Contacts of the strand formed by residues 64 - 70 (chain A) in PDB entry 1W59
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 ALA 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ILE* 3.1 30.7 - - + +
42A VAL* 4.4 9.0 - - + -
61A ILE* 3.6 26.6 + - + +
62A GLU 3.4 2.3 - - - +
63A GLY* 1.3 80.1 - - - +
65A LYS* 1.3 62.9 + - - +
66A THR 3.7 0.9 + - - -
82A ASP* 3.9 4.2 - - - +
223A VAL* 4.0 18.2 - - + -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE 2.8 13.7 + - - +
41A THR* 3.3 17.3 - - + +
42A VAL* 2.9 26.3 + - - +
64A ALA* 1.3 72.7 - - - +
66A THR* 1.3 62.6 + - - +
67A VAL* 3.8 13.9 - - - -
82A ASP* 3.3 18.8 - - + +
83A LYS* 4.2 17.2 - - - +
117A ALA 4.6 1.8 + - - -
118A ALA* 2.6 40.4 + - - +
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Residues in contact with THR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.6 8.1 - - + -
53A ILE* 3.9 20.0 - - + -
56A LEU* 4.4 15.3 - - + -
57A LYS* 3.6 13.1 - - + +
61A ILE* 3.7 29.8 - - + -
65A LYS* 1.3 73.7 - - - +
67A VAL* 1.3 63.2 + - - +
81A ALA* 3.6 5.1 - - - -
82A ASP* 2.7 60.3 + - - +
83A LYS 3.1 8.0 + - - -
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 3.7 22.7 - - + -
42A VAL 2.8 12.2 + - - +
43A VAL* 3.1 15.7 - - + +
44A GLY 2.7 32.2 + - - -
53A ILE* 3.7 5.5 - - - +
65A LYS* 3.8 19.3 - - - -
66A THR* 1.3 79.9 - - - +
68A ALA* 1.3 57.1 + - - +
69A ILE* 3.9 21.8 - - + -
83A LYS* 3.3 12.1 - - + +
85A ILE* 4.4 5.6 - - + -
115A ILE* 6.6 0.2 - - + -
118A ALA* 4.2 24.2 - - + +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLY 3.5 5.4 - - - +
50A ASN* 3.3 17.0 - - - +
53A ILE* 4.1 6.1 - - + -
67A VAL* 1.3 73.9 - - - +
69A ILE* 1.3 62.3 + - - +
76A LEU* 3.7 8.8 - - + +
79A THR* 3.8 24.2 - - + -
81A ALA* 3.9 12.3 - - + +
83A LYS 3.0 7.2 + - - +
84A LYS* 3.2 6.0 - - + -
85A ILE 2.9 23.6 + - - -
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 4.0 7.2 - - + -
44A GLY 3.0 7.8 + - - +
45A CYS* 3.3 36.6 - - + -
46A GLY 3.2 18.7 + - - -
50A ASN* 3.5 2.1 - - - +
67A VAL* 3.9 15.9 - - + -
68A ALA* 1.3 79.4 - - - +
70A ASN* 1.3 63.8 + - - +
85A ILE* 3.2 30.7 - - + +
87A ILE* 4.1 17.0 - - + -
115A ILE* 4.7 8.7 - - + -
139A SER* 3.9 15.0 - - - +
143A VAL* 3.6 20.9 - - + -
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Residues in contact with ASN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY* 3.8 5.7 - - - -
50A ASN* 2.6 31.6 + - - +
69A ILE* 1.3 70.8 - - - +
71A THR* 1.3 80.7 + - - +
72A ASP* 2.9 26.7 - - - +
75A GLN* 2.7 29.7 + - - +
76A LEU* 3.7 13.2 - - + +
85A ILE 3.1 5.5 + - - -
86A LEU* 3.4 11.0 - - - +
87A ILE* 3.0 26.0 + - - +
135A THR* 3.6 21.3 + - - +
500A SO4 4.7 0.6 + - - -
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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