Contacts of the strand formed by residues 50 - 54 (chain N) in PDB entry 6ULG
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 ILE 50 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N ARG* 3.6 28.3 - - - +
49N LEU* 1.3 79.4 - - - +
51N VAL* 1.3 65.5 - - - +
52N TYR* 3.6 31.9 - - + -
62N VAL* 4.2 7.0 - - + -
64N PHE 3.4 11.7 - - - +
65N ASP* 4.3 5.2 - - - +
135N VAL* 5.2 5.6 - - + -
138N LEU* 3.7 34.1 - - + -
142N MET* 4.8 3.6 - - - -
312N ALA 3.5 3.9 - - - +
313N ILE* 3.6 1.4 - - - -
314N SER* 3.0 38.6 + - - +
316N ILE* 3.8 16.2 - - + -
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Residues in contact with VAL 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49N LEU* 4.3 7.2 - - + -
50N ILE* 1.3 79.0 - - - +
52N TYR* 1.3 59.0 + - - +
62N VAL* 3.9 0.7 - - - -
63N LEU* 2.8 59.5 + - + +
64N PHE* 3.3 26.1 + - + +
311N ILE* 4.0 17.9 - - + -
312N ALA 3.8 2.9 - - - +
313N ILE* 4.2 13.7 - - + -
351N ILE* 3.9 31.6 - - + -
355N MET* 5.3 1.6 - - - -
371N TYR* 5.1 1.8 - - - +
375N LEU* 4.3 5.8 - - + -
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Residues in contact with TYR 52 (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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50N ILE* 3.6 30.3 - - + -
51N VAL* 1.3 76.2 - - - +
53N GLN* 1.3 62.3 + - - +
60N ARG* 3.9 31.7 - - + +
61N GLN 3.9 6.7 - - - -
62N VAL* 3.6 21.0 - - + +
63N LEU* 4.7 0.9 - - - -
135N VAL* 2.7 37.0 + - + +
136N ASN* 3.9 6.6 + - - -
138N LEU 4.8 0.4 - - - -
139N GLY* 3.6 23.8 - - - -
142N MET* 3.7 19.5 - - + -
143N PHE* 3.6 31.0 - + + -
311N ILE* 3.3 14.6 - - - +
312N ALA 3.2 25.6 + - - +
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Residues in contact with GLN 53 (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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52N TYR* 1.3 77.9 - - - +
54N ASP* 1.3 61.5 + - - +
55N CYS 4.2 0.4 - - - +
56N ASP* 5.2 4.9 + - - -
59N GLY 4.4 0.3 - - - +
60N ARG* 3.3 5.2 - - - +
61N GLN* 3.0 64.5 + - + +
63N LEU* 3.9 28.7 - - + +
143N PHE* 4.2 2.0 - - - -
309N LYS* 2.9 35.3 + - - +
310N LYS 3.3 13.2 - - - +
311N ILE* 4.2 5.9 - - + +
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Residues in contact with ASP 54 (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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53N GLN* 1.3 76.2 - - - +
55N CYS* 1.3 67.6 + - - +
59N GLY 4.3 8.5 - - - +
60N ARG* 2.5 49.7 + - + +
143N PHE* 3.6 27.1 - - + -
310N LYS* 3.0 31.5 + - - +
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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