Contacts of the helix formed by residues 73 - 81 (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 GLY 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLN* 3.7 5.4 - - - +
71A CYS 3.4 0.8 + - - -
72A LYS* 1.3 77.9 - - - +
74A LEU* 1.3 65.0 + - - +
75A ARG 3.4 2.5 - - - -
76A GLN* 3.4 12.7 + - - +
77A LYS* 3.2 28.3 + - - +
111A MET* 5.0 7.4 + - - +
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Residues in contact with LEU 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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11A ILE* 5.4 2.9 - - + -
43A GLN* 3.6 34.7 + - + +
46A PHE* 5.0 5.6 - - + -
47A ILE* 3.7 26.9 - - + -
58A ILE* 4.9 4.5 - - + -
60A VAL* 3.8 24.0 - - + -
71A CYS 3.5 3.4 + - - +
72A LYS 3.4 4.0 + - - -
73A GLY* 1.3 76.7 - - - +
75A ARG* 1.3 59.4 + - - +
77A LYS* 3.1 2.8 + - - +
78A CYS* 2.9 37.7 + - - -
88A LEU* 4.1 15.7 - - + -
111A MET 5.4 0.6 + - - -
113A TYR* 3.5 34.1 - - + +
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Residues in contact with ARG 75 (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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73A GLY 3.4 0.4 - - - -
74A LEU* 1.3 77.6 - - - +
76A GLN* 1.3 65.7 + - - +
78A CYS* 3.1 4.2 + - - +
79A ASP* 3.0 38.5 + - - +
83A LEU 4.7 1.0 + - - -
85A GLY* 4.0 9.3 - - - +
86A ILE* 2.8 36.6 + - - +
88A LEU* 3.4 26.0 - - + +
111A MET 3.9 19.8 + - - +
112A GLY* 2.9 35.5 + - - +
113A TYR* 5.7 1.2 - - + -
114A ASP* 2.8 34.6 + - - -
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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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73A GLY* 3.4 12.9 + - - +
74A LEU 3.2 0.6 - - - -
75A ARG* 1.3 82.1 - - - +
77A LYS* 1.3 63.8 + - + +
79A ASP* 3.3 10.1 + - + +
80A GLU* 2.7 52.8 + - + +
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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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43A GLN* 2.5 42.2 + - + +
44A GLU* 3.6 25.7 + - + +
47A ILE* 3.4 20.5 - - + +
72A LYS 4.7 3.0 + - - -
73A GLY* 3.2 14.1 + - - +
74A LEU 3.1 6.8 + - - +
76A GLN* 1.3 77.3 - - + +
78A CYS* 1.3 62.9 + - - +
80A GLU* 3.4 16.6 + - - +
81A ALA* 2.9 24.8 + - - +
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Residues in contact with CYS 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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47A ILE* 3.8 21.8 - - - -
58A ILE* 4.0 19.5 - - - -
74A LEU* 2.9 32.0 + - - +
75A ARG* 3.5 11.2 - - - +
77A LYS* 1.3 74.8 - - - +
79A ASP* 1.3 61.7 + - - +
81A ALA* 3.1 6.4 + - - +
82A GLY 3.1 5.4 + - - -
83A LEU* 2.8 46.0 + - + +
86A ILE* 4.3 9.2 - - + -
88A LEU* 4.1 11.2 - - + -
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Residues in contact with ASP 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 ARG* 3.0 37.8 + - - +
76A GLN* 3.6 10.1 - - - +
78A CYS* 1.3 76.2 - - - +
80A GLU* 1.3 59.9 + - + +
82A GLY* 2.7 18.5 + - - -
83A LEU 4.7 1.0 - - - +
84A GLU* 3.3 50.4 - - + +
85A GLY 4.4 2.8 + - - -
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Residues in contact with GLU 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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76A GLN* 2.7 53.4 + - + +
77A LYS* 3.8 18.1 - - - +
79A ASP* 1.3 78.4 - - + +
81A ALA* 1.3 59.8 + - - +
82A GLY 3.1 0.7 + - - -
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Residues in contact with ALA 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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47A ILE* 3.6 27.6 - - + -
51A ILE* 4.2 19.8 - - + +
77A LYS 2.9 17.8 + - - +
78A CYS* 3.1 5.8 + - - +
80A GLU* 1.3 76.1 - - - +
82A GLY* 1.3 59.6 + - - +
83A LEU* 3.5 5.3 + - + +
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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