Contacts of the strand formed by residues 57 - 67 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C ASN* 3.7 7.2 - - - -
54C THR* 2.8 45.6 + - - +
55C GLN 4.3 6.5 - - - +
56C GLY* 1.3 83.0 - - - +
58C ASP* 1.3 63.8 + - - +
60C GLU* 3.6 7.9 + - - +
77C ARG* 3.4 28.2 - - - +
123C TYR* 2.7 43.6 + - - -
124C PHE 4.6 2.8 + - - -
126C GLU* 3.3 29.3 + - - +
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Residues in contact with ASP 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C ASN* 3.1 11.2 + - - +
56C GLY 4.2 0.6 - - - -
57C ARG* 1.3 71.4 - - - +
59C ASN* 1.3 71.1 + - - +
60C GLU 3.2 0.2 - - - -
77C ARG* 2.7 41.5 + - + +
137C GLN 2.7 12.3 - - - +
138C ASP* 3.4 20.0 - - - +
305C CA 2.3 29.9 - - - -
343C CPJ 3.1 7.1 - - - +
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Residues in contact with ASN 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C TYR 4.6 0.2 - - - -
53C ASN* 3.0 10.3 + - - -
58C ASP* 1.3 81.1 + - - +
60C GLU* 1.3 62.9 + - - +
61C LEU* 3.3 3.6 - - - +
62C LEU* 3.9 15.3 - - + -
74C TYR* 3.9 27.7 - - + +
76C GLY 3.6 1.0 + - - -
77C ARG* 3.0 29.6 + - + +
136C GLU* 3.0 9.4 - - - +
305C CA 2.4 25.8 - - - -
343C CPJ 3.1 35.1 + - - +
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Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C TYR* 3.4 21.5 + - + +
53C ASN* 4.0 0.2 + - - -
54C THR* 3.8 29.4 - - + +
57C ARG* 3.6 14.3 + - - +
58C ASP 3.2 1.8 + - - -
59C ASN* 1.3 76.0 - - - +
61C LEU* 1.3 60.5 + - - +
75C ILE* 3.5 4.0 - - - +
76C GLY* 2.9 20.6 + - - +
77C ARG* 3.0 22.8 + - - +
123C TYR* 2.7 30.6 + - - -
125C VAL* 3.2 12.7 - - + +
126C GLU* 2.7 34.9 + - - +
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 4.7 0.4 - - + -
33C PHE* 3.6 46.0 - - + -
35C LEU* 5.1 0.4 - - + -
50C PHE* 3.9 17.3 - - + +
52C TYR* 2.9 63.6 + - + +
60C GLU* 1.3 79.4 - - - +
62C LEU* 1.3 64.2 + - - +
63C VAL* 4.5 4.5 - - + -
73C LEU* 3.9 13.0 - - + -
74C TYR 3.2 7.2 - - - +
75C ILE* 4.5 4.0 - - + -
125C VAL* 4.5 11.0 - - + -
159C MET* 3.7 24.0 - - + -
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C SER* 3.3 22.4 - - - +
50C PHE 3.3 16.8 - - - +
51C SER* 4.1 6.3 - - - -
52C TYR 5.3 0.4 - - - +
59C ASN* 3.7 15.9 - - - +
61C LEU* 1.3 76.6 - - - +
63C VAL* 1.3 68.3 + - - +
64C TYR* 4.0 7.9 - - + -
72C SER 3.6 1.0 - - - +
73C LEU* 3.3 7.4 - - - +
74C TYR* 2.8 63.9 + - + -
136C GLU* 3.5 22.4 - - + +
343C CPJ 3.4 33.2 - - + -
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Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 3.7 29.2 - - + -
37C PHE* 4.1 19.1 - - + -
48C SER* 3.8 2.1 - - - -
49C LEU* 2.8 39.3 + - + -
50C PHE* 2.9 22.5 + - + +
61C LEU* 4.5 3.6 - - + -
62C LEU* 1.3 75.4 - - - +
64C TYR* 1.3 57.6 + - - +
71C TYR* 5.4 3.1 - - + -
72C SER 3.5 8.3 - - - +
73C LEU* 4.2 9.2 - - + -
94C ILE* 4.9 2.5 - - + -
96C VAL* 4.0 15.0 - - + -
107C PHE* 4.1 18.8 - - + -
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Residues in contact with TYR 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ALA* 3.4 32.1 - - + +
47C TYR 3.5 22.7 - - - -
48C SER* 3.7 13.5 - - - -
49C LEU* 4.9 1.8 - - - -
62C LEU* 4.0 6.7 - - + -
63C VAL* 1.3 76.2 - - - +
65C LYS* 1.3 61.4 + - - +
66C GLU* 3.6 31.0 + - - -
71C TYR* 4.0 1.2 - - - -
72C SER* 2.9 38.8 + - - +
74C TYR* 4.0 25.8 - + + -
136C GLU* 4.5 0.4 - - + -
148C GLN* 3.1 42.6 + - + +
343C CPJ 4.2 25.3 - - + -
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Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU 5.8 1.4 + - - -
45C ARG 4.4 0.9 - - - +
46C ALA* 3.1 2.3 - - - +
47C TYR* 2.8 72.1 + - + +
49C LEU* 3.9 16.2 - - + +
64C TYR* 1.3 73.0 - - - +
66C GLU* 1.3 60.2 + - - +
67C ARG* 3.5 21.1 - - - +
68C VAL* 3.9 13.1 - - - +
69C GLY 4.1 0.7 - - - +
70C GLU 3.7 9.9 - - - +
71C TYR* 3.5 38.1 + - + +
86C GLU* 2.8 29.7 + - - -
88C PHE* 5.8 3.2 - - - -
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C SER 4.7 0.2 - - - +
45C ARG 4.2 0.3 - - - -
46C ALA* 3.3 29.5 + - - +
64C TYR* 3.7 20.1 - - - +
65C LYS* 1.3 72.1 - - - +
67C ARG* 1.3 86.5 + - - +
70C GLU* 3.6 17.5 + - + +
72C SER* 2.7 36.2 + - - +
74C TYR* 3.8 4.4 + - - -
79C LYS* 3.6 22.1 + - - -
81C THR* 4.8 4.7 - - + -
343C CPJ 6.1 0.3 - - - +
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Residues in contact with ARG 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C SER 4.4 12.6 - - - +
45C ARG 5.4 0.7 - - - -
65C LYS* 3.5 12.1 - - - -
66C GLU* 1.3 95.1 + - - +
68C VAL* 1.3 78.0 + - - +
69C GLY 3.4 0.2 + - - -
70C GLU* 2.9 59.3 + - - +
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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