Contacts of the strand formed by residues 57 - 67 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53F ASN* 3.5 8.9 - - - +
54F THR* 2.8 46.6 + - - +
55F GLN 4.4 5.2 - - - -
56F GLY* 1.3 86.0 + - - +
58F ASP* 1.3 62.7 + - - +
60F GLU* 3.7 7.7 - - - +
77F ARG* 3.5 39.4 - - - +
123F TYR* 4.2 8.9 + - - -
126F GLU* 3.2 27.8 + - - -
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Residues in contact with ASP 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345E CPJ 3.2 7.1 - - - +
53F ASN* 3.1 11.2 + - - +
56F GLY 4.2 0.8 - - - -
57F ARG* 1.3 70.1 - - - +
59F ASN* 1.3 72.8 + - - +
60F GLU 3.2 3.1 - - - -
77F ARG* 2.7 40.8 + - + +
137F GLN 2.8 11.4 - - - +
138F ASP* 3.4 19.6 - - - +
312F CA 2.4 31.0 - - - -
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Residues in contact with ASN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345E CPJ 2.8 37.6 + - - +
52F TYR 4.6 0.4 - - - -
53F ASN* 3.0 9.7 + - - -
58F ASP* 1.3 80.0 + - - +
60F GLU* 1.3 63.1 + - - +
61F LEU* 3.3 3.8 - - - +
62F LEU* 3.9 15.5 - - + -
74F TYR* 3.9 28.2 - - + +
76F GLY 3.5 0.9 + - - -
77F ARG* 2.9 28.7 + - + +
136F GLU* 3.0 9.6 - - - +
312F CA 2.3 24.8 - - - -
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Residues in contact with GLU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F TYR* 3.3 22.7 + - + +
54F THR* 3.9 33.0 - - + +
57F ARG* 3.7 7.8 - - - +
58F ASP 3.1 1.0 + - - -
59F ASN* 1.3 76.4 - - - +
61F LEU* 1.3 61.0 + - - +
75F ILE* 3.5 4.2 - - - +
76F GLY* 2.8 21.3 + - - +
77F ARG* 2.9 24.8 + - - -
123F TYR* 2.5 33.9 + - - -
125F VAL* 3.4 7.1 - - + +
126F GLU* 2.9 34.9 + - - +
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Residues in contact with LEU 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LEU* 4.6 4.9 - - + -
33F PHE* 3.6 45.3 - - + -
35F LEU* 5.1 1.1 - - + -
50F PHE* 3.8 10.5 - - + +
52F TYR* 3.0 64.5 + - + +
60F GLU* 1.3 77.7 - - - +
62F LEU* 1.3 66.4 + - - +
63F VAL* 4.6 7.6 - - + -
73F LEU* 3.7 14.6 - - + -
74F TYR 3.2 7.2 - - - +
75F ILE* 4.5 3.6 - - + -
125F VAL* 4.6 5.4 - - + -
159F MET* 3.7 26.0 - - + -
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Residues in contact with LEU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345E CPJ 3.5 32.1 - - + -
48F SER* 3.3 32.1 - - - +
50F PHE 3.3 10.8 - - - +
51F SER* 4.1 6.5 - - - -
52F TYR 5.2 0.4 - - - +
59F ASN* 3.8 15.7 - - - +
61F LEU* 1.3 76.7 - - - +
63F VAL* 1.3 68.5 + - - +
64F TYR* 4.0 10.1 - - + -
72F SER 3.6 1.4 - - - +
73F LEU* 3.3 6.9 - - - +
74F TYR* 2.7 60.2 + - + -
136F GLU* 3.6 17.9 - - + +
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Residues in contact with VAL 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LEU* 4.0 18.6 - - + -
37F PHE* 4.1 20.4 - - + -
48F SER 3.8 0.5 - - - -
49F LEU* 2.8 37.3 + - + -
50F PHE* 2.9 21.0 + - + -
61F LEU* 4.6 3.8 - - + -
62F LEU* 1.3 79.2 - - - +
64F TYR* 1.3 61.8 + - - +
71F TYR* 5.4 1.8 - - + -
72F SER 3.4 7.6 - - - +
73F LEU* 4.1 9.6 - - + -
94F ILE* 5.0 2.0 - - + -
96F VAL* 3.8 26.0 - - + -
107F PHE* 4.1 17.9 - - + -
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Residues in contact with TYR 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345E CPJ 4.0 25.5 - - + -
46F ALA* 3.4 31.7 - - + +
47F TYR 3.6 20.6 - - - -
48F SER* 3.6 16.8 - - - -
49F LEU* 5.2 0.7 - - - -
62F LEU* 4.0 15.9 - - + -
63F VAL* 1.3 77.1 - - - +
65F LYS* 1.3 60.8 + - - +
66F GLU* 3.5 32.7 + - + -
71F TYR* 4.0 1.4 - - - +
72F SER* 2.8 40.0 + - - +
74F TYR* 4.1 15.7 - + + -
136F GLU* 4.4 0.4 - - + -
148F GLN* 3.2 40.2 + - + +
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Residues in contact with LYS 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LEU 6.0 0.4 + - - -
45F ARG 4.4 0.9 - - - +
46F ALA* 3.1 4.5 - - - -
47F TYR* 2.8 81.6 + - + +
49F LEU* 4.3 9.7 - - + +
64F TYR* 1.3 73.2 - - - +
66F GLU* 1.3 58.9 + - - +
67F ARG* 3.2 24.5 - - - +
68F VAL* 4.0 12.3 - - - +
69F GLY 4.0 1.3 - - - +
70F GLU 3.8 8.5 - - - +
71F TYR* 3.4 34.3 + - + +
86F GLU* 2.8 29.7 + - - -
88F PHE* 5.9 1.6 - - - -
92F VAL* 6.2 0.4 - - - +
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Residues in contact with GLU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345E CPJ 6.1 0.6 - - - +
44F SER 4.7 0.2 - - - +
45F ARG* 4.2 0.7 - - - -
46F ALA* 3.4 30.5 + - + +
64F TYR* 3.5 25.4 - - + +
65F LYS* 1.3 73.0 - - - +
67F ARG* 1.3 87.3 + - + +
70F GLU* 3.7 14.1 + - - +
72F SER* 3.1 28.9 + - - +
74F TYR* 3.6 15.5 + - - -
79F LYS* 4.1 11.7 + - - +
81F THR* 5.0 2.9 - - + -
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Residues in contact with ARG 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F SER 4.4 12.1 - - - +
45F ARG 5.4 0.9 - - - -
65F LYS* 3.2 16.6 - - - -
66F GLU* 1.3 96.0 + - - +
68F VAL* 1.3 72.6 + - - +
70F GLU* 2.8 67.0 + - - +
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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