Contacts of the helix formed by residues 75 - 83 (chain A) in PDB entry 1COZ
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 GLU 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ASN* 3.2 9.2 + - + +
74A TRP* 1.3 81.7 - - + +
76A GLN* 1.3 62.1 + - - +
77A LYS* 3.3 4.2 + - - -
78A LYS* 4.3 6.6 + - - +
79A GLN* 5.2 1.6 + - - +
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Residues in contact with GLN 76 (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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7A TYR* 4.3 8.7 - - + -
34A ALA* 5.0 1.0 - - - +
69A ILE* 5.1 0.8 - - - +
70A PRO 3.2 21.1 + - - +
71A GLU* 3.7 8.2 - - + +
72A LYS* 2.7 35.5 + - - +
73A ASN* 2.9 29.5 + - - +
74A TRP 3.4 0.4 - - - -
75A GLU* 1.3 76.4 - - - +
77A LYS* 1.3 68.7 + - + +
78A LYS 3.5 0.4 - - - -
79A GLN* 3.3 10.0 + - + +
80A ASP* 2.9 50.4 + - - +
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Residues in contact with LYS 77 (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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7A TYR* 3.8 45.2 - - + +
71A GLU* 3.8 19.0 + - - -
73A ASN 5.2 0.8 + - - -
74A TRP* 4.3 30.4 + - - +
75A GLU 3.3 3.0 + - - -
76A GLN* 1.3 78.5 - - + +
78A LYS* 1.3 61.8 + - - +
80A ASP* 3.3 1.4 + - - +
81A ILE* 3.0 30.0 + - - +
89A PHE* 3.9 17.7 - - + -
91A MET* 4.7 2.8 - - - +
99A PHE* 3.6 42.8 - - + -
101A PHE* 5.4 5.6 - - + -
102A LEU* 4.4 13.0 - - + -
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Residues in contact with LYS 78 (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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75A GLU 4.3 5.7 + - - +
76A GLN 3.5 0.8 - - - -
77A LYS* 1.3 78.1 - - - +
79A GLN* 1.3 61.8 + - - +
81A ILE* 3.4 5.2 + - - +
82A ILE* 3.3 30.6 + - + +
101A PHE* 4.0 28.5 + - + -
102A LEU* 3.9 20.3 - - + +
104A ASP* 4.4 5.1 + - - -
105A GLN* 2.9 39.9 + - - +
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Residues in contact with GLN 79 (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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75A GLU 5.2 1.0 + - - +
76A GLN* 3.3 11.4 + - + +
78A LYS* 1.3 77.1 - - - +
80A ASP* 1.3 58.1 + - - +
81A ILE 3.3 0.2 - - - -
82A ILE* 3.5 26.0 - - - +
83A ASP* 2.6 68.4 + - - +
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Residues in contact with ASP 80 (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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5A ILE* 4.2 7.6 - - + -
7A TYR* 2.6 32.6 + - - +
69A ILE* 4.1 15.7 - - - +
76A GLN* 2.9 47.9 + - - +
77A LYS 3.5 3.8 - - - +
78A LYS 3.3 0.2 - - - -
79A GLN* 1.3 74.8 - - - +
81A ILE* 1.3 61.4 + - + +
83A ASP* 4.3 3.8 - - - +
84A HIS* 2.9 44.9 + - + +
86A ILE* 4.0 1.6 - - - +
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Residues in contact with ILE 81 (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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5A ILE* 4.0 24.2 - - + -
7A TYR* 4.2 6.3 - - - +
77A LYS 3.0 22.2 + - - +
78A LYS* 3.6 7.9 - - - +
80A ASP* 1.3 80.9 - - + +
82A ILE* 1.3 60.1 + - + +
85A ASN* 3.2 6.9 + - - -
86A ILE* 3.0 48.6 + - + +
89A PHE* 4.1 12.8 - - + -
102A LEU* 4.8 7.6 - - + -
105A GLN* 4.0 33.9 - - + +
106A CYS* 3.9 20.9 - - - -
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Residues in contact with ILE 82 (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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78A LYS* 3.3 26.0 + - + +
79A GLN* 3.3 32.6 + - - +
80A ASP 3.1 0.4 - - - -
81A ILE* 1.3 76.7 - - + +
83A ASP* 1.3 69.0 + - - +
85A ASN* 3.2 22.7 + - - +
105A GLN* 4.5 9.2 - - + +
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Residues in contact with ASP 83 (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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79A GLN* 2.6 55.1 + - - +
80A ASP* 4.0 5.1 - - - +
82A ILE* 1.3 74.9 - - - +
84A HIS* 1.3 74.0 + - + +
85A ASN* 3.4 6.5 + - - -
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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