Contacts of the helix formed by residues 70 - 82 (chain H) in PDB entry 2I2R
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 ASN 70 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68H VAL* 3.6 7.1 + - + +
69H VAL* 1.3 75.1 - - - +
71H GLU* 1.3 65.2 + - - +
72H ASP* 3.2 28.2 + - - +
73H THR* 2.7 37.8 + - - +
74H PHE* 3.1 5.0 + - - +
95H PHE* 3.6 11.2 - - + -
105H SER* 4.2 8.1 - - - +
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Residues in contact with GLU 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H ASN* 1.3 79.3 - - - +
72H ASP* 1.3 59.8 + - - +
74H PHE* 3.1 4.9 - - + +
75H LYS* 2.7 34.7 + - + +
88H SER 5.0 2.4 - - - +
91H ALA* 4.4 5.1 - - + +
92H HIS* 3.2 51.0 + - - +
95H PHE* 3.6 38.6 - - + +
96H ASN* 5.3 0.7 + - - -
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Residues in contact with ASP 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H ASN* 3.2 19.0 + - - +
71H GLU* 1.3 80.6 - - - +
73H THR* 1.3 65.2 + - + +
75H LYS* 3.4 8.1 + - - +
76H GLN* 2.9 27.4 + - - +
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Residues in contact with THR 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H GLU 5.2 1.3 - - - +
64H CYS* 4.5 17.9 - - + -
66H SER* 5.6 3.1 - - - -
68H VAL 5.1 3.1 - - - +
69H VAL* 3.1 16.3 - - - +
70H ASN* 2.7 36.9 + - - +
72H ASP* 1.3 76.3 - - + +
74H PHE* 1.3 49.6 + - - +
76H GLN* 3.2 23.5 + - - +
77H ILE* 2.7 54.6 + - - +
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Residues in contact with PHE 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D TRP* 3.9 23.6 - + - -
11D PHE* 6.1 0.7 - + - -
69H VAL* 3.6 21.8 - - + -
70H ASN 3.1 4.8 + - - +
71H GLU* 3.1 13.9 - - + +
73H THR* 1.3 81.9 + - - +
75H LYS* 1.3 62.2 + - - +
77H ILE* 3.5 8.5 + - + +
78H TYR* 3.2 40.5 - + - -
91H ALA* 4.2 12.2 - - + +
94H LEU* 3.5 31.0 - - + -
95H PHE* 3.6 23.8 - + + -
98H PHE* 3.8 31.4 - + - -
106H VAL* 4.1 15.7 - - + -
111H PHE* 6.1 0.2 - + - -
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Residues in contact with LYS 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H GLU* 2.7 15.0 + - + +
72H ASP* 3.6 11.2 - - - +
74H PHE* 1.3 73.2 - - - +
76H GLN* 1.3 57.8 + - - +
78H TYR* 2.9 23.2 + - - +
79H ALA* 3.2 7.8 + - - -
87H ALA* 4.9 4.7 - - - +
88H SER* 4.7 15.3 - - - +
91H ALA* 3.6 20.6 - - + +
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Residues in contact with GLN 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H GLU 5.5 2.8 + - - -
72H ASP 2.9 17.0 - - - +
73H THR* 3.3 29.0 + - - +
75H LYS* 1.3 76.7 - - - +
77H ILE* 1.3 60.0 + - - +
78H TYR 3.1 0.6 + - - -
79H ALA* 3.3 21.6 + - + +
80H GLN* 3.0 18.5 + - - +
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Residues in contact with ILE 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 5.7 5.5 - - + +
8D TRP* 4.1 46.4 - - + +
63H GLU* 4.0 43.2 - - + +
64H CYS* 5.2 0.7 - - + -
69H VAL* 4.3 11.9 - - + -
73H THR* 2.7 50.6 + - - +
74H PHE* 3.7 11.7 - - - +
75H LYS 3.1 0.4 - - - -
76H GLN* 1.3 76.5 - - + +
78H TYR* 1.3 62.3 + - + +
80H GLN* 2.9 16.8 - - - +
81H PHE* 4.5 4.0 + - - +
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Residues in contact with TYR 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D TRP* 3.3 44.5 + + + -
9D LEU* 5.4 2.5 - - + -
11D PHE* 3.7 5.2 - - - +
12D ALA* 4.4 13.6 + - + -
74H PHE* 3.2 43.3 - + - -
75H LYS* 2.9 9.5 + - - +
77H ILE* 1.3 83.0 - - + +
79H ALA* 1.3 66.2 + - - +
80H GLN 2.8 4.0 + - - -
81H PHE* 2.8 35.4 + - + +
82H PHE* 3.7 13.7 + + - -
87H ALA* 3.8 22.3 - - + +
90H TYR* 4.4 13.7 - + - -
91H ALA* 5.6 2.7 - - + -
94H LEU* 3.3 23.7 - - + +
157H MET* 4.4 5.6 - - - -
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Residues in contact with ALA 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H LYS 3.2 7.0 + - - +
76H GLN* 3.3 24.4 + - + +
78H TYR* 1.3 75.7 - - - +
80H GLN* 1.3 58.3 + - + +
82H PHE 2.9 21.1 - - - +
83H PRO 4.1 4.2 - - - +
85H GLY 5.2 5.5 - - - +
87H ALA* 5.3 2.7 - - - +
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Residues in contact with GLN 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 5.9 8.5 - - + -
63H GLU* 3.9 19.1 + - - -
76H GLN 3.0 14.7 + - - +
77H ILE* 2.9 25.1 - - - +
78H TYR 2.8 0.8 + - - -
79H ALA* 1.3 74.2 - - + +
81H PHE* 1.3 55.1 + - - +
82H PHE* 2.4 27.9 + - - +
83H PRO* 4.1 1.2 - - - +
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Residues in contact with PHE 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 5.1 10.3 - - + +
77H ILE 4.5 1.9 + - - +
78H TYR* 2.8 31.3 + - + +
80H GLN* 1.3 75.9 - - - +
82H PHE* 1.3 100.2 + - + -
83H PRO* 4.7 1.2 - - - +
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Residues in contact with PHE 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 4.4 20.2 - - + -
12D ALA* 4.8 6.1 - - + -
78H TYR* 3.7 8.6 + + - +
79H ALA 2.9 16.5 - - - +
80H GLN 2.4 9.3 + - - +
81H PHE* 1.3 106.8 - - + +
83H PRO* 1.3 82.1 - - + +
85H GLY* 4.3 8.3 + - - +
87H ALA* 5.0 2.5 - - + -
157H MET* 3.0 65.7 - - + +
158H MET* 4.7 12.8 - - + +
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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