Contacts of the strand formed by residues 57 - 67 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53I ASN* 3.6 7.9 - - - -
54I THR* 2.9 45.2 + - - +
55I GLN 3.7 7.4 - - - +
56I GLY* 1.3 83.0 - - - +
58I ASP* 1.3 63.3 + - - +
60I GLU* 3.3 21.1 + - - +
76I GLY* 4.2 8.3 + - - -
77I ARG* 3.5 40.1 - - - +
120I ARG* 4.6 2.6 - - - +
123I TYR* 2.7 35.6 + - - -
126I GLU* 3.8 23.6 + - + +
139I SER 6.5 0.2 - - - -
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Residues in contact with ASP 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B CPJ 3.2 6.6 - - - +
53I ASN* 2.9 13.5 + - - +
56I GLY 4.2 1.2 + - - -
57I ARG* 1.3 75.1 - - - +
59I ASN* 1.3 77.3 + - - +
60I GLU* 3.2 1.6 + - - +
77I ARG* 3.1 33.8 + - + +
137I GLN 2.8 11.3 - - - +
138I ASP* 3.3 20.0 - - - +
317I CA 2.4 32.0 - - - -
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Residues in contact with ASN 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B CPJ 3.1 31.1 + - - +
53I ASN* 3.0 13.2 + - - -
58I ASP* 1.3 78.6 + - - +
60I GLU* 1.3 63.5 + - - +
61I LEU* 3.3 4.4 + - - +
62I LEU* 3.8 15.7 - - + -
74I TYR* 3.8 36.5 - - + +
76I GLY 3.5 1.2 + - - -
77I ARG* 2.9 25.8 + - + +
136I GLU* 3.0 8.3 - - - +
317I CA 2.4 26.3 - - - -
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Residues in contact with GLU 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I TYR* 3.3 28.2 + - + +
53I ASN* 3.9 0.2 + - - -
54I THR* 3.8 22.9 - - - +
57I ARG* 3.3 23.6 + - - +
58I ASP 3.2 2.1 - - - +
59I ASN* 1.3 76.0 - - - +
61I LEU* 1.3 62.0 + - - +
75I ILE* 3.4 5.7 - - - +
76I GLY* 2.9 23.6 + - - +
77I ARG* 6.1 0.2 - - - +
123I TYR* 2.8 27.6 + - - -
125I VAL* 3.3 12.8 - - + +
126I GLU* 2.7 40.6 + - - +
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Residues in contact with LEU 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I LEU* 4.8 0.2 - - + -
33I PHE* 3.6 45.5 - - + -
35I LEU* 5.2 0.9 - - + -
50I PHE* 3.9 17.1 - - + +
52I TYR* 2.8 66.2 + - + +
60I GLU* 1.3 78.7 - - - +
62I LEU* 1.3 65.1 + - - +
63I VAL* 4.6 4.3 - - + -
73I LEU* 3.8 13.0 - - + -
74I TYR 3.2 7.9 - - - +
75I ILE* 4.5 3.1 - - + -
125I VAL* 4.6 10.1 - - + -
159I MET* 3.7 24.9 - - + -
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Residues in contact with LEU 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B CPJ 3.7 24.5 - - + -
48I SER* 3.4 23.1 - - - +
50I PHE 3.3 16.8 - - - +
51I SER* 3.9 8.1 - - - +
52I TYR 5.1 0.4 - - - +
59I ASN* 3.7 15.9 - - - +
61I LEU* 1.3 77.7 - - - +
63I VAL* 1.3 68.7 + - - +
64I TYR* 4.1 8.3 - - + -
72I SER 3.7 0.7 - - - +
73I LEU* 3.3 5.9 - - - +
74I TYR* 2.7 60.9 + - + -
136I GLU* 3.4 28.9 - - + +
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Residues in contact with VAL 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I LEU* 3.9 19.7 - - + -
37I PHE* 4.2 11.4 - - + -
48I SER* 3.8 2.1 - - - -
49I LEU* 2.8 46.1 + - + -
50I PHE* 2.9 23.7 + - + +
61I LEU* 4.6 3.6 - - + -
62I LEU* 1.3 74.9 - - - +
64I TYR* 1.3 61.8 + - - +
71I TYR* 5.4 2.7 - - + -
72I SER 3.5 8.7 - - - +
73I LEU* 4.2 9.9 - - + -
94I ILE* 4.9 1.8 - - + -
96I VAL* 3.9 24.2 - - + -
107I PHE* 4.2 17.9 - - + -
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Residues in contact with TYR 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B CPJ 3.9 26.0 + - + -
46I ALA* 3.4 31.6 - - + +
47I TYR 3.7 17.9 - - - -
48I SER* 3.8 16.2 - - - -
49I LEU* 5.1 0.9 - - - -
62I LEU* 4.1 7.0 - - + -
63I VAL* 1.3 76.6 - - - +
65I LYS* 1.3 60.5 + - - +
66I GLU* 3.5 34.8 + - - -
71I TYR* 4.0 1.1 - - - -
72I SER* 2.8 38.9 + - - +
74I TYR* 3.9 23.6 - - + -
136I GLU* 4.4 0.9 - - + -
148I GLN* 3.1 43.0 + - + +
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Residues in contact with LYS 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I LEU 5.8 1.6 + - - -
45I ARG 5.6 0.4 - - - +
46I ALA* 3.2 3.6 - - - +
47I TYR* 2.8 79.5 + - + +
49I LEU* 4.1 9.7 - - + +
64I TYR* 1.3 72.1 - - - +
66I GLU* 1.3 62.9 + - - +
67I ARG* 3.2 23.5 - - - +
68I VAL* 4.1 9.1 - - - +
69I GLY 3.9 1.6 - - - +
70I GLU 3.6 8.3 - - - +
71I TYR* 3.4 35.3 + - + +
86I GLU* 3.0 28.4 + - - -
88I PHE* 5.9 2.8 - - - -
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Residues in contact with GLU 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I SER 4.9 0.2 - - - +
45I ARG 4.5 0.2 - - - -
46I ALA* 3.4 25.3 + - - +
64I TYR* 3.5 22.3 - - - +
65I LYS* 1.3 71.5 - - - +
67I ARG* 1.3 88.5 + - - +
70I GLU* 3.5 18.6 + - + +
72I SER* 2.7 36.7 + - - +
74I TYR* 3.8 4.9 + - - -
79I LYS* 3.6 20.6 + - - -
81I THR* 4.4 7.2 - - + -
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Residues in contact with ARG 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I SER 4.3 14.1 - - - +
45I ARG 5.3 1.6 - - - -
65I LYS* 3.2 16.9 - - - -
66I GLU* 1.3 91.4 + - - +
68I VAL* 1.3 73.1 - - - +
70I GLU* 2.8 66.3 + - - +
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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