Contacts of the strand formed by residues 77 - 86 (chain B) in PDB entry 2EWY
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 ARG 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B SER 3.5 25.7 + - - -
75B THR* 3.8 17.7 + - - +
76B TYR* 1.3 86.8 + - - +
78B SER* 1.3 64.7 + - - +
97B GLY* 3.4 1.9 - - - -
98B GLU* 3.0 52.3 + - + +
112B LEU* 6.4 1.1 - - + -
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B TYR* 3.8 21.5 + - - -
77B ARG* 1.3 75.2 - - - +
79B LYS* 1.3 63.3 + - - +
80B GLY* 3.3 13.6 + - - -
95B PHE* 5.7 3.3 - - - +
96B VAL 4.3 2.9 + - - -
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ARG 3.7 1.8 + - - -
78B SER* 1.3 73.2 - - - +
80B GLY* 1.3 60.1 + - - +
81B PHE* 3.6 23.6 - - + -
96B VAL* 3.0 40.9 + - + +
97B GLY 4.1 2.7 - - - +
98B GLU* 3.9 31.4 - - + -
114B ASN* 3.0 28.5 + - - +
148B SER 5.7 2.8 + - - -
149B LEU* 4.3 10.3 - - - +
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B SER* 3.2 14.8 + - - -
79B LYS* 1.3 79.0 - - - +
81B PHE* 1.3 61.4 + - - +
96B VAL 4.0 1.0 + - - -
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Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 3.6 32.1 - - + -
80B GLY* 1.3 80.5 - - - +
82B ASP* 1.3 78.4 + - - +
95B PHE* 3.8 1.0 - - - +
96B VAL* 2.8 57.4 + - + +
145B PRO* 3.9 26.9 - - + -
149B LEU* 4.4 9.9 - - + -
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PHE* 1.3 93.8 - - - +
83B VAL* 1.3 60.4 + - - +
93B THR* 4.9 5.6 - - + -
94B GLY 3.2 7.0 - - - +
95B PHE* 3.2 29.6 - - - -
119B PHE* 3.8 27.9 - - + -
145B PRO* 5.5 2.4 - - - +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ASN* 4.7 4.5 - - - +
82B ASP* 1.3 76.0 - - - +
84B THR* 1.3 67.1 + - - +
85B VAL* 5.0 0.4 - - + -
92B TRP* 3.6 24.7 - - + -
93B THR* 3.3 4.6 - - - +
94B GLY 2.8 30.4 + - - +
96B VAL* 3.6 24.0 - - + -
116B ALA* 4.2 7.0 - - + -
144B LYS* 3.4 15.3 - - + +
145B PRO* 3.2 40.8 - - + -
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 1.3 80.5 - - - +
85B VAL* 1.3 66.9 + - - +
86B LYS 4.3 0.3 + - - -
91B SER* 5.2 3.1 - - - -
92B TRP 3.1 16.0 + - - -
93B THR* 3.5 18.5 + - - -
144B LYS* 4.1 13.2 - - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B SER* 5.8 0.4 - - - -
53B ASN* 4.0 13.9 - - + +
83B VAL* 5.0 1.1 - - + -
84B THR* 1.3 79.7 + - - +
86B LYS* 1.3 63.8 + - - +
87B TYR* 3.6 37.3 + - + +
91B SER* 3.2 26.2 - - - -
92B TRP* 3.2 41.9 + - + +
144B LYS* 3.8 27.1 - - + -
1002B DBO 4.4 11.0 - - + -
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B THR 4.3 0.8 + - - -
85B VAL* 1.3 77.2 - - - +
87B TYR* 1.3 76.1 + - - +
88B THR 4.4 8.3 + - - -
89B GLN* 4.4 1.4 - - - +
90B GLY 3.7 22.5 + - - +
91B SER* 3.9 9.6 + - - -
1002B DBO 3.2 20.1 - - - +
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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