Contacts of the strand formed by residues 357 - 363 (chain A) in PDB entry 4N0N
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 PHE 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A VAL* 3.6 37.9 - - + -
335A ILE* 5.5 0.2 - - + -
347A ARG* 5.6 2.7 - - - -
352A ILE* 4.3 26.2 - - + -
355A CYS* 3.7 31.2 - - + -
356A THR* 1.3 81.8 - - - +
358A PRO* 1.3 73.2 - - + +
359A VAL 4.0 15.5 - - - +
360A VAL* 4.0 18.6 - - + -
381A ARG* 2.8 10.5 + - + -
382A ALA* 3.2 4.9 - - - -
383A SER* 2.9 26.8 + - - -
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Residues in contact with PRO 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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356A THR 4.9 0.2 - - - +
357A PHE* 1.3 90.5 - - + +
359A VAL* 1.3 65.6 + - + +
382A ALA* 4.5 0.2 - - - -
383A SER* 3.5 13.3 + - - +
384A GLN* 2.9 48.8 + - - +
385A GLU 2.9 10.7 + - - +
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Residues in contact with VAL 359 (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 LYS* 3.5 41.7 - - + +
332A GLY* 3.5 7.9 - - - +
333A VAL* 3.0 21.9 + - - +
357A PHE* 4.0 5.2 - - - +
358A PRO* 1.3 91.7 - - + +
360A VAL* 1.3 70.5 + - - +
384A GLN* 5.0 3.4 - - + +
385A GLU* 3.3 29.8 - - + +
387A TYR* 3.9 18.4 - - + -
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Residues in contact with VAL 360 (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 LYS 3.7 2.2 - - - -
333A VAL* 3.2 14.6 - - + +
335A ILE* 3.8 26.7 - - + -
357A PHE* 4.0 27.1 - - + -
359A VAL* 1.3 80.7 - - - +
361A THR* 1.3 73.8 + - - +
362A LEU 4.0 0.4 - - - +
378A ALA 5.0 0.4 - - - +
381A ARG* 4.1 12.6 - - + -
382A ALA* 3.8 21.8 - - + +
385A GLU 3.1 5.9 + - - +
386A LEU* 3.5 16.6 - - + +
387A TYR* 3.0 27.5 + - - -
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Residues in contact with THR 361 (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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324A VAL* 5.4 3.8 - - + -
329A PHE* 3.7 40.3 - - + +
330A GLU* 4.4 0.4 - - - -
331A LYS* 2.7 37.7 + - - +
333A VAL 2.9 8.1 + - - +
334A VAL* 3.2 12.6 - - + +
335A ILE 2.8 28.6 + - - +
360A VAL* 1.3 74.6 + - - +
362A LEU* 1.3 62.1 + - - +
363A ARG* 4.0 16.4 - - + -
387A TYR* 3.3 9.9 - - + +
389A TYR* 5.5 0.9 - - + +
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Residues in contact with LEU 362 (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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335A ILE* 3.5 25.1 - - + +
349A ILE* 3.9 12.8 - - + -
360A VAL 4.0 1.4 - - - -
361A THR* 1.3 71.3 - - - +
363A ARG* 1.3 62.9 + - - +
364A LEU* 4.0 19.7 - - + -
378A ALA* 3.8 38.6 - - + +
379A VAL* 4.0 17.3 - - + -
386A LEU* 4.2 11.0 - - + -
387A TYR 2.8 12.4 + - - +
388A ILE* 3.5 7.8 - - + -
389A TYR* 2.9 28.9 + - - +
395A LEU* 4.0 20.2 - - + -
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Residues in contact with ARG 363 (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 PRO* 2.7 36.4 + - - +
329A PHE 4.2 15.7 - - - -
330A GLU* 4.8 2.7 - - - -
334A VAL* 3.9 25.4 - - + -
335A ILE 2.8 12.7 + - - +
336A THR* 2.7 35.4 + - - +
341A ASP* 4.1 13.5 + - - +
346A HIS* 4.3 18.4 + - - -
361A THR* 4.0 9.9 - - + -
362A LEU* 1.3 75.7 - - - +
364A LEU* 1.3 64.2 + - - +
365A PRO* 3.4 29.3 - - + +
389A TYR* 3.7 28.9 - - + -
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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