Contacts of the strand formed by residues 66 - 73 (chain N) in PDB entry 6E0P
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 GLY 66 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N LYS 3.6 0.7 - - - +
61N GLN* 3.4 7.1 - - - -
62N THR* 2.8 37.7 + - - +
63N PRO* 4.8 1.5 - - - +
64N ARG 3.7 1.8 - - - +
65N GLN* 1.3 78.8 - - - +
67N LEU* 1.3 62.3 + - - -
68N GLU* 3.9 1.6 + - - +
245N TYR* 5.0 13.9 - - - -
258N SER* 5.2 7.9 - - - -
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Residues in contact with LEU 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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59N VAL* 3.7 16.6 - - + -
60N LYS 3.5 1.1 - - - -
61N GLN* 3.7 34.3 - - + +
65N GLN 3.7 2.8 + - - +
66N GLY* 1.3 74.0 - - - -
68N GLU* 1.3 65.9 + - - +
117N TYR* 4.9 6.3 - - + -
132N TRP* 5.1 1.6 - - + -
194N TYR* 5.9 1.6 - - + -
196N GLN* 4.6 3.1 - - - +
202N PRO* 4.7 13.9 - - + -
245N TYR* 3.7 46.8 - - + -
256N PHE* 3.5 53.7 + - + +
257N GLY 4.9 2.8 + - - +
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Residues in contact with GLU 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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59N VAL* 3.3 6.2 - - - +
60N LYS* 2.8 67.1 + - + +
62N THR* 5.5 1.1 - - - -
65N GLN* 2.9 36.0 - - + +
66N GLY 4.9 1.3 - - - +
67N LEU* 1.3 80.2 - - - +
69N TRP* 1.3 64.1 + - - +
70N ILE 3.7 0.2 + - - -
83N ASN* 5.6 2.2 - - - +
85N LYS* 2.8 37.4 + - - -
86N PHE* 4.2 8.6 - - + -
256N PHE* 4.1 2.9 - - - +
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Residues in contact with TRP 69 (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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57N GLN* 2.5 29.0 + - + +
58N TRP 3.9 12.3 - - - -
59N VAL* 4.7 7.0 - - + -
68N GLU* 1.3 72.9 - - - +
70N ILE* 1.3 59.4 + - - +
71N GLY* 3.5 21.0 + - - -
72N TYR* 3.5 27.1 - + - -
81N LYS* 4.2 19.1 - - + -
82N TYR 4.2 2.2 - - - -
83N ASN* 3.0 53.7 + - + +
86N PHE* 4.1 2.4 - - - -
129N LEU* 5.6 3.8 - - + -
247N LEU* 6.1 0.7 - - + -
252N SER 3.3 24.9 - - - -
253N PRO* 4.0 4.9 - - + -
254N TYR* 3.3 61.3 + + + +
256N PHE* 4.0 13.9 - + + -
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Residues in contact with ILE 70 (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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58N TRP* 2.8 22.8 + - + +
59N VAL 4.0 3.4 - - - -
60N LYS* 3.7 27.6 - - + +
69N TRP* 1.3 77.1 - - - +
71N GLY* 1.3 56.7 + - - +
82N TYR* 3.6 5.8 - - + +
83N ASN* 2.7 33.8 + - - +
86N PHE* 3.9 33.7 - - + +
90N ALA* 3.9 16.4 - - + -
92N LEU* 5.7 2.5 - - + -
103N MET* 3.7 26.5 - - + -
116N TYR* 3.7 27.6 - - + -
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Residues in contact with GLY 71 (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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57N GLN* 3.4 2.3 - - - -
58N TRP* 2.8 28.5 + - - +
69N TRP* 3.5 17.7 + - - -
70N ILE* 1.3 84.8 - - - +
72N TYR* 1.3 61.0 + - - -
81N LYS 3.2 14.1 - - - -
82N TYR* 4.2 1.8 - - - -
92N LEU* 3.9 9.6 - - - -
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Residues in contact with TYR 72 (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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55N THR* 3.8 26.0 - - + -
56N ILE 3.3 15.0 - - - +
57N GLN* 3.3 30.3 - - - +
69N TRP* 3.5 17.0 - + - -
71N GLY* 1.3 73.9 - - - -
73N ILE* 1.3 67.7 + - - +
74N TYR* 4.5 4.9 - - + -
79N GLY 4.4 10.1 - - - -
80N THR* 3.3 8.2 + - - -
81N LYS* 3.1 78.0 + - + +
92N LEU* 3.5 9.7 - - - +
254N TYR* 4.7 10.5 + + - -
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Residues in contact with ILE 73 (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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55N THR* 3.4 2.9 - - - -
56N ILE* 3.0 31.7 + - + +
72N TYR* 1.3 76.2 - - - +
74N TYR* 1.3 65.1 + - - +
75N PRO* 3.6 3.9 - - + +
78N ALA* 4.2 17.0 - - + +
79N GLY 3.4 5.6 - - - +
80N THR* 3.7 16.8 - - + -
92N LEU* 3.6 22.6 - - + +
93N THR* 3.6 27.8 - - - -
94N SER* 3.7 14.1 - - - +
101N VAL* 3.7 39.5 - - + -
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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