Contacts of the helix formed by residues 81 - 92 (chain C) in PDB entry 2H5X
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 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C LEU* 3.4 5.6 - - - -
79C GLY 4.0 1.0 + - - -
80C VAL* 1.3 73.9 - - - +
82C PRO* 1.3 76.2 - - - +
83C ARG 3.4 2.9 + - - -
84C LEU 3.4 1.4 + - - -
85C ALA* 3.0 23.0 + - - +
503C GOL 3.1 31.4 + - - -
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Residues in contact with PRO 82 (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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51C ILE* 4.3 27.8 - - + -
53C ARG* 5.2 7.6 - - - +
60C TYR* 3.1 35.0 - - + +
71C PHE* 4.2 4.0 - - + -
75C LEU* 3.8 18.8 - - + -
81C GLY* 1.3 80.0 - - - +
83C ARG* 1.3 64.8 + - + +
85C ALA* 3.5 3.4 - - + +
86C MET* 2.9 30.8 + - - +
503C GOL 3.7 15.7 - - - +
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Residues in contact with ARG 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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60C TYR* 4.9 2.4 + - - +
82C PRO* 1.3 74.6 - - + +
84C LEU* 1.3 60.3 + - - +
86C MET* 3.2 5.2 + - - +
87C ALA* 2.8 29.9 + - - +
503C GOL 2.8 63.1 + - - +
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Residues in contact with LEU 84 (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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79C GLY 4.2 18.4 - - - +
80C VAL* 4.2 18.8 - - + -
81C GLY 3.4 3.9 + - - +
82C PRO 3.4 0.2 - - - -
83C ARG* 1.3 79.1 - - - +
85C ALA* 1.3 52.9 + - - +
87C ALA* 3.2 7.3 + - + +
88C ALA* 2.8 34.8 + - - +
113C PRO 3.3 26.9 - - - +
114C GLY* 3.6 28.3 - - - +
115C ILE* 3.9 19.5 - - + -
123C MET* 5.4 0.7 - - + -
503C GOL 3.5 16.7 + - - +
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Residues in contact with ALA 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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71C PHE* 3.7 23.6 - - + -
74C LEU* 4.2 22.4 - - + +
75C LEU* 4.3 5.6 - - + -
80C VAL* 4.2 7.7 - - + +
81C GLY 3.0 18.7 + - - +
82C PRO* 3.5 5.8 - - + +
84C LEU* 1.3 76.9 - - - +
86C MET* 1.3 62.8 + - - +
88C ALA* 3.2 9.1 + - - +
89C LEU* 3.0 26.6 + - - +
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Residues in contact with MET 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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29C ASN* 3.6 11.9 - - + +
30C ALA* 3.4 43.3 - - - +
31C THR* 3.8 14.4 - - + +
60C TYR* 3.9 19.1 - - + -
62C PHE* 3.8 23.3 - - + -
71C PHE* 3.7 21.1 - - + -
82C PRO 2.9 20.3 + - - +
83C ARG* 3.6 4.9 - - - +
85C ALA* 1.3 74.7 - - - +
87C ALA* 1.3 52.4 + - - +
89C LEU* 3.1 6.3 + - - +
90C ALA* 2.7 36.6 + - - +
158D LEU* 5.4 2.9 - - + -
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Residues in contact with ALA 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 ARG 2.8 14.1 + - - +
84C LEU* 3.3 14.1 - - + +
86C MET* 1.3 76.4 - - - +
88C ALA* 1.3 63.4 + - - +
90C ALA* 3.0 9.3 + - - +
91C VAL* 2.9 27.9 + - + +
112C VAL* 4.0 11.0 - - + -
113C PRO 4.7 4.5 - - - +
158D LEU* 4.3 34.7 - - + +
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Residues in contact with ALA 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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74C LEU* 5.4 5.4 - - + -
84C LEU 2.8 16.7 + - - +
85C ALA* 3.2 12.8 - - - +
87C ALA* 1.3 73.7 - - - +
89C LEU* 1.3 57.6 + - - +
91C VAL* 3.0 5.9 + - - +
92C HIS* 2.8 30.1 + - - +
97C LEU* 4.3 18.3 - - + +
109C LEU* 6.0 0.7 - - + -
112C VAL* 3.4 23.8 - - + +
115C ILE* 4.4 11.7 - - + -
123C MET* 6.1 2.0 - - - -
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Residues in contact with LEU 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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31C THR* 4.1 13.5 - - + +
33C ALA* 6.0 1.6 - - - +
62C PHE* 3.5 35.7 - - + -
67C THR* 4.2 11.7 - - + +
70C LEU* 4.3 16.6 - - + -
71C PHE* 4.3 20.0 - - + -
74C LEU* 4.6 6.1 - - + -
85C ALA 3.0 14.5 + - - +
86C MET* 3.1 9.4 + - - +
88C ALA* 1.3 75.8 - - - +
90C ALA* 1.3 60.4 + - - +
92C HIS 2.9 24.2 - - - +
93C ASP* 4.0 5.4 + - - +
94C ALA* 4.4 9.9 - - - +
97C LEU* 3.6 23.8 - - + -
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Residues in contact with ALA 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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31C THR* 4.0 13.4 - - + +
32C PRO* 4.1 21.7 - - + +
33C ALA* 6.5 0.4 - - - -
86C MET 2.7 17.2 + - - +
87C ALA* 3.0 13.6 + - - +
89C LEU* 1.3 74.3 - - - +
91C VAL* 1.3 61.0 + - + +
93C ASP* 5.7 0.9 - - - +
158D LEU* 4.3 20.2 - - + -
189D LEU* 3.6 22.5 - - + +
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Residues in contact with VAL 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 ALA* 2.9 16.0 + - + +
88C ALA 3.5 5.8 - - - +
90C ALA* 1.3 83.0 - - + +
92C HIS* 1.3 84.7 + - + +
93C ASP* 5.4 0.8 - - - +
111C ARG 4.5 9.6 - - - +
112C VAL* 3.8 21.3 - - + -
113C PRO* 4.1 9.6 - - + -
158D LEU* 5.9 1.3 - - + -
160D PHE* 4.1 26.9 - - + -
189D LEU* 4.9 11.1 - - + +
190D SER* 5.8 1.4 - - - -
192D LEU 4.8 1.8 - - - +
193D GLY* 3.9 23.2 - - - +
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Residues in contact with HIS 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 ALA 2.8 7.7 + - - +
89C LEU* 2.9 28.3 - - - +
90C ALA 3.5 0.2 - - - -
91C VAL* 1.3 107.9 + - + +
93C ASP* 1.3 67.0 + - - +
94C ALA 3.7 0.2 + - - -
96C ALA* 4.6 7.2 - - + -
97C LEU* 3.9 30.0 - - + +
100C VAL* 4.3 14.6 - - + +
108C ALA* 3.2 42.6 + - + +
109C LEU* 4.9 1.6 - - - +
111C ARG* 4.7 1.8 + - + -
112C VAL* 4.1 12.8 - - + +
193D GLY* 4.1 19.3 + - - -
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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