Contacts of the helix formed by residues 124 - 132 (chain C) in PDB entry 3WHD
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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92C GLN* 4.9 5.6 + - - +
122C ILE* 3.7 6.8 - - - +
123C SER* 1.3 90.0 - - - +
125C GLU* 1.3 65.1 + - - +
126C ALA* 3.7 9.2 + - - +
127C GLU* 3.1 30.3 + - - +
128C GLN 3.2 9.5 + - - -
166C ARG* 3.7 19.3 - - - +
168C PHE* 3.9 7.4 - - - -
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Residues in contact with GLU 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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124C THR* 1.3 73.9 - - - +
126C ALA* 1.3 58.1 + - - +
128C GLN* 3.1 7.6 + - + +
129C ASN* 2.8 50.3 + - - +
166C ARG* 5.8 0.4 - - - +
168C PHE* 3.4 34.3 - - + -
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Residues in contact with ALA 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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91C PHE* 3.6 18.8 - - + -
92C GLN* 4.6 8.5 - - - +
124C THR* 3.2 8.9 + - - +
125C GLU* 1.3 78.8 - - - +
127C GLU* 1.3 61.9 + - - +
129C ASN* 3.9 9.2 - - - +
130C PHE* 3.0 22.9 + - - +
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Residues in contact with GLU 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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91C PHE* 3.7 17.0 - - + -
92C GLN* 5.5 1.1 - - - +
94C ASN* 5.7 0.7 - - - -
96C TYR* 2.4 36.3 + - + +
120C MET* 3.8 11.6 - - + +
121C THR 3.1 12.3 - - - +
122C ILE* 4.1 1.6 - - + -
123C SER* 2.9 31.1 + - - -
124C THR* 3.1 23.1 + - - +
126C ALA* 1.3 76.9 - - - +
128C GLN* 1.3 60.8 + - - +
130C PHE* 3.3 5.2 + - - +
131C ILE* 3.2 21.5 + - - +
208C LYS* 2.8 23.2 + - - -
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Residues in contact with GLN 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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122C ILE* 3.8 22.0 - - + +
124C THR 3.2 6.4 + - - +
125C GLU* 3.1 12.8 + - - +
127C GLU* 1.3 73.9 - - - +
129C ASN* 1.3 70.7 + - - +
131C ILE* 3.1 18.3 + - - +
132C ILE* 3.1 34.3 + - + +
168C PHE* 3.8 29.3 - - + +
185C LEU* 3.7 11.0 - - + +
192C TRP* 3.8 20.6 + - - +
193C ALA* 4.6 1.2 - - - +
194C TRP* 2.9 30.7 + - - -
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Residues in contact with ASN 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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125C GLU* 2.8 48.0 + - - +
126C ALA* 3.9 8.3 - - - +
128C GLN* 1.3 77.3 + - - +
130C PHE* 1.3 62.4 + - - +
132C ILE* 3.6 22.8 - - + +
133C GLN* 3.6 19.4 + - - +
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Residues in contact with PHE 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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89C ARG* 3.8 13.9 - - + -
90C ALA 3.1 26.5 - - - -
91C PHE* 3.5 43.1 - + + -
96C TYR* 4.0 21.1 - + - -
126C ALA 3.0 14.2 + - - +
127C GLU 3.4 9.2 - - - +
128C GLN 3.1 0.2 - - - -
129C ASN* 1.3 76.4 - - - +
131C ILE* 1.3 73.7 + - + +
132C ILE 3.4 0.5 + - - -
133C GLN* 3.5 22.5 + - - +
134C PHE* 3.4 45.1 - + - -
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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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89C ARG* 5.5 0.9 - - + -
96C TYR* 3.6 32.3 - - + -
98C PRO* 4.8 10.8 - - + -
120C MET* 3.7 30.3 - - + -
122C ILE* 4.6 0.4 - - + -
127C GLU 3.2 2.5 + - - +
128C GLN* 3.1 15.7 + - - +
130C PHE* 1.3 84.8 - - + +
132C ILE* 1.3 60.3 + - - +
133C GLN 3.1 0.4 - - - -
134C PHE* 3.0 34.3 + - + +
135C LEU* 3.5 8.4 - - + +
185C LEU* 3.8 26.0 - - + -
206C ILE* 3.8 27.8 - - + -
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Residues in contact with ILE 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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128C GLN* 3.2 33.0 - - + +
129C ASN* 3.6 27.4 - - - +
131C ILE* 1.3 79.6 - - + +
133C GLN* 1.3 67.9 + - + +
134C PHE 3.2 0.6 + - - -
135C LEU* 3.4 18.9 + - - +
185C LEU* 4.1 11.0 - - + -
192C TRP* 3.5 59.7 + - + +
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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