Contacts of the strand formed by residues 329 - 336 (chain A) in PDB entry 6JZB
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 GLN 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A PHE* 3.7 9.8 - - - -
271A ILE* 3.3 31.8 - - + +
273A TYR* 3.9 14.5 - - + +
290A ILE* 4.0 9.3 - - - +
291A PRO 2.9 25.5 + - - -
292A THR* 3.2 22.5 + - - -
293A VAL 4.3 1.7 + - - -
312A ARG* 3.9 0.3 - - - -
313A LEU* 2.8 43.4 + - + +
316A LYS* 3.5 28.1 - - + +
317A GLY 3.7 2.2 - - - +
328A ASP* 1.3 71.8 - - - +
330A TYR* 1.3 67.7 + - - +
331A VAL* 4.6 0.8 - - + +
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Residues in contact with TYR 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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270A THR* 3.9 28.5 - - + -
271A ILE 2.9 9.7 + - - +
272A PHE* 3.5 17.2 - + + +
273A TYR 3.0 24.3 + - - +
310A LYS* 4.9 24.0 - - + +
311A PHE 3.3 7.6 - - - -
312A ARG* 3.5 50.4 + - + -
328A ASP* 4.2 14.3 + - + -
329A GLN* 1.3 75.0 - - - +
331A VAL* 1.4 62.9 + - - +
332A THR* 4.3 6.9 + - - +
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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
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273A TYR* 3.3 17.7 - - + +
275A LEU* 3.9 34.8 - - + -
290A ILE* 3.8 30.5 - - + -
299A LEU* 4.2 12.1 - - + -
309A LYS 3.6 1.2 - - - +
310A LYS* 3.3 3.3 - - - -
311A PHE* 2.7 53.7 + - + +
313A LEU* 4.4 15.3 - - + -
329A GLN* 4.6 2.2 - - + +
330A TYR* 1.4 71.4 - - - +
332A THR* 1.3 68.6 + - - +
333A VAL* 4.9 0.2 - - + -
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Residues in contact with THR 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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272A PHE* 5.7 3.3 - - - -
273A TYR 2.9 11.4 + - - -
274A ASN* 3.4 16.4 + - - +
275A LEU 2.8 23.8 + - - -
308A GLY* 3.9 20.2 - - - +
309A LYS 3.5 2.2 - - - +
310A LYS* 4.3 18.9 + - + +
330A TYR* 4.3 8.1 + - - +
331A VAL* 1.3 78.1 + - - +
333A VAL* 1.3 69.4 + - - +
334A ASN* 3.7 0.5 + - - +
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Residues in contact with VAL 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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275A LEU* 3.5 17.9 - - + -
277A LEU* 3.3 37.2 - - + -
301A ILE* 4.7 1.1 - - + -
305A THR* 4.1 13.5 - - + -
306A GLN 4.3 3.1 - - - +
307A THR* 3.6 0.3 + - - -
308A GLY* 3.0 25.1 + - - -
309A LYS 3.0 19.8 + - - +
311A PHE* 3.7 32.5 - - + -
331A VAL* 4.9 0.7 - - + -
332A THR* 1.3 78.6 - - - +
334A ASN* 1.3 69.5 - - - +
335A VAL* 4.3 8.7 - - + -
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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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274A ASN* 5.7 4.7 - - + -
275A LEU 2.7 12.8 + - - +
276A ASN* 3.0 28.5 + - - +
277A LEU 2.8 27.0 + - - -
307A THR* 3.6 6.7 + - - -
332A THR 3.7 1.8 + - - +
333A VAL* 1.3 75.8 - - - +
335A VAL* 1.3 71.3 + - - +
336A VAL* 3.7 14.0 + - - +
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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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277A LEU* 3.5 8.5 - - + +
279A PHE* 3.6 32.5 - - + +
282A ALA* 4.2 26.5 - - + -
305A THR 4.4 3.4 - - - +
307A THR* 3.0 39.6 + - - +
333A VAL* 4.3 9.9 - - + -
334A ASN* 1.3 82.4 + - - +
336A VAL* 1.3 63.7 + - - +
337A THR* 3.7 3.3 + - - -
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Residues in contact with VAL 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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276A ASN* 3.8 25.6 - - + +
277A LEU 2.9 15.2 + - - +
278A ASN* 4.3 4.8 - - + +
279A PHE* 3.5 21.6 + - - -
334A ASN* 3.7 21.1 - - - +
335A VAL* 1.3 71.8 - - - +
337A THR* 1.3 76.8 + - - +
338A PRO* 3.5 3.6 - - + +
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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