Contacts of the strand formed by residues 369 - 375 (chain N) in PDB entry 5IYB
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 369 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340N ASP* 6.0 2.5 - - - -
353N LEU 3.6 11.4 - - - +
354N LYS* 3.9 8.1 - - + +
367N PHE* 3.7 4.5 - - - -
368N SER* 1.3 92.6 + - - +
370N ALA* 1.3 61.9 + - - +
371N ILE* 5.4 6.5 - - + -
55O ARG* 3.4 49.0 - - - +
56O VAL 3.7 2.9 + - - +
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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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351N PHE 3.9 0.5 - - - +
352N HIS 3.5 0.3 - - - -
353N LEU* 2.6 51.4 + - + +
367N PHE* 3.4 28.9 - - + -
369N LYS* 1.3 74.6 - - - +
371N ILE* 1.3 64.7 + - - +
56O VAL* 3.7 16.8 - - + +
58O PHE* 3.8 16.4 - - + -
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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 3.4 9.4 - - - +
352N HIS* 4.0 30.1 - - + +
353N LEU 5.3 1.3 - - - +
369N LYS* 5.4 5.6 - - + -
370N ALA* 1.3 81.7 - - - +
372N GLY* 1.3 62.0 + - - +
55O ARG* 5.8 5.8 - - - +
56O VAL 4.0 3.0 + - - -
57O ASN* 3.1 25.7 - - - +
58O PHE* 3.5 10.9 + - - -
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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
----------------------------------------------------------
350N LYS* 3.3 9.0 - - - +
351N PHE* 2.7 38.7 + - - +
352N HIS* 5.6 0.5 + - - -
371N ILE* 1.3 80.8 - - - +
373N ASP* 1.3 61.2 + - - +
57O ASN* 4.5 0.8 + - - -
58O PHE* 3.5 22.4 - - - -
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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* 5.2 5.9 - - - +
349N TRP 3.0 18.2 + - - +
350N LYS* 3.5 22.6 - - + +
351N PHE* 4.1 5.3 - - - -
372N GLY* 1.3 75.2 - - - +
374N ALA* 1.3 67.5 + - - +
58O PHE* 3.6 8.7 + - - +
59O ARG* 3.4 34.1 - - + +
60O GLY 3.6 1.4 + - - -
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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 2.7 - - - +
349N TRP* 2.4 43.3 + - + +
351N PHE* 3.4 27.8 - - + -
373N ASP* 1.3 81.5 + - - +
375N GLU* 1.3 57.8 + - - +
60O GLY 3.2 18.2 - - - +
62O LEU* 4.4 8.3 - - + +
76O LEU* 4.2 11.0 - - + -
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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* 2.9 43.1 + - - +
348N LYS* 3.5 26.9 + - + +
349N TRP* 4.6 0.2 - - - -
374N ALA* 1.3 76.0 - - - +
376N TRP* 1.3 60.7 + - - +
60O GLY 3.4 7.9 + - - +
61O SER* 3.4 11.2 + - - +
62O LEU* 2.6 32.0 + - - +
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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