Contacts of the strand formed by residues 57 - 67 (chain N) in PDB entry 2A3W
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 57 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53N ASN* 3.6 7.4 - - - -
54N THR* 2.8 41.4 + - - +
55N GLN 4.1 6.5 - - - +
56N GLY* 1.3 84.5 - - - +
58N ASP* 1.3 63.6 + - - +
60N GLU* 2.9 28.2 + - - +
76N GLY* 3.8 6.3 - - - -
77N ARG* 3.1 45.3 - - - +
120N ARG* 4.4 3.0 - - - +
123N TYR* 2.7 32.5 + - - -
126N GLU* 4.1 16.4 - - - +
139N SER 6.5 0.2 - - - -
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Residues in contact with ASP 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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53N ASN* 2.9 19.6 + - - +
56N GLY 4.2 0.6 - - - -
57N ARG* 1.3 70.4 - - - +
59N ASN* 1.3 76.4 + - - +
60N GLU* 3.0 6.6 + - - +
77N ARG* 3.2 27.4 - - + +
137N GLN 2.7 11.6 - - - +
138N ASP* 3.3 19.3 - - - +
327N CA 2.5 30.2 - - - -
349N CPJ 3.1 7.8 - - - +
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Residues in contact with ASN 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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53N ASN* 3.0 12.3 + - - +
58N ASP* 1.3 77.5 + - - +
60N GLU* 1.3 64.6 + - - +
61N LEU* 3.3 3.5 + - - +
62N LEU* 4.0 15.9 - - + -
74N TYR* 3.6 31.1 - - + +
76N GLY 3.7 0.3 + - - -
77N ARG* 3.1 23.1 + - + +
136N GLU* 2.9 8.7 - - - +
327N CA 2.3 26.5 - - - -
349N CPJ 3.1 37.9 + - - +
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Residues in contact with GLU 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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52N TYR* 3.4 26.2 + - + +
53N ASN* 3.9 0.2 + - - -
54N THR* 3.9 17.5 - - - +
57N ARG* 2.9 43.1 + - - +
58N ASP 3.0 3.8 + - - +
59N ASN* 1.3 76.5 - - - +
61N LEU* 1.3 60.4 + - - +
74N TYR 3.9 0.2 - - - -
75N ILE* 3.3 7.1 - - - +
76N GLY* 2.9 24.1 + - - +
123N TYR* 2.6 21.1 + - - -
125N VAL* 3.5 9.7 - - + +
126N GLU* 2.8 35.7 + - - +
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Residues in contact with LEU 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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30N LEU* 4.7 0.7 - - + -
33N PHE* 3.5 46.9 - - + -
35N LEU* 5.6 1.1 - - + -
50N PHE* 3.9 13.9 - - + +
52N TYR* 2.9 65.2 + - + +
59N ASN 3.3 0.2 - - - -
60N GLU* 1.3 78.6 - - - +
62N LEU* 1.3 64.3 + - - +
63N VAL* 4.9 3.1 - - + -
73N LEU* 3.8 14.6 - - + -
74N TYR 3.1 5.4 - - - +
75N ILE* 4.3 2.0 - - + -
125N VAL* 4.4 11.4 - - + -
159N MET* 3.7 23.8 - - + -
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Residues in contact with LEU 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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48N SER* 3.3 23.1 - - - +
50N PHE 3.2 21.3 - - - +
51N SER* 3.9 9.0 - - - +
52N TYR 5.1 0.7 - - - +
53N ASN* 6.0 0.2 - - - +
59N ASN* 3.8 13.9 - - - +
61N LEU* 1.3 76.6 - - - +
63N VAL* 1.3 67.9 + - - +
64N TYR* 4.1 8.5 - - + -
72N SER 3.7 0.5 - - - +
73N LEU* 3.3 6.7 - - - +
74N TYR* 2.7 61.6 + - + +
136N GLU* 3.4 20.6 - - + +
349N CPJ 3.3 33.7 - - + -
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Residues in contact with VAL 63 (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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35N LEU* 4.0 18.8 - - + -
37N PHE* 4.2 10.8 - - + -
49N LEU* 3.0 45.7 + - + -
50N PHE* 3.0 22.2 + - + +
61N LEU* 4.9 3.6 - - + -
62N LEU* 1.3 77.0 - - - +
64N TYR* 1.3 61.9 + - - +
71N TYR* 5.3 2.7 - - + -
72N SER 3.5 8.1 - - - +
73N LEU* 4.1 9.9 - - + -
94N ILE* 5.0 3.1 - - + -
96N VAL* 3.8 25.8 - - + -
107N PHE* 4.3 16.8 - - + -
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Residues in contact with TYR 64 (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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46N ALA* 3.5 27.4 - - + +
47N TYR 3.6 22.2 - - - -
48N SER* 3.9 11.4 - - - -
49N LEU* 4.9 1.8 - - - -
62N LEU* 4.1 13.7 - - + -
63N VAL* 1.3 74.9 - - - +
65N LYS* 1.3 60.9 + - - +
66N GLU* 3.5 35.0 - - - -
71N TYR* 3.8 1.6 - - - +
72N SER* 2.7 41.1 + - - -
74N TYR* 3.8 26.2 - + + -
136N GLU* 4.4 2.2 - - + -
148N GLN* 2.9 44.0 + - + +
349N CPJ 3.9 17.4 - - + -
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Residues in contact with LYS 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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43N LEU 5.7 1.4 + - - -
45N ARG 4.5 0.5 - - - +
46N ALA* 3.2 3.8 - - - +
47N TYR* 2.9 71.8 + - + +
49N LEU* 3.9 15.3 - - + +
64N TYR* 1.3 72.1 - - - +
66N GLU* 1.3 62.1 + - - +
67N ARG* 3.3 23.8 - - - +
68N VAL* 3.9 14.3 - - - +
69N GLY 3.9 2.5 - - - +
70N GLU 3.8 6.5 - - - +
71N TYR* 3.4 36.7 + - + +
86N GLU* 2.8 28.8 + - - -
88N PHE* 5.7 3.2 - - - -
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Residues in contact with GLU 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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44N SER 4.8 0.3 - - - +
45N ARG 4.3 0.2 - - - -
46N ALA* 3.4 27.5 + - - +
64N TYR* 3.5 23.7 - - - +
65N LYS* 1.3 71.4 - - - +
67N ARG* 1.3 91.3 + - + +
70N GLU* 3.5 16.3 + - + +
72N SER* 2.7 35.7 + - - +
74N TYR* 3.9 3.1 + - - -
79N LYS* 2.9 22.2 + - - +
81N THR* 4.6 7.0 - - + -
349N CPJ 5.8 0.7 - - - +
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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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44N SER 4.3 13.9 - - - +
45N ARG 5.4 1.1 - - - -
65N LYS* 3.3 17.9 - - - -
66N GLU* 1.3 94.1 + - - +
68N VAL* 1.3 74.7 + - + +
70N GLU* 2.8 62.6 + - + +
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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