Contacts of the strand formed by residues 339 - 345 (chain A) in PDB entry 3JRQ
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 ASP 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ILE* 5.5 1.1 - - - -
266A LEU* 3.9 11.7 - - - +
267A CYS 3.6 4.7 - - - +
268A ARG* 3.1 35.0 + - - +
335A ARG* 3.3 21.2 + - - +
336A VAL 2.8 41.0 + - - +
337A LYS 3.0 1.1 - - - +
338A GLU* 1.3 70.5 - - - +
340A ASP* 1.3 61.2 + - - +
422A LEU* 4.0 24.2 - - + +
423A LYS* 3.2 25.8 + - - +
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Residues in contact with ASP 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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267A CYS* 2.7 26.9 + - - +
269A GLY* 3.1 25.1 + - - -
338A GLU 3.6 6.3 - - - +
339A ASP* 1.3 73.2 - - - +
341A CYS* 1.3 58.1 + - + +
363A ARG* 3.4 32.5 - - + -
367A LEU* 5.8 1.6 - - - +
421A ASP* 3.0 13.0 - - - +
422A LEU* 2.7 30.3 + - - +
423A LYS* 3.1 31.0 + - + -
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Residues in contact with CYS 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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265A VAL 4.1 0.3 - - - +
266A LEU* 3.6 2.8 - - - +
267A CYS* 2.9 45.3 + - - -
340A ASP* 1.3 86.6 - - - +
342A LEU* 1.3 60.3 + - - +
343A ILE* 4.8 8.1 - - - +
359A CYS 4.8 0.7 - - - -
362A ALA* 4.4 13.0 - - - -
363A ARG* 4.2 23.3 - - - -
366A ILE* 4.1 17.7 - - + -
419A VAL* 4.4 4.5 - - + -
420A VAL 3.1 13.7 - - - +
422A LEU* 3.5 9.2 - - - +
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Residues in contact with LEU 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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173A PHE* 6.2 0.2 - - + -
247A ALA* 3.7 30.5 - - + -
249A VAL* 4.1 13.2 - - + -
254A ILE* 3.8 20.0 - - + -
256A VAL* 5.1 0.4 - - + -
264A ALA* 4.6 2.0 - - + -
265A VAL 3.3 24.0 - - - +
266A LEU* 4.3 4.5 - - + -
275A LEU* 4.1 20.6 - - + -
341A CYS* 1.3 73.5 - - - +
343A ILE* 1.3 61.8 + - - +
344A LEU* 4.1 14.4 - - + -
418A VAL 3.6 0.3 - - - +
419A VAL* 3.4 5.5 - - - +
420A VAL* 2.9 46.7 + - + +
422A LEU* 3.6 14.3 - - + +
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Residues in contact with ILE 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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263A ARG 3.8 0.7 - - - +
264A ALA* 3.2 4.7 - - - -
265A VAL* 2.8 53.1 + - + +
341A CYS* 4.8 8.1 - - - +
342A LEU* 1.3 78.2 - - - +
344A LEU* 1.3 71.8 + - - +
345A ALA* 4.3 1.6 - - + -
350A TRP* 4.0 20.0 - - + -
358A ALA* 3.8 15.5 - - + +
359A CYS* 3.7 33.7 - - - +
362A ALA* 4.1 15.0 - - + -
402A LEU* 4.3 7.4 - - + -
417A VAL* 4.2 14.6 - - + -
418A VAL 3.4 5.8 - - - +
419A VAL* 4.9 4.7 - - + -
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Residues in contact with LEU 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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173A PHE* 3.7 25.8 - - + +
175A VAL* 3.6 18.4 - - + +
245A VAL* 3.6 33.7 - - + +
247A ALA* 4.1 23.3 - - + +
263A ARG 3.6 3.4 - - - -
264A ALA* 3.6 22.4 - - + -
342A LEU* 4.1 11.7 - - + -
343A ILE* 1.3 80.9 - - - +
345A ALA* 1.3 61.4 + - - +
417A VAL* 3.1 4.3 - - - +
418A VAL* 2.7 49.1 + - + +
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Residues in contact with ALA 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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175A VAL* 4.3 3.6 - - - +
245A VAL* 4.8 0.6 - - - +
262A SER* 3.4 4.6 - - - -
263A ARG 2.9 23.4 + - - -
343A ILE* 4.1 3.8 - - + -
344A LEU* 1.3 77.4 - - - +
346A SER* 1.3 63.2 + - - +
349A VAL* 3.9 6.7 - - + -
350A TRP* 2.7 42.5 + - + +
416A SER 3.1 11.7 - - - +
417A VAL* 3.7 16.2 - - + -
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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