Contacts of the helix formed by residues 84 - 95 (chain C) in PDB entry 3Q2K
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 LEU 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C THR* 3.8 11.9 - - - +
81C PRO* 3.1 38.1 + - + +
83C GLY* 1.3 73.8 - - - +
85C HIS* 1.3 66.1 + - - +
86C PRO* 3.2 4.5 - - - -
87C TRP* 3.1 13.1 + - + +
88C GLN* 2.8 33.3 + - + +
180C TRP* 3.9 26.6 - - + -
500C NAI 3.7 32.5 - - - +
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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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78C LEU* 3.7 15.7 + - + +
80C THR* 2.8 43.2 + - - -
81C PRO 3.3 7.5 + - - -
82C SER* 3.3 10.7 + - - +
84C LEU* 1.3 73.3 - - - +
86C PRO* 1.3 59.0 - - + +
88C GLN* 4.5 1.6 - - - -
89C ALA* 2.6 39.7 + - - +
101C SER* 3.2 15.1 + - - +
102C GLU* 3.1 36.5 + - + +
104C PRO 3.1 11.7 + - - -
105C MET 3.3 14.6 - - - +
115C MET* 4.3 0.7 - - - -
500C NAI 3.2 20.9 - - - -
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Residues in contact with PRO 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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82C SER 3.5 9.2 - - - +
83C GLY* 3.6 10.5 - - - +
84C LEU 3.2 5.2 - - - -
85C HIS* 1.3 96.9 - - + +
87C TRP* 1.3 65.3 + - + +
89C ALA* 3.8 1.4 - - - +
90C ILE* 3.0 36.7 + - + +
105C MET 3.6 2.0 - - - +
106C ALA* 3.4 27.1 - - + -
107C THR 5.1 0.2 - - - +
111C ASP* 3.7 25.4 - - + +
115C MET* 3.1 24.6 - - + +
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Residues in contact with TRP 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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117B LYS* 3.3 40.9 - - - +
121B GLU* 6.0 1.1 - - - -
83C GLY 3.5 22.1 + - - -
84C LEU* 3.1 13.7 + - + +
86C PRO* 1.3 76.8 - - + +
88C GLN* 1.3 68.9 + - + +
90C ILE* 3.3 17.1 + - + +
91C GLU* 3.2 23.3 + - - +
111C ASP* 3.7 33.8 + - + -
114C ARG* 3.7 32.3 - - - -
180C TRP* 6.0 1.6 - + - -
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Residues in contact with GLN 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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16C VAL* 3.8 11.2 - - - +
64C LEU* 3.9 23.7 - - + +
78C LEU* 3.9 24.4 - - + +
80C THR* 2.6 34.4 + - - +
84C LEU* 2.8 28.2 + - + +
85C HIS 3.9 2.0 - - - +
87C TRP* 1.3 78.2 - - + +
89C ALA* 1.3 63.1 + - - +
90C ILE 3.2 0.2 + - - -
91C GLU* 3.3 3.5 + - - +
92C VAL* 2.9 27.6 + - - +
500C NAI 3.4 32.9 + - - -
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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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78C LEU* 3.7 15.0 - - + +
85C HIS 2.6 22.8 + - - +
86C PRO 3.8 2.2 - - - +
88C GLN* 1.3 75.1 - - - +
90C ILE* 1.3 57.9 + - - +
92C VAL* 3.8 1.4 - - - +
93C ALA* 2.9 29.6 + - - +
99C VAL* 3.9 19.7 - - + +
115C MET* 3.7 27.6 - - + -
119C CYS* 4.5 6.9 - - - -
126C LEU* 5.3 0.2 - - + -
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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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86C PRO* 3.0 27.3 + - + +
87C TRP* 3.8 21.3 - - + +
88C GLN 3.2 0.2 - - - -
89C ALA* 1.3 75.3 - - - +
91C GLU* 1.3 57.3 + - - +
93C ALA* 3.1 2.9 + - - +
94C GLN* 2.8 53.6 + - - +
111C ASP 5.4 0.2 - - - +
114C ARG* 4.0 40.6 - - + +
115C MET* 4.0 10.3 - - + +
118C ALA* 3.9 25.1 - - + +
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Residues in contact with GLU 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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64C LEU* 3.7 17.3 - - - +
65C SER* 3.5 32.6 + - - -
68C LEU* 3.6 17.3 - - + +
87C TRP 3.2 15.2 + - - +
88C GLN* 3.9 3.9 - - - +
90C ILE* 1.3 73.6 - - - +
92C VAL* 1.3 67.9 + - - +
94C GLN* 3.3 14.1 + - - +
95C ALA* 3.1 20.7 + - + +
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Residues in contact with VAL 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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64C LEU* 4.3 14.4 - - + -
68C LEU* 4.1 11.0 - - + -
76C LEU* 3.7 38.4 - - + -
78C LEU* 4.6 7.2 - - + -
88C GLN 2.9 22.4 + - - +
89C ALA 3.8 3.8 - - - +
91C GLU* 1.3 75.8 - - - +
93C ALA* 1.3 64.7 + - - +
95C ALA* 3.0 12.6 + - - +
96C GLY 3.1 8.3 + - - -
97C ARG* 3.4 25.8 + - + +
98C HIS 3.7 9.2 - - - +
99C VAL* 3.6 15.3 - - + -
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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
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89C ALA 2.9 18.7 + - - +
90C ILE* 3.1 4.9 + - - +
92C VAL* 1.3 80.2 - - - +
94C GLN* 1.3 57.9 + - + +
96C GLY* 2.8 19.9 + - - -
97C ARG 4.1 9.4 - - - +
99C VAL* 5.0 0.4 - - + -
118C ALA* 4.4 4.0 - - + +
119C CYS* 4.0 17.9 - - - +
122C ALA* 3.4 21.8 - - + +
124C VAL* 3.8 21.8 - - + -
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Residues in contact with GLN 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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90C ILE* 2.8 39.5 + - + +
91C GLU* 3.8 13.5 - - + +
92C VAL 3.3 0.2 - - - -
93C ALA* 1.3 75.6 - - + +
95C ALA* 1.3 56.6 + - - +
96C GLY 3.2 0.9 - - - -
118C ALA* 5.8 3.5 - - + +
122C ALA* 5.3 2.0 - - - -
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Residues in contact with ALA 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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68C LEU* 4.2 30.1 - - + +
91C GLU* 3.1 10.2 + - + +
92C VAL 3.0 10.2 + - - +
94C GLN* 1.3 75.9 - - - +
96C GLY* 1.3 60.7 + - - +
97C ARG* 3.4 20.7 + - - +
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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