Contacts of the helix formed by residues 66 - 74 (chain A) in PDB entry 1I7H
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 SER 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A CYS* 4.6 3.5 - - - -
64A GLU 3.6 2.6 + - - -
65A SER* 1.3 76.7 - - - +
67A GLU* 1.3 73.9 + - - +
68A GLN* 3.4 6.6 + - - +
69A GLU* 3.0 27.1 + - - +
70A ASP* 3.0 29.0 + - - +
88A GLN* 5.0 4.0 + - - -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A SER* 1.3 86.7 - - - +
68A GLN* 1.3 87.3 + - + +
70A ASP* 3.4 10.9 + - - +
71A ASP* 3.1 31.7 + - - +
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A SER 4.3 7.4 + - - +
46A CYS* 3.6 35.9 + - - +
47A ALA* 5.9 1.2 - - - +
66A SER* 3.8 4.8 + - - +
67A GLU* 1.3 94.9 + - + +
69A GLU* 1.3 63.6 + - - +
71A ASP* 3.5 9.6 + - - +
72A MET* 3.4 21.8 + - + +
88A GLN* 5.4 0.3 - - - +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A CYS* 3.6 12.0 - - - -
65A SER* 3.6 10.9 - - - -
66A SER* 3.0 23.4 + - - +
68A GLN* 1.3 75.7 - - - +
70A ASP* 1.3 66.2 + - - +
72A MET* 3.0 5.4 + - - +
73A LEU* 2.9 30.6 + - + +
84A ARG* 2.8 48.0 + - - -
85A LEU* 2.9 45.1 + - + -
88A GLN* 3.3 18.8 - - + +
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Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER* 2.7 29.2 + - - +
66A SER 3.0 22.1 + - - +
67A GLU* 3.6 11.3 - - - +
68A GLN 3.4 0.2 - - - -
69A GLU* 1.3 76.5 - - - +
71A ASP* 1.3 64.0 + - - +
73A LEU* 3.2 24.2 + - - +
74A ASP* 3.1 20.5 + - - +
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Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLU* 3.1 20.4 + - - +
68A GLN* 3.8 9.6 - - - +
69A GLU 3.2 0.4 - - - -
70A ASP* 1.3 78.6 - - - +
72A MET* 1.3 65.4 + - + +
74A ASP* 3.4 24.1 + - - +
75A LYS* 4.0 12.1 - - - +
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Residues in contact with MET 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A CYS 3.3 25.4 - - - +
47A ALA* 3.3 16.8 - - - +
48A CYS* 3.2 44.4 - - - +
49A THR* 3.0 24.1 - - + +
68A GLN* 3.4 10.3 + - + +
69A GLU 3.0 8.1 + - - +
71A ASP* 1.3 76.7 - - + +
73A LEU* 1.3 62.1 + - - +
75A LYS* 2.9 41.3 + - + +
85A LEU* 4.0 9.0 - - + -
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A HIS* 4.4 14.6 - - + -
65A SER* 5.2 3.1 - - - +
69A GLU* 2.9 32.7 + - + +
70A ASP* 3.2 19.5 + - - +
72A MET* 1.3 71.2 - - - +
74A ASP* 1.3 57.8 + - - +
75A LYS 2.9 5.4 - - - -
76A ALA* 2.9 29.2 + - + +
79A LEU* 3.7 31.0 - - + +
83A SER 3.9 19.5 - - - +
84A ARG* 4.3 11.2 - - - +
85A LEU* 3.6 29.2 - - + -
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Residues in contact with ASP 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASP* 3.1 17.5 + - - +
71A ASP* 3.6 20.0 - - - +
72A MET 3.1 0.8 - - - -
73A LEU* 1.3 76.8 - - - +
75A LYS* 1.3 59.7 + - + +
79A LEU* 4.7 12.7 - - - +
3B LYS* 3.6 19.5 + - - -
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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