Contacts of the strand formed by residues 363 - 375 (chain N) in PDB entry 5IY6
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 ARG 363 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359N ASN* 2.8 7.8 - - - +
360N LEU 2.8 37.0 + - - +
361N ASN* 3.8 16.4 - - - +
362N GLY* 1.3 78.6 - - - +
364N ASP* 1.3 60.7 + - - +
365N TYR* 3.0 29.1 + - + +
86O GLU* 2.5 39.6 + - - -
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Residues in contact with ASP 364 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N VAL* 5.6 2.9 - - - +
14N TYR* 3.3 30.7 + - + +
50N LEU* 5.4 8.9 - - + +
357N ILE* 5.5 5.9 - - + +
358N MET 3.4 4.9 - - - +
359N ASN* 3.2 32.7 + - - -
362N GLY 4.0 3.9 + - - +
363N ARG* 1.3 74.2 - - - +
365N TYR* 1.3 71.8 + - - +
10O THR* 4.3 17.1 + - - +
11O LEU* 5.1 5.5 + - - +
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Residues in contact with TYR 365 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N VAL* 6.0 3.8 - - + -
14N TYR* 3.3 7.0 + - - -
357N ILE* 3.5 6.8 - - - +
358N MET* 2.5 65.3 + - + +
360N LEU* 3.5 52.1 + - + +
363N ARG* 3.0 46.1 + - + -
364N ASP* 1.3 81.5 - - - +
366N ILE* 1.3 59.7 + - - +
86O GLU* 3.0 32.1 + - + -
88O ILE* 3.5 14.2 - - + +
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Residues in contact with ILE 366 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10N VAL* 4.7 8.7 - - + +
13N LEU* 5.3 13.2 - - + -
14N TYR* 3.9 25.6 - - + +
356N GLY 3.2 14.1 - - - +
357N ILE* 3.5 22.7 - - + -
358N MET* 4.6 1.9 - - - +
365N TYR* 1.3 78.7 - - - +
367N PHE* 1.3 64.3 + - - +
44O ILE* 6.1 3.1 - - + -
48O LEU* 3.8 7.9 - - + -
52O VAL* 3.5 34.1 - - + -
54O ASN* 2.6 41.9 + - - +
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Residues in contact with PHE 367 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335N VAL* 4.3 6.7 - - + -
337N CYS* 3.6 18.6 - - + -
353N LEU* 5.0 1.8 - - + -
354N LYS* 3.9 14.8 - - - -
355N ASP* 3.2 2.4 - - - -
356N GLY* 2.7 60.1 + - - +
358N MET* 3.5 34.8 - - + -
366N ILE* 1.3 75.6 - - - +
368N SER* 1.3 58.0 + - - +
369N LYS 3.6 17.5 - - - -
370N ALA* 3.5 23.1 - - + -
52O VAL* 3.6 10.1 - - - +
54O ASN* 3.2 12.6 - - - +
55O ARG* 4.3 0.9 - - - -
56O VAL* 3.5 36.3 - - + +
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Residues in contact with SER 368 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354N LYS* 3.1 6.6 - - - +
355N ASP* 2.6 39.8 + - - +
367N PHE* 1.3 66.2 - - - +
369N LYS* 1.3 70.0 + - - +
48O LEU 5.1 0.9 + - - -
52O VAL* 3.7 16.1 + - - +
53O ARG* 3.6 24.4 + - - -
54O ASN 2.2 29.5 + - - -
55O ARG* 5.2 0.4 - - - -
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Residues in contact with LYS 369 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353N LEU 3.3 7.0 - - - +
354N LYS* 3.7 13.9 - - + +
367N PHE* 3.6 5.1 - - - -
368N SER* 1.3 92.4 - - - +
370N ALA* 1.3 61.5 + - - +
371N ILE* 6.1 2.7 - - + -
53O ARG* 5.8 6.8 - - - +
55O ARG* 3.2 29.8 - - + +
56O VAL 2.8 27.2 + - - +
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Residues in contact with ALA 370 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352N HIS* 3.5 0.3 - - - -
353N LEU* 2.2 65.8 + - + +
367N PHE* 3.5 25.8 - - + -
369N LYS* 1.3 72.4 - - - +
371N ILE* 1.3 62.7 + - - +
56O VAL* 3.1 14.8 - - + +
58O PHE* 3.5 20.5 - - + -
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Residues in contact with ILE 371 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351N PHE 3.2 9.4 - - - +
352N HIS* 3.6 38.4 - - + +
353N LEU 5.3 0.9 - - - +
369N LYS* 6.1 2.2 - - + -
370N ALA* 1.3 81.0 - - - +
372N GLY* 1.3 63.3 + - - +
55O ARG* 6.4 0.4 - - - +
56O VAL 3.7 5.3 + - - -
57O ASN* 2.9 27.2 - - + +
58O PHE* 3.3 8.8 + - - -
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Residues in contact with GLY 372 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350N LYS* 3.4 5.9 - - - +
351N PHE* 2.4 53.5 + - - +
352N HIS* 5.7 0.2 - - - -
371N ILE* 1.3 73.5 - - - +
373N ASP* 1.3 59.9 + - - +
57O ASN* 4.8 0.2 - - - -
58O PHE* 3.4 29.5 - - - -
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Residues in contact with ASP 373 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348N LYS* 2.6 38.1 + - - +
349N TRP 2.6 26.2 - - - +
350N LYS* 4.4 6.2 - - + +
351N PHE* 4.1 3.5 - - - -
372N GLY* 1.3 75.4 - - - +
374N ALA* 1.3 72.8 + - - +
375N GLU* 4.3 0.2 - - - +
58O PHE* 3.9 5.1 + - - -
59O ARG* 2.9 44.6 + - - +
60O GLY 3.6 6.4 + - - -
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Residues in contact with ALA 374 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348N LYS* 3.4 1.4 - - - -
349N TRP* 2.3 43.4 + - + +
351N PHE* 3.3 26.0 - - + -
373N ASP* 1.3 78.7 + - - +
375N GLU* 1.3 62.5 + - - +
59O ARG* 3.9 5.2 - - - +
60O GLY 3.0 27.1 - - - +
62O LEU* 4.1 10.8 - - + +
76O LEU* 4.3 0.9 - - + -
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Residues in contact with GLU 375 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347N ASN* 3.0 25.6 - - - +
348N LYS* 3.6 30.7 + - + +
349N TRP* 4.3 1.3 - - - -
373N ASP* 4.6 0.7 - - - -
374N ALA* 1.3 78.3 - - - +
376N TRP* 1.3 60.7 + - - +
59O ARG* 2.3 41.2 + - - +
61O SER* 3.8 12.8 - - - +
62O LEU 3.2 21.3 + - - +
205P ARG* 5.3 3.5 + - - -
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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