Contacts of the strand formed by residues 353 - 358 (chain A) in PDB entry 4JJ7
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 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A PHE* 3.5 8.5 - - + +
340A PHE* 3.1 36.0 + - + +
341A THR* 5.1 1.3 - - - +
342A GLY* 5.2 4.0 - - - +
348A LEU* 2.9 43.9 + - + -
349A ALA* 4.4 1.8 - - - +
350A GLY 4.4 4.0 - - - +
351A LYS 2.8 23.7 + - - +
352A PRO* 1.3 73.6 - - - +
354A VAL* 1.3 60.5 + - - +
355A PHE* 4.1 10.7 - - + -
397A ALA 3.8 13.3 + - - -
398A ASP* 2.9 8.2 + - - +
399A PHE* 3.3 35.4 - - + +
400A LEU 2.9 25.3 + - - +
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Residues in contact with VAL 354 (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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309A CYS* 4.3 14.1 - - - -
310A PHE 2.9 13.9 + - - +
311A ILE* 3.2 11.8 - - + +
312A CYS 2.8 25.8 + - - -
352A PRO* 4.6 0.9 - - + -
353A LYS* 1.3 79.0 - - - +
355A PHE* 1.3 66.7 + - - +
356A PHE* 3.5 38.4 - - + -
400A LEU* 3.3 22.7 - - + +
470A LEU* 5.8 0.2 - - + -
474A LEU* 3.8 28.0 - - + -
476A PHE* 4.5 7.0 - - + -
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Residues in contact with PHE 355 (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 LEU* 5.6 0.7 - - + -
310A PHE* 4.2 9.4 - + - -
312A CYS* 3.2 35.0 - - + +
314A ILE* 5.5 0.7 - - + -
336A LEU* 4.1 12.3 - - + -
337A THR* 3.8 33.4 - - + -
340A PHE* 3.7 27.6 - + - -
353A LYS* 4.1 16.8 - - + -
354A VAL* 1.3 77.8 - - - +
356A PHE* 1.3 58.9 + - - +
357A ILE* 4.2 10.8 - - + -
399A PHE* 3.7 26.7 - + - -
400A LEU 2.8 10.4 + - - +
401A LEU* 3.4 20.3 - - + +
402A GLY* 2.8 32.2 + - - +
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Residues in contact with PHE 356 (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 PHE* 3.9 26.0 - + - -
311A ILE* 4.1 7.6 - - + -
312A CYS 2.9 6.5 + - - -
313A CYS* 3.3 26.7 - - + +
314A ILE 2.9 27.9 + - - +
315A LEU* 5.7 0.2 - - - +
354A VAL* 3.5 29.4 - - + -
355A PHE* 1.3 75.5 - - - +
357A ILE* 1.3 62.3 + - - +
358A GLN 4.0 0.7 - - - -
400A LEU* 5.2 0.7 - - + -
402A GLY* 3.4 7.6 - - - +
421A TYR* 3.5 24.9 - - + -
422A ILE* 4.7 6.7 - - + -
425A LEU* 3.6 40.2 - - + -
429A LEU* 5.1 0.2 - - + -
439A ILE* 4.8 13.7 - - + -
443A LEU* 4.2 13.2 - - + -
476A PHE* 5.7 1.3 - + - -
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Residues in contact with ILE 357 (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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314A ILE* 3.6 38.4 - - + +
323A ILE* 3.7 27.6 - - + -
333A ILE* 4.2 13.2 - - + -
336A LEU* 4.9 3.4 - - + -
355A PHE* 4.7 10.1 - - + -
356A PHE* 1.3 75.1 - - - +
358A GLN* 1.3 60.5 + - - +
359A ALA* 3.8 9.4 + - + +
401A LEU* 3.7 27.1 - - + -
402A GLY 2.9 9.5 + - - -
403A MET* 3.7 27.0 - - + +
404A ALA* 3.0 27.9 + - - +
421A TYR* 4.4 3.5 - - - -
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Residues in contact with GLN 358 (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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260A ARG* 4.2 5.6 - - - +
266A ASP* 4.2 1.6 - - - +
314A ILE 2.9 15.3 + - - +
315A LEU* 3.8 7.0 - - + -
316A SER 3.0 27.5 + - - +
356A PHE 4.0 1.2 - - - -
357A ILE* 1.3 70.2 - - - +
359A ALA* 1.3 60.3 + - - +
404A ALA* 3.3 21.6 - - + +
411A SER* 3.1 25.6 + - - -
412A TYR 4.1 3.5 + - - +
419A THR* 3.5 34.7 + - + +
421A TYR* 3.4 15.2 - - - +
422A ILE* 3.7 20.4 - - + -
462A GLN* 4.7 0.3 + - - -
506B 1U8 2.8 24.6 + - - +
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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