Contacts of the strand formed by residues 64 - 68 (chain N) in PDB entry 1UCY
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 LEU 64 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33N LEU* 3.9 16.8 - - + -
34N PHE 3.6 0.9 - - - -
36N LYS* 5.1 0.7 - - - -
41N LEU* 3.5 32.3 - - + -
58N CYS 5.9 0.2 - - - +
59N LEU* 3.3 31.6 - - + -
60N THR* 3.6 29.0 - - + +
61N VAL 3.7 9.7 + - - +
62N ASP 3.5 1.8 - - - +
63N ASP* 1.3 83.2 - - - +
65N LEU* 1.3 72.3 + - - +
84N MET* 4.2 12.1 - - - +
85N LEU* 3.5 33.5 + - + -
88N ILE* 3.9 10.8 - - + -
106N LEU* 5.2 0.7 - - + -
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Residues in contact with LEU 65 (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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33N LEU* 3.8 5.5 - - - +
34N PHE* 2.8 54.5 + - + +
36N LYS* 4.1 42.0 - - + +
38N GLN* 6.2 1.3 - - + -
64N LEU* 1.3 84.3 - - - +
66N VAL* 1.3 64.7 + - - +
67N ARG* 4.1 2.2 - - + -
82N ILE* 4.5 19.5 - - + -
83N SER 3.3 6.3 - - - +
84N MET* 3.7 24.5 - - + -
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Residues in contact with VAL 66 (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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31N VAL* 3.5 20.6 - - + -
32N MET 3.6 2.9 - - - -
33N LEU* 4.6 12.8 - - + -
52N VAL* 4.5 5.2 - - + -
65N LEU* 1.3 76.8 - - - +
67N ARG* 1.3 62.0 + - - +
68N ILE* 3.4 28.9 - - + -
81N LYS 3.7 0.9 - - - +
82N ILE* 3.3 3.3 - - - +
83N SER* 2.7 37.9 + - - +
85N LEU* 3.5 33.0 - - + -
106N LEU* 4.9 4.5 - - + -
108N LEU* 4.0 15.5 - - + -
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Residues in contact with ARG 67 (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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30N GLN 4.4 0.9 - - - +
31N VAL* 3.9 0.9 - - - -
32N MET* 2.9 39.1 + - + +
34N PHE* 3.3 62.5 - - + -
65N LEU* 5.0 0.9 - - + -
66N VAL* 1.3 77.0 - - - +
68N ILE* 1.3 64.1 + - - +
70N LYS* 3.4 36.6 - - + +
73N ARG 5.1 3.6 + - - -
74N THR 6.2 1.0 - - - -
75N ARG 4.2 1.6 + - - +
76N TYR* 3.7 21.8 - - - +
80N GLU* 2.9 41.3 + - - +
81N LYS 3.5 4.0 - - - -
82N ILE* 4.2 19.6 - - + +
141N TRP* 5.6 0.2 - - - -
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Residues in contact with ILE 68 (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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28N PRO 4.5 5.2 - - - +
30N GLN 4.1 11.9 - - - +
31N VAL* 4.0 12.3 - - + -
46N LEU* 4.4 17.0 - - + -
52N VAL* 5.2 0.2 - - + -
66N VAL* 3.4 30.5 - - + +
67N ARG* 1.3 71.7 - - - +
69N GLY* 1.3 65.5 + - - +
70N LYS 3.3 3.1 - - - -
80N GLU* 3.2 6.6 - - - +
81N LYS 2.7 40.6 + - - +
83N SER* 4.9 0.2 - - - -
108N LEU* 4.5 10.8 - - + -
112N ILE* 3.3 33.2 - - + -
118N ILE* 3.5 33.9 - - + -
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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