Contacts of the helix formed by residues 125 - 137 (chain C) in PDB entry 7CAL
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 125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C LYS* 3.8 3.8 - - - +
51C ILE* 5.4 0.2 - - - +
123C VAL* 3.6 13.4 + - - +
124C ASP* 1.3 76.8 - - - +
126C PRO* 1.3 66.9 - - - +
127C LYS* 3.0 9.7 + - - +
128C LYS* 3.3 33.5 + - - +
129C ILE* 3.0 24.9 + - - +
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Residues in contact with PRO 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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49C LYS* 3.9 27.1 - - + -
50C HIS* 5.2 11.4 - - + +
51C ILE* 4.8 15.0 - - + -
110C PHE 5.1 6.4 - - - +
111C PHE* 6.0 3.1 - - + -
125C SER* 1.3 82.9 - - - +
127C LYS* 1.3 61.6 + - - +
129C ILE* 4.1 14.7 - - + +
130C ALA* 3.4 19.4 + - - +
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Residues in contact with LYS 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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125C SER* 3.1 2.4 - - - +
126C PRO* 1.3 83.0 - - + +
128C LYS* 1.3 62.6 - - + +
129C ILE 3.2 0.2 - - - -
130C ALA* 3.0 21.6 + - + +
131C ILE* 3.0 39.4 + - + +
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Residues in contact with LYS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C TYR* 4.0 18.3 + - - +
116C ASP* 5.0 6.7 + - - -
123C VAL* 4.2 16.4 - - + +
125C SER* 3.2 24.5 + - - +
127C LYS* 1.3 78.3 - - + +
129C ILE* 1.3 64.3 + - - +
131C ILE* 4.1 12.9 - - + +
132C ARG* 3.4 23.0 + - - +
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Residues in contact with ILE 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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51C ILE* 4.1 19.3 - - + -
109C THR 4.4 4.0 - - - +
110C PHE* 3.6 35.0 - - - +
112C VAL* 3.3 33.0 - - + +
114C TYR* 4.1 19.2 - - + -
123C VAL* 4.0 13.9 - - + +
125C SER 3.0 29.0 + - - +
126C PRO* 4.1 9.2 - - + +
128C LYS* 1.3 77.8 - - - +
130C ALA* 1.3 61.5 + - - +
132C ARG* 3.5 3.5 + - - +
133C TYR* 3.1 22.3 + - - +
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Residues in contact with ALA 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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110C PHE* 3.9 28.3 - - + -
126C PRO 3.4 14.0 + - - +
127C LYS* 3.0 16.6 + - + +
129C ILE* 1.3 78.6 - - - +
131C ILE* 1.3 62.0 + - + +
133C TYR* 3.4 0.7 + - - -
134C LEU* 3.0 41.6 + - + +
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Residues in contact with ILE 131 (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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127C LYS* 3.0 41.2 + - + +
128C LYS* 3.9 12.5 + - + +
130C ALA* 1.3 77.7 - - + +
132C ARG* 1.3 60.1 + - - +
134C LEU* 4.0 6.7 - - + -
135C SER* 2.8 38.7 + - - +
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Residues in contact with ARG 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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112C VAL* 6.4 0.2 - - - +
114C TYR* 3.4 62.2 + - + +
128C LYS 3.4 17.1 + - - +
129C ILE* 3.7 4.5 - - - +
130C ALA 3.2 0.8 - - - -
131C ILE* 1.3 78.8 - - - +
133C TYR* 1.3 64.0 + - - +
135C SER* 3.3 2.8 + - - -
136C THR* 3.3 44.6 + - + +
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Residues in contact with TYR 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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105C ASP 4.5 1.2 + - - -
106C ILE* 3.9 28.1 - - + +
109C THR* 3.1 43.7 + - + +
110C PHE* 3.7 24.2 - + + -
129C ILE* 3.1 14.6 + - + +
130C ALA 4.1 2.7 - - - +
132C ARG* 1.3 82.2 - - - +
134C LEU* 1.3 61.0 + - - +
135C SER 3.4 0.7 + - - -
136C THR* 4.2 4.7 - - - -
137C TRP* 3.2 41.0 + + + -
138C PHE* 3.3 35.0 + + - +
141C ASP* 4.2 10.7 - - - +
176C ARG* 4.6 8.6 + - - -
177C ARG* 5.2 3.3 + - - -
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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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110C PHE* 4.0 20.2 - - + -
130C ALA* 3.0 29.7 + - + +
131C ILE* 3.7 7.4 + - + +
133C TYR* 1.3 77.1 - - - +
135C SER* 1.3 60.4 + - - +
138C PHE* 3.6 49.5 + - + +
139C ALA* 5.0 4.2 + - - +
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Residues in contact with SER 135 (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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131C ILE* 2.8 30.0 + - - +
132C ARG* 3.3 3.8 + - - -
133C TYR 3.2 0.4 - - - -
134C LEU* 1.3 81.5 - - - +
136C THR* 1.3 65.2 + - - +
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Residues in contact with THR 136 (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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132C ARG* 3.3 34.0 + - + +
133C TYR* 4.1 5.5 + - - -
135C SER* 1.3 85.4 - - - +
137C TRP* 1.3 105.2 + - - +
138C PHE 3.8 1.5 + - - -
139C ALA 5.5 0.2 + - - -
140C PHE* 4.6 4.9 + - - +
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Residues in contact with TRP 137 (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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133C TYR* 3.2 28.0 + + + -
136C THR* 1.3 116.0 + - - +
138C PHE* 1.3 59.3 + - - +
139C ALA 4.0 0.2 - - - -
140C PHE* 3.6 47.8 - + - -
141C ASP* 3.3 19.4 - - + +
176C ARG* 3.8 48.9 - - + +
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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