Contacts of the helix formed by residues 122 - 134 (chain C) 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 PRO 122 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C GLY 3.3 9.4 - - - +
121C THR* 1.3 99.1 - - + +
123C PRO* 1.3 71.4 - - + +
124C GLU* 3.5 19.3 - - + +
125C VAL* 3.1 28.0 + - + +
126C GLY 3.8 1.4 + - - -
800C CNC 5.2 0.7 - - - +
471D PHE* 6.4 0.2 - - + -
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Residues in contact with PRO 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 4.2 13.7 - - + -
23C LEU* 4.0 21.3 - - + -
26C ALA* 3.7 24.9 - - + -
27C PHE* 4.0 3.4 - - + -
121C THR 3.6 1.8 - - - +
122C PRO* 1.3 83.7 - - + +
124C GLU* 1.3 68.0 + - - +
126C GLY* 3.0 4.8 + - - +
127C ILE* 2.9 33.4 + - + +
800C CNC 3.6 35.9 - - + +
471D PHE* 5.1 5.6 - - + -
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Residues in contact with GLU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ALA* 4.7 8.7 - - - +
122C PRO* 3.1 20.5 - - + +
123C PRO* 1.3 91.7 - - - +
125C VAL* 1.3 62.4 + - + +
127C ILE* 3.8 14.3 - - + +
128C ALA* 3.0 24.6 + - - +
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C TYR* 3.9 21.5 - - + -
121C THR* 3.9 7.9 - - + -
122C PRO* 3.1 34.6 + - + +
124C GLU* 1.3 78.0 - - + +
126C GLY* 1.3 64.1 + - - +
128C ALA* 3.3 5.2 + - - +
129C ASP* 3.0 30.4 + - - +
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Residues in contact with GLY 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 3.8 8.1 - - - -
89C TYR* 4.1 4.3 - - - -
117C TYR* 3.9 16.6 - - - -
122C PRO 3.8 3.4 + - - -
123C PRO 3.0 6.4 + - - -
125C VAL* 1.3 80.3 - - - +
127C ILE* 1.3 62.3 + - - +
129C ASP* 3.3 1.7 + - - +
130C LEU* 2.9 26.0 + - - +
800C CNC 4.0 20.7 - - - +
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ALA* 3.7 35.4 - - + +
27C PHE* 3.6 29.6 - - + -
30C ALA* 3.7 23.1 - - + -
32C PHE* 4.4 3.5 - - + -
123C PRO 2.9 27.2 + - - +
124C GLU* 3.8 14.4 - - + +
126C GLY* 1.3 76.4 - - - +
128C ALA* 1.3 63.0 + - - +
130C LEU* 3.4 2.1 + - - +
131C LYS* 3.0 41.0 + - + +
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Residues in contact with ALA 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLU 3.0 18.0 + - - +
125C VAL* 3.9 4.9 - - - +
127C ILE* 1.3 78.2 - - - +
129C ASP* 1.3 65.8 + - - +
131C LYS* 3.4 8.1 + - - +
132C LYS* 3.0 23.0 + - - +
137C GLU* 5.0 1.4 - - - +
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Residues in contact with ASP 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C TYR* 3.3 2.5 - - - +
115C ARG* 3.7 30.2 + - - +
117C TYR* 2.7 41.1 + - - +
125C VAL* 3.0 22.3 + - - +
126C GLY 3.8 1.1 - - - +
128C ALA* 1.3 80.0 - - - +
130C LEU* 1.3 55.9 + - - +
132C LYS* 3.2 16.2 + - - +
133C ASP* 2.8 33.6 + - - +
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Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 3.5 30.5 - - + -
27C PHE* 3.9 15.0 - - + -
32C PHE* 3.5 20.9 - - + -
57C ALA* 3.9 20.2 - - + -
59C LEU* 4.5 7.2 - - + -
87C LEU* 4.0 7.0 - - + -
89C TYR* 3.1 21.5 + - + +
126C GLY 2.9 17.0 + - - +
127C ILE 3.9 3.6 - - - +
129C ASP* 1.3 74.2 - - - +
131C LYS* 1.3 61.5 + - - +
133C ASP 3.7 0.4 - - - +
134C LEU* 2.9 58.3 + - + +
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Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET* 2.8 33.2 - - + +
30C ALA* 2.9 23.7 + - - +
31C GLY 5.6 0.2 - - - -
32C PHE* 3.7 21.1 - - + -
127C ILE* 3.0 36.6 + - + +
128C ALA* 3.8 7.6 - - - +
130C LEU* 1.3 76.5 - - - +
132C LYS* 1.3 63.3 + - - +
134C LEU 3.5 0.2 + - - -
135C ASN 3.0 3.5 + - - -
136C ILE* 2.9 47.9 + - + +
137C GLU* 3.3 20.2 + - + -
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Residues in contact with LYS 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ARG* 3.2 37.7 - - - +
128C ALA 3.0 15.8 + - - +
129C ASP* 3.7 14.0 + - - +
131C LYS* 1.3 77.4 - - - +
133C ASP* 1.3 64.2 + - - +
135C ASN* 3.0 22.2 + - - +
137C GLU* 3.2 35.5 - - - +
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Residues in contact with ASP 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU* 3.8 29.0 - - + +
89C TYR* 2.6 25.9 + - - +
114C ASP* 5.5 0.9 - - - +
115C ARG* 2.8 36.9 + - - +
129C ASP 2.8 15.8 + - - +
130C LEU 3.3 2.2 + - - +
132C LYS* 1.3 80.1 - - - +
134C LEU* 1.3 61.2 + - - +
135C ASN* 3.8 8.9 + - - -
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LYS* 3.9 38.6 + - + +
6C ILE* 5.7 0.7 - - + -
32C PHE* 4.1 6.5 - - + -
56C ASP* 4.0 26.7 - - + +
87C LEU* 3.6 21.1 - - + -
130C LEU* 2.9 44.7 + - + +
133C ASP* 1.3 75.9 - - - +
135C ASN* 1.3 71.9 + - - +
136C ILE* 3.3 20.6 + - + +
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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