Contacts of the strand formed by residues 54 - 62 (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 TYR 54 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92G GLU* 4.8 2.5 + - - -
104H GLY* 5.3 2.8 - - - -
105H GLU* 2.8 47.9 + - + +
49N TYR* 3.4 37.6 - + + +
50N THR* 3.6 9.0 - - - -
51N PHE 3.7 6.7 + - - +
52N THR 3.2 1.4 - - - -
53N SER* 1.3 94.8 - - - +
55N THR* 1.3 64.6 + - - +
56N ILE* 4.7 2.6 - - - +
74N TYR* 3.9 4.9 - - - -
75N PRO* 3.3 19.1 - - - +
120N ARG* 3.5 44.1 + - + -
121N LYS 3.6 2.7 - - - +
122N SER* 3.5 22.2 - - - +
130N ASP* 5.0 1.1 - - - -
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Residues in contact with THR 55 (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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54N TYR* 1.3 77.1 - - - +
56N ILE* 1.3 64.2 + - - +
57N GLN* 3.1 24.6 + - - +
72N TYR* 3.8 22.9 - - + -
73N ILE 3.4 10.3 - - - -
74N TYR* 3.5 24.0 - - + -
120N ARG* 3.9 1.9 - - - -
121N LYS* 2.7 50.8 + - - +
122N SER* 4.2 7.2 + - - +
123N SER* 4.8 7.2 - - - -
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Residues in contact with ILE 56 (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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26N LEU* 4.9 4.5 - - + -
44N CYS* 4.2 17.3 - - - +
46N ALA* 4.6 2.9 - - + -
49N TYR* 3.9 16.6 - - - +
51N PHE* 3.6 30.7 - - + -
54N TYR 3.9 4.2 + - - +
55N THR* 1.3 77.2 - - - +
57N GLN* 1.3 65.1 + - - +
58N TRP* 3.6 22.0 + - - +
72N TYR* 3.3 3.4 - - - -
73N ILE* 3.0 30.8 + - - +
75N PRO* 4.7 2.0 - - + +
101N VAL* 3.7 25.6 - - + -
118N CYS* 4.1 14.8 - - + -
119N ALA 3.4 10.3 - - - +
120N ARG* 5.0 0.9 - - - -
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Residues in contact with GLN 57 (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* 3.1 20.0 + - - +
56N ILE* 1.3 74.6 - - - +
58N TRP* 1.3 63.0 + - - +
59N VAL* 4.3 0.4 - - + -
69N TRP* 2.5 40.6 + - + +
71N GLY 3.4 6.7 - - - -
72N TYR* 3.3 26.4 - - - +
118N CYS* 3.3 5.5 - - - +
119N ALA* 2.8 34.8 + - + +
121N LYS* 3.6 28.6 - - + +
129N LEU* 3.6 30.5 - - + +
254N TYR* 3.4 10.6 + - - -
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Residues in contact with TRP 58 (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 GLN* 3.8 21.3 - - - -
42N MET* 3.9 35.2 - - + -
43N PRO 4.7 1.1 - - - -
44N CYS* 3.8 17.0 - - + -
56N ILE* 3.6 13.7 + - + +
57N GLN* 1.3 77.8 - - - +
59N VAL* 1.3 59.5 + - - +
69N TRP* 3.9 2.8 - - - -
70N ILE* 2.8 45.5 + - + -
71N GLY 2.8 13.2 + - - +
92N LEU* 3.4 33.9 - - + +
101N VAL* 3.5 38.2 - - + +
103N MET* 3.6 28.3 - - + -
116N TYR* 4.7 3.8 - - + -
117N TYR 3.3 18.2 - - - -
118N CYS* 3.8 15.0 - - + -
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Residues in contact with VAL 59 (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 5.2 0.4 - - - -
58N TRP* 1.3 79.5 - - - +
60N LYS* 1.3 63.4 + - - +
61N GLN 4.1 0.2 + - - -
67N LEU* 3.7 30.1 - - + -
68N GLU 3.3 12.6 - - - +
69N TRP* 4.7 5.8 - - + -
70N ILE* 4.0 3.8 - - - +
115N VAL 3.7 0.9 - - - +
116N TYR* 3.5 3.6 - - - -
117N TYR* 2.8 37.4 + - + +
119N ALA* 5.2 4.0 - - + -
129N LEU* 4.1 9.9 - - + -
132N TRP* 4.0 24.2 - - + -
256N PHE* 3.9 31.0 - - + -
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Residues in contact with LYS 60 (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* 1.3 73.3 - - - +
61N GLN* 1.3 63.4 + - - +
62N THR* 3.7 19.9 + - + +
65N GLN* 5.3 3.6 + - - -
66N GLY 3.6 1.2 - - - +
67N LEU* 3.5 1.6 - - - -
68N GLU* 2.8 59.3 + - + +
70N ILE* 3.7 19.6 - - + +
85N LYS* 5.8 1.2 - - - +
86N PHE* 3.6 29.8 - - + -
111N GLU* 3.9 19.8 + - - +
112N ASP* 4.6 5.9 + - - -
114N ALA* 3.7 14.1 - - + -
115N VAL 3.6 3.1 - - - -
116N TYR* 3.5 31.6 - - + +
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Residues in contact with GLN 61 (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 4.1 0.2 + - - -
60N LYS* 1.3 72.5 - - - +
62N THR* 1.3 63.0 + - - +
63N PRO* 3.9 6.0 - - + +
66N GLY* 3.4 10.5 - - - +
67N LEU* 3.7 19.4 - - + +
114N ALA* 3.3 16.3 - - - +
115N VAL* 2.9 30.3 + - + +
117N TYR* 3.2 18.7 + - + -
196N GLN* 2.7 46.1 + - - +
245N TYR* 3.8 13.7 + - - -
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Residues in contact with THR 62 (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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60N LYS* 3.7 27.1 - - + +
61N GLN* 1.3 76.2 - - - +
63N PRO* 1.3 65.1 - - - +
64N ARG* 3.0 8.6 + - - -
65N GLN* 3.2 30.9 + - - +
66N GLY* 2.8 34.0 + - - +
68N GLU* 5.5 1.0 - - - -
111N GLU 4.3 9.9 - - - +
113N SER 4.8 2.9 - - - +
114N ALA* 3.7 20.4 - - + -
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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