Contacts of the helix formed by residues 78 - 89 (chain C) in PDB entry 2PYO
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 ILE 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C LYS* 5.1 11.9 - - - +
76C ARG* 3.8 15.7 - - + +
77C ILE* 1.3 81.8 - - - +
79C PRO* 1.4 77.2 - - + +
80C ARG* 4.0 20.6 - - + +
81C HIS* 2.9 42.9 + - + +
82C LEU* 3.4 3.6 + - - +
52D SER* 3.7 14.8 - - - +
55D ALA* 3.9 5.2 - - - -
59J C 5.9 2.2 - - - +
60J A 5.2 7.6 - - - +
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Residues in contact with PRO 79 (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 ILE* 1.4 88.8 - - + +
80C ARG* 1.3 63.2 + - - +
82C LEU* 2.9 16.3 + - + +
83C GLN* 2.8 22.2 + - - +
101C ILE* 4.2 3.5 - - + +
102C ALA 3.4 19.1 - - - +
103C GLN* 3.3 25.4 - - + +
104C GLY* 4.2 1.8 - - - -
52D SER* 3.9 10.3 - - - +
54D LYS* 3.9 26.2 - - + -
55D ALA* 4.0 7.8 - - + +
58D ILE* 4.4 6.1 - - + -
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Residues in contact with ARG 80 (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 ILE* 3.1 19.2 + - + +
79C PRO* 1.3 77.8 - - - +
81C HIS* 1.3 58.7 + - + +
83C GLN* 3.2 2.3 + - - +
84C LEU* 2.7 62.8 + - + +
103C GLN 3.7 2.7 + - - +
104C GLY* 3.0 29.2 + - - -
105C GLY* 3.7 3.2 - - - -
106C VAL 2.6 32.3 + - - +
108C PRO* 3.8 18.0 - - - +
55E GLN 3.1 23.2 + - - -
56E LYS* 4.0 19.6 + - - +
57E SER 4.5 0.6 + - - -
58E THR* 3.4 20.1 - - + +
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Residues in contact with HIS 81 (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 ALA* 4.0 16.7 - - + +
68C ALA* 4.2 12.0 - - + +
69C ALA* 3.6 29.9 - - + +
72C ASN* 4.4 11.0 + - + +
74C LYS* 4.2 17.7 - - + +
76C ARG 3.4 20.0 - - - -
77C ILE* 3.5 12.4 - - + -
78C ILE* 2.9 43.4 + - + +
80C ARG* 1.3 83.3 - - + +
82C LEU* 1.3 64.2 - - - +
84C LEU* 3.7 10.6 - - + +
85C ALA* 3.0 26.2 + - - +
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Residues in contact with LEU 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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61C VAL* 4.0 18.4 - - + -
62C LEU* 5.5 1.6 - - + -
65C ALA* 3.5 27.4 - - + -
77C ILE* 3.9 9.9 - - + -
78C ILE 4.0 9.2 - - - +
79C PRO* 2.9 7.0 + - + +
81C HIS* 1.3 75.5 - - - +
83C GLN* 1.3 64.4 + - - +
85C ALA* 3.5 2.2 + - - +
86C ILE* 3.0 35.8 + - + +
101C ILE* 4.5 10.5 - - + -
55D ALA* 3.8 19.1 - - + +
58D ILE* 3.5 39.0 - - + -
59D MET* 4.2 15.3 - - + -
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Residues in contact with GLN 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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79C PRO 2.8 11.2 + - - +
80C ARG* 3.5 6.3 - - - +
82C LEU* 1.3 77.1 - - - +
84C LEU* 1.3 65.5 + - + +
86C ILE* 4.6 0.4 - - - +
87C ARG* 2.9 77.5 + - + +
101C ILE* 3.7 22.8 - - + +
104C GLY* 3.1 34.3 - - - +
105C GLY 2.9 20.3 + - - +
106C VAL* 4.2 11.7 - - - +
107C LEU* 5.8 0.2 - - + -
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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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68C ALA* 5.1 10.1 - - + -
80C ARG* 2.7 66.2 + - + +
81C HIS* 3.7 13.7 - - + +
83C GLN* 1.3 74.4 - - + +
85C ALA* 1.3 62.7 + - - +
87C ARG* 3.3 0.7 + - - -
88C ASN* 3.0 36.7 + - - +
106C VAL 5.4 0.2 - - - -
107C LEU* 3.6 24.8 - - + +
108C PRO* 4.5 5.6 - - + -
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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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61C VAL* 4.9 3.6 - - + +
64C LEU* 3.7 41.6 - - + +
65C ALA* 4.2 3.8 - - + +
68C ALA* 5.3 3.8 - - + +
81C HIS 3.0 16.3 + - - +
82C LEU* 4.0 3.1 - - - +
84C LEU* 1.3 77.0 - - - +
86C ILE* 1.3 65.1 + - + +
88C ASN* 3.4 3.7 + - - +
89C ASP* 3.2 25.8 + - - +
92C LEU* 4.7 3.3 - - + +
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Residues in contact with ILE 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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61C VAL* 4.9 15.7 - - + -
82C LEU* 3.0 28.5 + - + +
83C GLN* 3.8 3.1 - - - +
85C ALA* 1.3 78.5 - - + +
87C ARG* 1.3 91.8 + - - +
89C ASP* 3.3 9.2 - - - +
92C LEU* 4.0 24.0 - - + +
93C ASN* 3.3 15.9 + - - +
96C LEU* 3.6 33.0 - - + -
101C ILE* 3.3 24.9 - - + -
58D ILE* 5.9 1.1 - - + -
62D PHE* 6.2 1.1 - - + -
98F TYR* 6.0 1.1 - - + -
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Residues in contact with ARG 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 GLN* 2.9 57.4 + - + +
86C ILE* 1.3 92.3 - - - +
88C ASN* 1.3 61.7 + - - +
89C ASP 3.6 0.9 + - - -
93C ASN* 3.0 36.6 + - - +
96C LEU* 3.4 21.6 + - - +
97C SER* 4.5 4.6 + - - +
99C VAL* 2.8 31.7 + - - +
100C THR* 4.7 1.2 - - - +
101C ILE* 4.5 8.9 - - - +
107C LEU* 3.5 35.4 - - + +
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Residues in contact with ASN 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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84C LEU* 3.0 32.6 + - - +
85C ALA* 4.3 4.2 - - - +
87C ARG* 1.3 78.7 - - - +
89C ASP* 1.3 60.7 + - - +
90C GLU 3.6 2.6 + - - -
107C LEU* 3.3 30.4 - - - +
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Residues in contact with ASP 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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60C GLU* 5.5 1.3 - - - +
64C LEU* 4.4 12.4 - - + +
85C ALA 3.2 17.2 + - - +
86C ILE 3.4 0.2 + - - -
87C ARG 3.3 0.4 - - - -
88C ASN* 1.3 76.2 - - - +
90C GLU* 1.3 68.5 + - - +
91C GLU* 3.2 11.1 + - - +
92C LEU* 2.7 48.5 + - + +
93C ASN* 2.8 27.2 + - - +
103D LEU* 5.4 1.6 - - - +
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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