Contacts of the helix formed by residues 91 - 102 (chain C) in PDB entry 3N3B
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 GLY 91 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C SER* 3.3 11.2 - - - -
80C ALA* 3.3 15.1 - - - +
81C SER 4.1 5.2 - - - -
89C ALA 3.1 0.2 + - - -
90C TYR* 1.3 78.9 - - - +
92C ARG* 1.3 58.7 + - - +
93C ALA 3.1 3.6 - - - -
94C GLY* 3.0 18.7 + - - -
95C ASP* 4.0 0.2 - - - +
105C TRP* 3.2 22.2 - - - -
108C ARG* 5.3 2.0 - - - -
134C FMN 3.0 12.9 + - - -
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C SER* 3.4 2.2 + - - +
57C ALA* 4.0 13.5 - - + +
88C GLU* 3.8 35.5 + - - +
89C ALA* 3.2 35.4 + - + +
90C TYR 3.3 1.9 - - - -
91C GLY* 1.3 75.1 - - - +
93C ALA* 1.3 62.4 - - - +
94C GLY 3.1 0.4 - - - -
95C ASP* 2.9 29.3 - - - +
96C VAL* 3.1 27.2 + - + +
105C TRP* 5.4 0.2 - - - -
134C FMN 5.5 0.7 - - - +
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Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C VAL* 4.6 12.6 - - + +
47C PRO 3.9 8.7 - - - +
48C SER* 3.2 21.7 + - - +
57C ALA* 3.6 31.8 - - + +
58C VAL* 4.2 10.0 - - + +
91C GLY 3.1 1.0 - - - -
92C ARG* 1.3 76.9 - - - +
94C GLY* 1.3 61.6 + - - +
96C VAL* 3.9 1.3 - - - +
97C ILE* 3.3 30.9 + - - +
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Residues in contact with GLY 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C VAL* 6.2 0.4 - - - -
78C VAL* 3.4 16.7 - - - +
80C ALA* 3.6 23.6 - - - +
91C GLY 3.0 6.0 + - - -
93C ALA* 1.3 78.2 - - - +
95C ASP* 1.3 57.5 + - - +
96C VAL 3.4 0.2 + - - -
97C ILE* 3.4 2.3 + - - -
98C ALA* 2.9 27.2 + - - +
105C TRP* 3.6 15.3 - - - -
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Residues in contact with ASP 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLY 4.0 2.0 + - - +
92C ARG* 2.9 42.9 - - - +
94C GLY* 1.3 71.8 - - - +
96C VAL* 1.3 61.9 + - - +
98C ALA* 3.8 10.3 - - + +
99C ARG* 3.1 32.8 + - - +
105C TRP* 3.6 31.6 - - + -
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ALA* 5.0 7.0 - - + +
58C VAL* 3.8 22.0 - - + -
92C ARG* 3.1 30.8 + - + +
93C ALA* 3.9 4.5 - - - +
94C GLY 3.2 0.6 - - - -
95C ASP* 1.3 78.4 - - - +
97C ILE* 1.3 60.4 + - + +
99C ARG* 3.5 30.4 + - - +
100C LYS* 3.0 46.3 + - - +
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Residues in contact with ILE 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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44C LEU* 4.2 9.4 - - + -
46C VAL* 3.8 28.9 - - + -
58C VAL* 4.1 28.9 - - + -
62C VAL* 4.2 3.1 - - + -
66C LEU* 3.9 24.2 - - + -
75C LEU* 3.9 20.9 - - + -
78C VAL* 4.4 15.5 - - + -
93C ALA 3.3 20.0 + - - +
94C GLY 4.0 2.9 - - - +
96C VAL* 1.3 75.2 - - + +
98C ALA* 1.3 58.2 + - - +
100C LYS* 4.6 4.9 - - - +
101C CYS* 3.1 31.1 + - - +
103C VAL* 3.8 1.5 - - + +
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Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C VAL* 4.0 4.6 - - + +
94C GLY 2.9 19.1 + - - +
95C ASP* 3.9 7.0 - - + +
96C VAL 3.3 0.2 - - - -
97C ILE* 1.3 77.4 - - - +
99C ARG* 1.3 55.4 + - - +
102C GLY* 3.1 21.7 + - - -
103C VAL* 3.2 34.8 + - - +
105C TRP* 3.9 21.8 - - + +
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Residues in contact with ARG 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ASP* 3.1 21.3 + - - +
96C VAL* 3.7 41.0 + - - +
97C ILE 3.3 0.2 - - - -
98C ALA* 1.3 77.5 - - - +
100C LYS* 1.3 68.0 + - - +
101C CYS 3.6 0.3 + - - -
102C GLY* 3.9 5.4 + - - -
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Residues in contact with LYS 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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58C VAL* 5.6 4.0 - - - +
63C ILE* 5.7 10.1 - - - +
66C LEU* 6.5 0.4 - - + -
72C ARG* 6.1 0.2 - - - -
96C VAL* 3.0 34.0 + - - +
97C ILE* 4.3 3.1 - - - +
99C ARG* 1.3 85.8 - - - +
101C CYS* 1.3 68.9 + - - +
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Residues in contact with CYS 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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66C LEU* 4.5 11.9 - - - -
72C ARG* 4.3 28.4 - - + +
75C LEU* 3.8 28.7 - - + -
97C ILE* 3.1 27.8 + - - +
100C LYS* 1.3 88.8 - - - +
102C GLY* 1.3 62.5 + - - +
103C VAL* 3.4 8.0 - - + +
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Residues in contact with GLY 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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98C ALA 3.1 11.4 + - - -
99C ARG 3.9 5.2 + - - -
100C LYS 3.6 1.8 - - - -
101C CYS* 1.3 79.5 - - - +
103C VAL* 1.3 61.9 + - - +
104C PRO* 4.7 1.4 - - - +
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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