Contacts of the strand formed by residues 87 - 94 (chain C) in PDB entry 5NC5
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 87 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C SER* 6.4 0.7 - - - -
47C ALA 3.6 11.9 - - - +
48C SER* 4.4 6.6 + - - +
57C VAL* 4.5 0.6 - - - +
81C ASN* 3.9 1.7 - - - +
82C SER* 3.6 1.7 - - - -
83C ASP* 3.0 46.9 + - - +
85C THR* 2.8 17.8 + - - -
86C GLY* 1.3 79.2 - - - +
88C VAL* 1.3 71.4 + - - +
89C GLN* 4.9 8.5 - - + -
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Residues in contact with VAL 88 (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 ILE 4.3 0.7 - - - +
46C SER* 3.3 5.5 - - - -
47C ALA* 3.0 40.8 + - + +
57C VAL* 3.1 34.3 - - + -
61C VAL* 4.0 16.6 - - + -
62C THR* 3.4 23.8 - - + +
65C ILE* 5.4 0.9 - - + -
81C ASN 3.4 10.1 - - - +
82C SER* 4.3 1.3 - - - +
86C GLY 5.0 1.1 - - - +
87C THR* 1.3 73.9 - - - +
89C GLN* 1.3 69.9 + - - +
90C ILE* 3.7 28.5 - - + -
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Residues in contact with GLN 89 (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 THR* 3.9 22.5 - - + +
45C ILE 3.3 5.6 - - - +
46C SER* 4.0 14.5 + - - -
80C SER* 3.1 5.5 - - - -
81C ASN* 3.1 47.5 + - - +
87C THR* 4.9 11.0 - - + -
88C VAL* 1.3 78.0 - - - +
90C ILE* 1.3 62.3 + - - +
91C THR* 4.0 3.5 + - - +
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Residues in contact with ILE 90 (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 VAL 3.8 0.9 - - - +
44C THR* 3.3 2.6 - - - -
45C ILE* 2.7 51.6 + - + +
62C THR* 4.0 20.2 - - + +
65C ILE* 3.6 44.6 - - + -
66C GLU* 4.2 5.8 - - + -
69C MET* 5.4 0.2 - - + -
78C MET* 4.2 18.2 - - + -
79C SER 3.4 8.3 - - - +
80C SER* 3.8 10.3 - - - -
88C VAL* 3.7 13.0 - - + -
89C GLN* 1.3 75.8 - - - +
91C THR* 1.3 61.4 + - - +
92C LEU* 4.1 16.1 - - + +
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Residues in contact with THR 91 (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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42C ALA* 4.2 12.8 - - + -
43C VAL 3.4 8.7 - - - +
44C THR* 3.1 23.2 + - - +
77C TYR 3.9 0.9 - - - +
78C MET* 3.4 4.3 - - - -
79C SER* 2.7 46.9 + - - +
89C GLN* 4.0 4.4 - - - +
90C ILE* 1.3 73.9 + - - +
92C LEU* 1.3 69.6 + - - +
93C THR* 3.9 8.8 + - - +
132C SER* 4.5 0.9 - - - +
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Residues in contact with LEU 92 (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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42C ALA* 3.1 3.7 - - - +
43C VAL 2.7 48.4 + - - +
45C ILE* 4.4 14.1 - - + -
69C MET* 3.8 31.6 - - + -
72C ILE* 4.0 16.6 - - + -
75C LEU* 3.8 17.5 - - + -
77C TYR 3.8 4.0 - - - -
78C MET* 4.0 13.2 - - + -
90C ILE* 4.1 20.6 - - + +
91C THR* 1.3 77.0 - - - +
93C THR* 1.3 61.3 + - - +
94C PHE* 3.5 19.3 - - + -
107C VAL* 4.2 12.3 - - + -
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Residues in contact with THR 93 (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 PRO* 4.0 16.6 - - + +
41C PRO 3.5 8.5 - - - +
42C ALA* 4.1 9.7 - - + +
75C LEU* 3.7 2.6 - - - +
76C MET* 2.9 34.6 + - + +
77C TYR* 3.2 54.4 + - + +
79C SER* 5.3 0.9 + - - -
91C THR* 4.2 10.0 + - - +
92C LEU* 1.3 75.3 - - - +
94C PHE* 1.3 62.2 + - - +
674C LEU* 4.5 8.0 - - + +
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Residues in contact with PHE 94 (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 PRO* 2.9 22.9 - - - +
41C PRO* 2.7 26.8 + - + +
42C ALA* 4.6 1.6 - - - -
43C VAL* 4.3 10.3 - - + -
72C ILE* 3.6 32.3 - - + -
73C ASP 3.7 12.6 - - - -
74C ASN 3.4 15.0 - - - +
75C LEU* 4.1 8.7 - - + -
76C MET* 3.7 4.8 - - - +
92C LEU* 3.5 36.6 - - + -
93C THR* 1.3 78.3 - - - +
95C GLU* 1.3 67.5 + - - +
98C THR* 3.8 16.8 - - + -
103C ALA* 3.8 29.4 - - + -
107C VAL* 4.0 10.3 - - + -
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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