Contacts of the strand formed by residues 339 - 348 (chain A) in PDB entry 5OAQ
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 LYS 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A PRO* 5.6 0.2 - - - -
276A GLU* 5.5 4.9 + - - -
277A LYS* 5.6 5.7 - - - +
335A CYS* 3.2 4.1 - - - -
336A SER 2.9 32.2 + - - +
337A PHE 3.6 12.6 - - - +
338A GLY* 1.3 84.2 - - - +
340A GLN* 1.3 67.2 + - - +
341A VAL* 3.3 5.2 + - + +
501A GOL 5.0 6.1 - - - -
63L THR* 4.4 16.6 - - + +
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Residues in contact with GLN 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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275A PRO* 4.6 14.7 - - + +
333A LYS* 3.3 38.3 + - + +
334A VAL 3.7 5.2 - - - +
335A CYS* 4.3 5.7 - - - -
338A GLY 4.1 2.0 + - - -
339A LYS* 1.3 73.4 - - - +
341A VAL* 1.3 63.9 + - - +
342A VAL* 4.1 14.6 - - - +
343A GLU* 3.5 29.5 + - - +
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A VAL* 2.7 49.8 + - + +
335A CYS* 4.6 1.6 - - - -
336A SER* 3.9 20.6 - - - +
339A LYS* 3.7 11.2 - - + +
340A GLN* 1.3 79.8 - - - +
342A VAL* 1.3 67.7 + - + +
369A TYR* 3.8 29.8 - - + +
63L THR* 5.3 5.4 - - + +
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Residues in contact with VAL 342 (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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332A THR 3.9 0.6 - - - +
333A LYS* 3.4 2.9 - - - -
334A VAL* 2.9 53.1 + - + +
340A GLN* 4.1 7.1 - - - +
341A VAL* 1.3 90.9 - - + +
343A GLU* 1.3 63.0 + - - +
367A CYS* 4.0 22.0 - - + -
369A TYR* 4.3 20.4 - - + -
502A MYR 4.9 1.3 - - + -
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Residues in contact with GLU 343 (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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331A SER* 2.6 31.5 + - - +
332A THR 3.2 9.4 - - - +
333A LYS* 3.4 21.7 - - + -
340A GLN* 3.5 21.1 + - - +
342A VAL* 1.3 79.5 - - - +
344A LYS* 1.3 63.4 + - - +
345A VAL* 3.6 21.8 + - + +
502A MYR 5.6 1.6 - - - -
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Residues in contact with LYS 344 (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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316A VAL* 4.5 10.7 - - - +
330A CYS 3.6 1.4 - - - +
331A SER* 3.4 2.6 - - - -
332A THR* 2.8 47.5 + - - +
343A GLU* 1.3 73.7 - - - +
345A VAL* 1.3 65.6 + - - +
346A GLU* 3.6 27.2 + - + +
364A SER* 3.0 32.2 + - - +
365A PRO* 4.4 9.8 + - + +
502A MYR 3.9 51.7 - - + +
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Residues in contact with VAL 345 (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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329A THR* 4.9 11.9 - - + -
330A CYS 3.4 6.3 - - - +
331A SER* 4.4 6.1 - - - -
343A GLU* 3.6 31.2 + - + +
344A LYS* 1.3 81.6 - - - +
346A GLU* 1.3 74.4 + - - +
347A THR* 5.2 4.0 - - - +
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Residues in contact with GLU 346 (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 ILE 3.9 0.2 - - - +
329A THR* 3.2 4.2 - - - -
330A CYS* 2.7 53.2 + - + +
332A THR* 4.8 0.3 + - - -
344A LYS* 3.6 26.9 + - + +
345A VAL* 1.3 80.7 - - - +
347A THR* 1.3 63.2 + - - +
348A GLU* 3.8 14.2 + - - +
361A ILE* 3.3 27.4 - - + +
364A SER* 2.5 34.1 + - - -
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Residues in contact with THR 347 (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 ILE* 3.8 18.6 - - + -
328A ILE 3.4 5.2 - - - +
329A THR* 3.6 14.9 - - + +
345A VAL* 5.2 3.1 - - - +
346A GLU* 1.3 76.7 - - - +
348A GLU* 1.3 73.6 + - - +
349A TYR* 3.9 19.4 - - + +
402A ARG* 3.8 26.3 + - - +
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Residues in contact with GLU 348 (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 ILE* 3.7 4.2 - - - +
328A ILE* 2.8 58.1 + - + +
330A CYS* 5.6 0.7 - - + -
346A GLU* 3.8 16.9 - - - +
347A THR* 1.3 86.3 - - - +
349A TYR* 1.3 66.7 + - - +
359A TYR* 4.0 11.6 - - + -
360A ARG 3.2 17.1 - - - +
361A ILE* 3.5 44.0 - - + +
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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