 18.5 + - - +
605A SO4 4.2 2.3 + - - -
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Residues in contact with VAL 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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289A TYR 3.8 0.2 - - - +
290A GLU* 3.5 5.5 - - - -
291A LEU* 2.8 32.9 + - + +
310A LEU* 5.3 0.2 - - + -
312A ILE* 3.9 26.9 - - + -
313A GLY* 3.8 15.0 - - - -
333A PHE* 3.9 16.8 - - + -
334A ASN* 1.3 79.2 - - - +
336A ARG* 1.3 62.3 + - - +
337A ASN 4.2 0.4 - - - +
340A HIS* 3.9 7.4 - - + -
341A LEU* 3.5 33.7 - - + +
345A ILE* 4.7 7.6 - - + -
605A SO4 3.8 17.0 - - - +
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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