Contacts of the helix formed by residues 94 - 104 (chain C) in PDB entry 6B0Z
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 SER 94 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C THR* 3.3 30.1 - - - +
78C PRO* 4.3 2.3 - - - +
92C TRP 3.7 0.8 + - - -
93C LYS* 1.3 75.6 - - - +
95C PRO* 1.3 72.9 - - - +
96C ASN* 2.9 2.1 + - - -
97C GLY* 3.2 19.6 + - - -
98C THR* 3.4 8.8 + - - -
503C FLC 2.6 31.9 + - - -
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Residues in contact with PRO 95 (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 LEU* 4.4 13.0 - - + -
49C ARG* 3.3 45.5 - - - +
54C ASP* 5.0 1.3 - - - +
57C THR* 4.0 24.2 - - + +
72C LYS* 4.5 3.6 - - - -
75C THR* 3.8 22.4 - - + +
76C ILE 4.1 4.9 - - - +
93C LYS 3.4 4.5 - - - +
94C SER* 1.3 83.6 - - - +
96C ASN* 1.3 62.2 + - - +
98C THR* 3.4 3.6 + - - +
99C ILE* 3.0 32.0 + - + +
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Residues in contact with ASN 96 (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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72C LYS* 3.3 25.5 + - - +
75C THR* 3.8 6.3 + - - -
77C THR* 4.3 0.6 + - - -
94C SER* 2.9 4.6 + - - -
95C PRO* 1.3 77.5 - - - +
97C GLY* 1.3 63.7 + - - +
99C ILE* 3.3 6.1 + - - +
100C ARG* 2.9 54.9 + - - +
306C GLU* 3.7 7.8 - - - +
501C NDP 3.4 26.9 + - - -
503C FLC 3.0 36.0 + - - +
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Residues in contact with GLY 97 (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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93C LYS* 5.6 6.1 - - - -
94C SER* 3.2 13.9 + - - -
96C ASN* 1.3 79.3 - - - +
98C THR* 1.3 62.5 + - - +
100C ARG* 3.9 11.7 - - - +
101C ASN* 3.2 27.5 + - - +
140C ARG* 6.2 1.8 - - - -
503C FLC 4.8 0.4 + - - -
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Residues in contact with THR 98 (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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54C ASP* 4.7 5.3 + - - +
57C THR* 3.8 17.1 - - + +
58C LYS* 3.8 36.6 - - + -
93C LYS* 3.8 24.3 - - - +
94C SER 3.4 10.8 + - - -
95C PRO* 3.4 10.0 + - - +
96C ASN 3.2 0.6 - - - -
97C GLY* 1.3 78.0 - - - +
99C ILE* 1.3 65.3 + - + +
100C ARG 3.3 0.2 + - - -
101C ASN* 3.6 2.4 + - - +
102C ILE* 3.3 31.3 + - + +
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Residues in contact with ILE 99 (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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13C MET* 4.1 22.9 - - - -
44C LEU* 4.4 12.6 - - + -
57C THR* 4.5 10.8 - - + +
60C ALA* 5.7 0.4 - - + -
61C ALA* 4.3 21.3 - - + -
64C ILE* 4.2 7.2 - - + -
72C LYS* 4.2 16.2 - - + -
95C PRO* 3.0 22.9 + - + +
96C ASN* 3.9 4.5 - - - +
98C THR* 1.3 74.4 - - - +
100C ARG* 1.3 59.7 + - + +
102C ILE* 3.2 4.0 + - - +
103C LEU* 3.0 50.5 + - + +
304C GLU* 3.7 21.1 - - - +
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Residues in contact with ARG 100 (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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96C ASN* 2.9 47.7 + - - +
97C GLY* 3.9 9.5 - - - +
98C THR 3.2 0.2 - - - -
99C ILE* 1.3 77.1 - - + +
101C ASN* 1.3 57.1 + - - +
104C GLY* 2.6 37.4 + - - -
107C VAL* 4.3 16.2 - - - +
134C ALA* 4.1 28.2 - - + +
295C LEU* 4.3 22.0 - - + +
304C GLU* 5.1 5.1 + - - +
306C GLU* 4.2 15.6 + - - -
501C NDP 5.4 2.2 + - - -
503C FLC 2.9 32.7 + - - +
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Residues in contact with ASN 101 (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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93C LYS* 5.9 3.0 - - - +
97C GLY 3.2 16.2 + - - +
98C THR* 4.3 2.5 - - - +
100C ARG* 1.3 77.9 - - - +
102C ILE* 1.3 62.2 + - - +
104C GLY* 4.2 4.7 + - - -
134C ALA 5.9 2.8 - - - -
140C ARG* 4.5 21.5 + - - +
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Residues in contact with ILE 102 (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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58C LYS* 4.5 16.8 - - + +
61C ALA* 3.7 24.7 - - + -
62C GLU* 4.1 26.5 - - - +
65C LYS* 3.2 18.9 + - + +
98C THR* 3.3 27.6 + - + +
99C ILE 3.2 7.8 + - - +
100C ARG 3.1 0.8 - - - -
101C ASN* 1.3 81.1 - - + +
103C LEU* 1.3 78.9 + - + +
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Residues in contact with LEU 103 (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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61C ALA 3.4 22.7 - - - +
64C ILE* 3.7 26.0 - - + -
65C LYS* 3.7 36.0 + - + +
99C ILE* 3.0 35.4 + - + +
102C ILE* 1.3 86.3 - - + +
104C GLY* 1.3 66.8 + - - +
295C LEU* 4.2 13.7 - - + -
297C CYS* 3.7 27.9 - - - +
298C PRO* 4.6 4.0 - - - +
302C THR* 5.0 2.2 - - + -
304C GLU* 4.7 4.9 - - + +
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Residues in contact with GLY 104 (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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100C ARG 2.6 24.3 + - - -
101C ASN* 4.2 4.2 - - - -
102C ILE 3.4 2.2 + - - -
103C LEU* 1.3 78.1 - - - +
105C GLY* 1.3 61.1 + - - -
133C HIS* 6.0 0.4 - - - -
134C ALA* 5.6 2.0 - - - -
295C LEU* 3.6 14.9 - - - +
297C CYS* 3.6 13.2 - - - -
298C PRO* 4.5 2.2 - - - -
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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