Contacts of the strand formed by residues 57 - 64 (chain C) in PDB entry 3W58
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 THR 57 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C ASN 3.6 0.7 - - - +
48C ARG* 2.7 51.2 + - + +
55C ALA 3.8 10.1 - - - +
56C ASN* 1.3 75.1 - - - +
58C ILE* 1.3 58.4 + - - +
59C VAL* 4.1 15.3 - - + -
73C ARG* 3.4 50.8 + - - +
74C GLU 4.6 5.2 + - - -
76C VAL 5.5 0.2 - - - -
77C PHE* 3.3 13.4 - - - -
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Residues in contact with ILE 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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45C PHE* 3.6 31.2 - - + -
46C ASN 3.7 3.8 - - - -
47C PRO* 4.4 6.5 - - + -
57C THR* 1.3 73.8 + - - +
59C VAL* 1.3 64.9 + - - +
60C CYS* 4.0 11.7 - - - -
73C ARG* 3.4 1.7 - - - -
74C GLU* 2.9 42.8 + - + +
76C VAL 3.5 21.1 + - - +
77C PHE* 3.7 20.4 - - + -
78C PRO* 4.5 1.3 - - + -
79C PHE* 3.7 28.3 - - + -
100C LEU* 4.0 21.5 - - + -
106C PHE* 5.2 0.4 - - + -
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Residues in contact with VAL 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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44C HIS* 3.2 9.9 - - + +
46C ASN* 2.8 49.6 + - + +
48C ARG* 3.7 39.5 - - - +
57C THR* 4.1 11.2 - - + -
58C ILE* 1.3 74.4 - - - +
60C CYS* 1.3 66.8 + - - +
61C ASN* 5.5 0.4 - - + -
71C GLU* 3.3 40.6 - - + +
72C GLN 3.5 3.1 - - - +
73C ARG* 4.3 12.8 - - + +
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Residues in contact with CYS 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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43C LEU* 4.1 10.5 - - + -
44C HIS 3.1 4.7 - - - +
45C PHE* 3.9 18.6 - - - -
58C ILE* 3.9 2.7 + - - -
59C VAL* 1.3 82.0 - - - +
61C ASN* 1.3 64.6 + - - +
71C GLU* 3.5 1.2 - - - +
72C GLN* 2.9 34.4 + - - +
74C GLU* 3.5 27.8 - - - +
106C PHE* 3.9 25.8 - - - -
108C PHE* 3.8 16.4 - - + -
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Residues in contact with ASN 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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43C LEU* 3.6 4.9 - - - -
44C HIS* 2.7 42.0 + - + +
59C VAL* 5.5 0.2 - - + -
60C CYS* 1.3 75.7 - - - +
62C SER* 1.3 80.0 + - - +
68C TRP* 3.8 23.5 - - + +
69C GLY* 2.9 43.6 + - - +
70C THR 3.3 1.4 - - - +
71C GLU* 3.7 25.6 + - + +
108C PHE* 3.6 13.0 - - - -
111C ARG* 3.1 7.5 + - - +
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Residues in contact with SER 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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41C LEU* 3.4 14.1 - - - -
42C CYS 4.3 8.3 - - - -
44C HIS 4.9 0.2 - - - +
61C ASN* 1.3 83.9 + - - +
63C LYS* 1.3 62.1 + - - +
64C ASP* 5.4 1.2 + - - +
68C TRP* 3.2 12.9 - - - -
69C GLY* 2.9 27.6 + - - -
108C PHE* 4.3 1.3 - - - -
111C ARG* 2.9 40.1 + - - +
112C LEU* 4.0 13.0 - - - +
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Residues in contact with LYS 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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38C SER 3.9 18.6 + - - +
39C ASN* 3.5 18.9 + - - +
40C ASN* 3.2 5.4 - - - -
41C LEU* 2.8 52.4 + - + +
62C SER* 1.3 76.1 - - - +
64C ASP* 1.3 61.2 + - - +
66C GLY* 3.7 27.9 + - - -
67C ALA 3.4 5.6 - - - +
68C TRP* 3.3 51.7 - - + +
112C LEU* 3.6 5.1 - - - +
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Residues in contact with ASP 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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40C ASN* 3.6 7.9 - - - +
62C SER* 5.8 0.9 - - - +
63C LYS* 1.3 72.6 - - - +
65C GLY* 1.3 70.5 + - - +
67C ALA* 2.8 31.6 + - + +
111C ARG 5.0 2.8 - - - +
112C LEU* 4.1 28.1 - - + +
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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