Contacts of the helix formed by residues 82 - 93 (chain C) in PDB entry 3WA9
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 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C ARG* 3.7 13.2 - - + +
81C ILE* 1.3 81.0 - - - +
83C PRO* 1.3 75.2 - - - +
84C ARG* 3.4 19.2 + - - +
85C HIS* 2.8 36.1 + - + +
86C LEU* 3.2 9.5 + - - +
55D SER* 4.1 9.6 - - - +
58D ALA* 3.9 4.0 - - - -
278J C 5.8 0.4 - - - +
279J A 5.5 6.7 - - - +
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Residues in contact with PRO 83 (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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82C THR* 1.3 87.6 - - - +
84C ARG* 1.3 62.8 + - - +
86C LEU* 3.1 14.9 + - + +
87C GLN* 2.9 23.2 + - - +
104C ILE* 4.0 7.4 - - + +
105C ALA 3.4 25.4 - - - +
106C GLY* 3.8 11.2 - - - +
107C GLY* 4.1 2.7 - - - -
55D SER* 4.0 4.3 - - - +
57D LYS* 3.8 31.6 - - + +
58D ALA* 3.8 17.7 - - - +
61D ILE* 4.4 2.0 - - + -
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LEU* 5.2 4.5 - - + -
82C THR* 3.2 12.3 + - - +
83C PRO* 1.3 76.7 - - - +
85C HIS* 1.3 63.7 - - + +
87C GLN* 3.3 2.5 + - - +
88C LEU* 2.9 52.6 + - + +
106C GLY 3.7 3.8 + - - +
107C GLY* 2.8 29.8 + - - -
108C GLY* 3.5 3.4 - - - -
109C VAL 2.6 38.5 + - - +
111C PRO* 3.6 16.6 - - - +
55E GLN 3.1 18.8 + - - -
56E LYS* 3.8 16.2 + - - +
57E SER 4.7 0.2 + - - -
58E THR* 3.7 18.3 - - + +
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Residues in contact with HIS 85 (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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69C ALA* 4.1 17.0 - - - +
72C ALA* 4.2 4.6 - - + +
73C SER* 3.8 17.2 - - - -
76C LEU* 3.4 33.7 - - + +
78C VAL* 3.6 23.0 - - + +
80C ARG 3.5 18.4 - - - -
81C ILE* 3.4 11.5 - - + -
82C THR* 2.8 39.6 + - + +
84C ARG* 1.3 79.1 - - + +
86C LEU* 1.3 64.2 + - - +
88C LEU* 3.0 10.0 + - + +
89C ALA* 2.9 23.9 + - - +
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Residues in contact with LEU 86 (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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65C VAL* 3.6 31.2 - - + -
66C LEU* 5.1 2.0 - - + -
69C ALA* 3.9 17.0 - - + -
81C ILE* 4.2 8.1 - - + -
82C THR 3.2 8.0 + - - +
83C PRO* 3.1 10.5 + - + +
85C HIS* 1.3 78.6 - - - +
87C GLN* 1.3 56.0 + - - +
89C ALA* 3.5 1.6 + - - +
90C ILE* 2.9 37.7 + - + +
104C ILE* 4.2 10.8 - - + -
58D ALA* 3.6 23.3 - - + +
61D ILE* 3.4 39.7 - - + -
62D MET* 3.8 12.6 - - + -
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Residues in contact with GLN 87 (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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83C PRO 2.9 5.8 + - - +
84C ARG* 3.5 8.5 - - - +
86C LEU* 1.3 74.3 - - - +
88C LEU* 1.3 66.1 + - + +
90C ILE* 4.5 0.4 - - - +
91C ARG* 2.9 67.3 + - + +
104C ILE* 3.4 26.1 + - + +
107C GLY* 3.2 40.2 - - - +
108C GLY 3.0 19.8 + - - +
109C VAL* 4.3 10.1 - - - +
110C ILE* 5.4 0.4 - - + +
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Residues in contact with LEU 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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72C ALA* 4.4 15.5 - - + -
76C LEU* 4.5 22.0 - - + -
84C ARG* 2.9 56.5 + - + +
85C HIS* 3.4 7.2 - - - +
87C GLN* 1.3 76.5 - - + +
89C ALA* 1.3 56.9 + - - +
92C GLY* 2.9 28.6 + - - -
109C VAL 4.9 0.2 - - - +
110C ILE* 4.1 24.9 - - + +
111C PRO* 4.9 3.8 - - + -
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Residues in contact with ALA 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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65C VAL* 4.6 3.6 - - + +
68C LEU* 3.5 22.2 - - + +
69C ALA* 3.5 32.8 - - + +
72C ALA* 5.1 1.5 - - - +
85C HIS 2.9 14.0 + - - +
86C LEU* 3.7 4.3 - - - +
88C LEU* 1.3 78.8 - - - +
90C ILE* 1.3 65.7 + - + +
92C GLY* 4.0 0.7 - - - -
93C ASP* 3.4 24.9 + - - +
96C LEU* 4.5 2.3 - - + +
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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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65C VAL* 4.6 18.6 - - + -
86C LEU* 2.9 25.2 + - + +
87C GLN 4.2 1.8 - - - +
89C ALA* 1.3 78.7 - - + +
91C ARG* 1.3 84.1 + - - +
93C ASP 3.3 5.4 + - - +
96C LEU* 3.9 33.8 - - + +
97C ASP* 3.3 25.6 + - - +
100C ILE* 3.8 35.4 - - + -
104C ILE* 3.7 21.3 - - + -
61D ILE* 5.6 3.6 - - + -
62D MET* 6.4 0.2 - - - -
65D PHE* 6.0 1.6 - - + -
98F TYR* 5.9 2.0 - - + -
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Residues in contact with ARG 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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87C GLN* 2.9 57.0 + - + +
90C ILE* 1.3 88.8 - - - +
92C GLY* 1.3 61.2 + - - +
93C ASP 3.4 1.7 + - - +
97C ASP* 2.8 56.2 + - - +
100C ILE* 3.0 32.5 + - - +
101C LYS* 4.5 5.6 - - - +
102C ALA 3.2 20.8 + - - -
104C ILE* 4.7 4.8 - - - +
110C ILE* 3.2 31.0 - - + +
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Residues in contact with GLY 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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88C LEU 2.9 19.3 + - - -
89C ALA 4.0 1.8 - - - -
90C ILE 3.2 0.4 - - - -
91C ARG* 1.3 78.1 - - - +
93C ASP* 1.3 56.6 + - - +
94C GLU* 4.0 1.6 + - - +
110C ILE* 4.0 7.1 - - - +
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Residues in contact with ASP 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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64C GLU* 5.3 1.7 - - - +
68C LEU* 3.6 25.6 - - + +
89C ALA 3.4 15.9 + - - +
90C ILE 3.3 0.2 - - - +
91C ARG 3.3 1.9 - - - -
92C GLY* 1.3 76.6 - - - +
94C GLU* 1.3 67.6 + - - +
95C GLU* 3.1 12.6 + - - +
96C LEU* 2.8 39.2 + - + +
97C ASP* 2.9 26.6 + - - +
106D LEU* 5.5 1.0 - - - +
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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