Contacts of the helix formed by residues 124 - 132 (chain C) in PDB entry 1C7G
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 THR 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A VAL* 6.1 0.3 - - - +
284A VAL* 6.0 0.9 - - - -
122C TYR* 4.1 13.4 - - + -
123C PHE* 1.3 91.9 - - + +
125C THR* 1.3 73.8 + - - +
127C ARG* 3.4 2.2 + - - +
128C PHE* 3.1 23.5 + - - +
186C LEU* 5.9 0.6 - - - +
381C ARG* 5.9 4.3 - - - +
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Residues in contact with THR 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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283A VAL* 4.2 8.5 - - + +
284A VAL* 4.5 11.2 - - + -
100C ARG* 3.5 52.2 - - + +
103C GLU* 2.9 17.6 + - - -
123C PHE* 3.0 22.4 - - + -
124C THR* 1.3 83.7 + - - +
126C THR* 1.3 70.0 + - - +
128C PHE* 3.2 15.7 + - - +
129C HIS* 3.2 22.0 + - - -
1000C PLP 4.2 0.9 + - - -
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Residues in contact with THR 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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103C GLU* 2.9 38.3 - - - +
107C SER* 4.6 1.0 + - - -
122C TYR* 5.5 1.7 - - - +
123C PHE* 3.2 42.2 + - + +
125C THR* 1.3 74.3 + - - +
127C ARG* 1.3 62.6 + - - +
129C HIS* 3.6 3.6 + - - +
130C GLN* 3.2 37.1 + - - +
179C CYS* 4.7 6.9 - - - -
214C ASP* 3.6 14.0 + - - +
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Residues in contact with ARG 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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122C TYR* 3.5 45.5 - - + -
123C PHE 3.0 17.4 + - - +
124C THR* 3.9 2.9 - - - +
126C THR* 1.3 75.9 + - - +
128C PHE* 1.3 67.6 + - - +
130C GLN* 3.1 20.4 + - - +
131C GLU* 2.6 53.5 + - - +
137C PHE* 3.5 42.8 + - + +
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Residues in contact with PHE 128 (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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281A LEU* 5.3 6.5 - - + -
284A VAL* 3.6 49.4 - - + -
285A TYR* 4.2 8.5 - + - -
124C THR 3.1 14.3 + - - +
125C THR 3.2 7.2 + - - +
127C ARG* 1.3 77.8 - - - +
129C HIS* 1.3 78.5 + + - +
131C GLU* 3.3 6.3 + - - +
132C LYS* 2.6 63.7 + - + +
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Residues in contact with HIS 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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284A VAL 2.8 29.6 + - - -
285A TYR* 3.8 13.5 - + - -
100C ARG* 3.8 8.0 + - - +
103C GLU* 4.0 15.7 - - + +
104C ASN* 3.7 30.2 - - + -
107C SER* 3.4 21.9 - - - +
125C THR* 3.2 24.0 + - - -
126C THR 4.0 4.9 - - - +
128C PHE* 1.3 95.6 - + - +
130C GLN* 1.3 65.2 + - - +
132C LYS* 3.0 24.3 + - - +
133C ASN* 2.7 28.9 + - - +
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Residues in contact with GLN 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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107C SER* 3.9 2.5 - - - +
111C ILE* 3.8 15.0 - - + +
117C VAL* 3.5 33.3 - - + +
122C TYR* 5.8 0.4 - - - +
126C THR* 3.2 28.9 + - - +
127C ARG* 3.1 17.9 + - - +
129C HIS* 1.3 80.4 - - - +
131C GLU* 1.3 65.4 + - + +
133C ASN* 3.3 7.3 + - - -
134C GLY 3.7 0.5 + - - -
135C ALA* 3.3 23.1 + - + +
137C PHE* 3.6 28.8 - - + +
177C TYR* 3.7 22.7 + - - +
179C CYS* 4.0 13.5 - - - +
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Residues in contact with GLU 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 ARG* 2.6 61.7 + - + +
128C PHE* 4.0 5.1 - - - +
130C GLN* 1.3 75.3 - - + +
132C LYS* 1.3 66.8 + - - +
134C GLY* 3.0 14.4 + - - -
135C ALA 3.5 19.6 + - - +
136C THR* 5.3 0.4 - - - -
137C PHE* 4.5 8.1 + - - +
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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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285A TYR* 3.4 24.5 - - - +
104C ASN* 3.1 18.7 + - - -
108C GLN* 4.1 6.0 - - + +
128C PHE* 2.6 44.1 + - + +
129C HIS* 3.0 31.0 + - - +
131C GLU* 1.3 73.3 - - - +
133C ASN* 1.3 86.2 + - - +
134C GLY 3.5 2.6 + - - -
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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