Contacts of the helix formed by residues 66 - 72 (chain A) in PDB entry 1CCW
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 GLN 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A TYR* 3.3 28.4 + - + +
65A GLY* 1.3 74.8 - - - +
67A GLY* 1.3 62.5 + - - +
68A GLU* 3.2 3.1 - - - -
69A ILE* 3.2 6.0 + - + +
70A ASP* 3.0 25.5 + - - -
96B ASP* 3.8 4.5 - - - +
97B ALA* 4.1 0.2 - - - +
98B TYR* 3.2 51.4 - - - +
121B LEU 3.6 19.3 - - - +
122B LEU* 3.3 13.7 - - - +
123B ASN* 2.9 46.3 + - - +
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Residues in contact with GLY 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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62A SER* 3.2 23.4 + - - -
65A GLY 3.2 5.9 + - - -
66A GLN* 1.3 74.7 - - - +
68A GLU* 1.3 60.3 + - - +
70A ASP* 4.2 3.1 - - - -
71A CYS* 2.8 46.0 + - - +
94A ILE* 3.3 12.2 + - - -
108A PHE* 4.1 2.7 - - - -
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Residues in contact with GLU 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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65A GLY 4.5 2.6 + - - +
66A GLN 3.2 1.5 - - - -
67A GLY* 1.3 78.8 - - - +
69A ILE* 1.3 63.9 + - + +
72A LYS* 3.8 12.3 + - - +
94A ILE 3.5 4.4 + - - -
95A VAL* 3.6 16.1 - - + +
96A VAL 5.2 0.9 + - - -
99A GLN* 4.5 0.2 + - - -
107A ARG* 2.9 29.3 + - - +
108A PHE* 3.9 23.6 - - + -
111A MET* 3.8 21.9 - - + +
119B ARG* 2.7 40.5 + - - -
121B LEU* 3.8 21.3 - - + +
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Residues in contact with ILE 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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66A GLN* 3.2 4.1 + - + +
67A GLY 3.2 0.2 - - - -
68A GLU* 1.3 79.3 - - + +
70A ASP* 1.3 65.1 + - - +
71A CYS 3.3 0.7 + - - -
72A LYS* 3.5 18.1 + - - +
98B TYR* 3.2 28.9 - - + +
106B GLU* 5.6 2.5 - - + +
109B ASN* 4.3 18.8 - - - +
110B GLY* 4.1 23.1 - - - -
113B GLU* 5.2 3.8 - - + -
121B LEU* 3.6 48.5 - - + +
122B LEU* 4.3 5.2 - - + -
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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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11A ILE* 3.5 32.2 - - + +
12A GLY* 3.7 15.5 - - - -
43A GLN* 2.8 27.5 + - - +
64A TYR* 2.5 40.1 + - - -
66A GLN 3.0 15.3 + - - +
67A GLY* 4.1 2.2 + - - +
69A ILE* 1.3 79.5 - - - +
71A CYS* 1.3 53.0 + - - +
98B TYR* 2.7 26.7 + - - -
106B GLU* 4.7 3.1 - - - +
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Residues in contact with CYS 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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11A ILE* 4.3 17.3 - - - -
43A GLN* 3.7 1.3 + - - +
60A VAL* 4.3 5.2 - - - -
62A SER* 4.7 1.8 - - - -
67A GLY* 2.8 30.6 + - - +
70A ASP* 1.3 76.9 - - - +
72A LYS* 1.3 66.2 - - - +
73A GLY 3.4 1.9 + - - -
74A LEU 3.5 7.3 + - - -
90A VAL* 3.9 25.4 - - - -
108A PHE* 3.9 11.7 - - + -
111A MET* 4.0 3.9 - - - +
113A TYR* 2.7 45.4 + - + +
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Residues in contact with LYS 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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43A GLN* 2.8 20.1 + - - +
68A GLU 3.8 11.3 + - - +
69A ILE* 3.5 15.2 + - - +
70A ASP 3.4 1.1 - - - +
71A CYS* 1.3 79.1 - - - +
73A GLY* 1.3 61.4 + - - +
77A LYS* 4.7 2.1 + - - -
111A MET* 3.8 21.9 - - + -
113B GLU* 5.1 11.5 + - - -
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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