Contacts of the strand formed by residues 326 - 332 (chain A) in PDB entry 5J2M
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 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A ASP* 4.5 14.4 - - + +
325A LEU* 1.3 79.2 - - - +
327A ALA* 1.3 65.3 + - - +
328A GLU 4.2 0.2 - - - -
340A GLN 3.7 1.0 - - - +
341A ILE* 3.2 6.6 - - - +
342A TYR* 2.8 83.6 + - + +
343A GLN 4.5 12.6 - - - +
345A PRO* 6.6 0.2 - - + -
387A PRO* 4.6 0.4 - - - -
388A LYS* 3.1 10.1 - - + +
390A LYS* 3.8 38.8 - - + +
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Residues in contact with ALA 327 (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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326A ILE* 1.3 75.1 - - - +
328A GLU* 1.3 60.8 + - - +
329A ILE* 4.1 0.8 + - - -
339A TYR* 5.6 1.1 - - + -
340A GLN 3.5 5.2 - - - +
341A ILE* 4.2 10.1 - - + -
375A ILE* 4.0 20.9 - - + -
387A PRO* 4.2 8.0 - - + +
388A LYS 2.8 9.4 + - - +
389A PHE* 3.2 34.3 - - + -
390A LYS 2.8 23.8 + - - +
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Residues in contact with GLU 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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326A ILE 4.2 0.6 - - - -
327A ALA* 1.3 73.4 - - - +
329A ILE* 1.3 68.3 + - - +
339A TYR* 3.1 4.7 - - - +
340A GLN* 3.0 49.0 + - - +
342A TYR* 3.2 30.4 + - + -
390A LYS* 3.4 27.4 - - + +
417A VAL* 4.4 13.0 - - + +
419A THR* 3.9 24.7 + - - +
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Residues in contact with ILE 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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327A ALA 4.7 3.4 - - - +
328A GLU* 1.3 81.2 - - - +
330A GLN* 1.3 64.3 + - - +
337A TRP* 3.9 32.8 - - + -
338A THR 3.5 9.2 - - - +
339A TYR* 4.1 2.7 - - + -
340A GLN* 5.5 0.2 - - - -
368A LEU* 3.9 12.6 - - + -
371A ALA* 4.4 7.6 - - + -
372A VAL* 3.9 18.4 - - + -
375A ILE* 3.6 31.9 - - + -
389A PHE* 4.4 3.4 - - + -
390A LYS 3.2 7.6 + - - +
391A LEU* 3.7 28.7 - - + -
392A PRO* 3.2 24.4 - - + +
417A VAL* 5.2 0.3 - - - +
419A THR* 4.6 3.8 + - - -
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Residues in contact with GLN 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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328A GLU* 4.2 0.6 + - + -
329A ILE* 1.3 76.6 - - - +
331A LYS* 1.3 80.8 + - - +
332A GLN* 3.9 10.3 - - - +
337A TRP* 3.5 6.3 - - - +
338A THR* 2.7 56.3 + - + +
340A GLN* 4.5 9.9 - - - +
392A PRO* 4.9 1.7 - - - +
419A THR* 3.5 28.7 + - - +
420A PRO 3.3 19.5 + - - +
421A PRO* 3.6 4.2 - - - +
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Residues in contact with LYS 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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330A GLN* 1.3 97.2 + - - +
332A GLN* 1.3 79.8 + - - +
333A GLY* 5.0 4.9 - - - -
335A GLY 6.2 0.4 - - - +
337A TRP* 3.5 35.6 - - + -
364A ASP* 2.9 36.2 + - - -
392A PRO* 4.9 4.5 - - + +
421A PRO* 3.5 49.5 + - + +
422A LEU 4.9 5.8 + - - +
423A VAL* 4.5 7.9 - - + -
426A TRP* 5.4 7.9 - - - -
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Residues in contact with GLN 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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273A GLY* 4.3 13.1 - - - -
274A ILE 5.6 0.2 - - - +
275A LYS* 3.6 32.9 - - + +
330A GLN* 3.9 11.5 - - - +
331A LYS* 1.3 92.7 - - - +
333A GLY* 1.3 66.0 + - - +
335A GLY* 4.5 1.4 + - - -
336A GLN* 2.8 35.3 + - + +
337A TRP* 3.8 4.2 + - - -
338A THR* 3.3 44.3 + - - +
421A PRO* 5.4 2.0 - - - -
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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