Contacts of the helix formed by residues 124 - 135 (chain C) in PDB entry 4HRE
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 ASP 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C ALA 5.2 0.9 - - - +
117C SER* 2.8 42.5 + - - +
123C THR* 1.3 73.5 - - - +
125C GLU* 1.3 64.6 + - - +
126C ASP* 4.2 3.0 + - - +
127C SER* 2.4 34.7 + - - -
128C LEU 3.8 4.2 + - - -
286C LYS* 2.3 33.5 + - - -
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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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122C GLY* 4.3 6.6 - - - -
123C THR* 2.8 41.0 + - - +
124C ASP* 1.3 74.1 - - - +
126C ASP* 1.3 73.6 + - - +
128C LEU* 3.5 7.1 + - - +
129C ILE* 3.3 27.4 + - + +
167C PHE* 5.0 8.2 - - + -
251C ASP* 3.7 34.5 - - - +
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Residues in contact with ASP 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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124C ASP* 3.6 4.6 + - - +
125C GLU* 1.3 83.9 - - - +
127C SER* 1.3 58.8 - - - +
129C ILE* 3.2 10.0 + - - +
130C GLU* 2.9 27.7 + - - +
251C ASP* 5.5 0.3 - - - +
254C ASN* 3.6 25.2 + - - +
273C ARG* 4.1 24.8 + - - +
286C LYS* 6.5 0.2 - - - -
287C VAL* 6.0 4.3 - - + -
290C ARG* 5.7 0.7 - - - +
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Residues in contact with SER 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C GLU* 5.2 7.2 - - - -
114C LEU* 6.4 0.2 - - - -
117C SER* 4.5 8.3 - - - -
124C ASP* 2.4 28.7 + - - -
125C GLU 3.3 0.6 - - - -
126C ASP* 1.3 78.3 - - - +
128C LEU* 1.3 63.1 - - - +
130C GLU* 3.3 10.0 + - - +
131C ILE* 3.3 23.5 + - - +
286C LYS* 3.7 7.8 - - - -
287C VAL* 5.7 0.2 - - - +
290C ARG* 3.3 41.4 + - - +
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Residues in contact with LEU 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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114C LEU* 3.5 30.0 - - + +
117C SER* 4.1 17.3 + - - +
118C MET* 4.2 20.9 - - + -
123C THR* 4.4 13.5 - - + -
124C ASP 3.8 7.7 + - - +
125C GLU* 3.5 9.4 + - - +
126C ASP 3.3 0.2 - - - -
127C SER* 1.3 78.7 - - - +
129C ILE* 1.3 61.1 + - - +
131C ILE* 3.7 1.7 + - - +
132C ILE* 2.9 35.8 + - + +
159C ILE* 4.9 10.3 - - + -
163C THR* 4.1 25.8 - - + -
167C PHE* 4.5 10.3 - - + -
171C MET* 3.9 18.4 - - + -
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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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125C GLU 3.3 17.5 + - - +
126C ASP* 3.2 8.9 + - - +
128C LEU* 1.3 76.4 - - - +
130C GLU* 1.3 69.0 + - - +
133C CYS* 2.8 32.2 + - - +
167C PHE* 3.8 29.8 - - + -
171C MET* 3.7 10.5 - - + -
251C ASP* 4.0 4.5 - - - +
254C ASN* 3.8 20.9 - - + +
255C ALA* 3.7 24.5 - - + +
258C ASN* 3.3 36.8 - - + +
273C ARG* 5.7 0.2 - - - +
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Residues in contact with GLU 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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126C ASP 2.9 7.1 + - - +
127C SER 3.5 9.4 - - - +
128C LEU 3.3 0.4 - - - -
129C ILE* 1.3 77.6 - - - +
131C ILE* 1.3 61.7 + - - +
133C CYS* 3.7 1.2 - - - +
134C SER* 2.3 40.4 + - - +
135C ARG* 4.4 11.6 + - - -
258C ASN* 5.2 0.2 + - - -
269C TYR* 3.8 20.1 + - + +
270C PHE* 3.9 18.4 - - + -
273C ARG* 2.7 27.5 + - - +
290C ARG* 2.3 46.4 + - - +
291C ILE* 4.0 19.5 - - - +
294C SER* 4.8 2.4 + - - -
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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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110C ASP* 3.9 28.3 - - + +
113C GLU* 3.9 19.1 - - + -
114C LEU* 3.8 33.2 - - + +
127C SER* 3.3 18.5 + - - +
128C LEU 4.2 2.0 - - - +
130C GLU* 1.3 78.7 - - + +
132C ILE* 1.3 68.0 + - + +
134C SER* 3.8 3.8 - - - -
135C ARG* 2.8 66.6 + - + +
140C LEU* 5.9 0.2 - - + -
143C ILE* 4.0 7.2 - - + -
290C ARG* 4.9 8.3 - - - -
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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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114C LEU* 4.3 19.7 - - + -
128C LEU* 2.9 29.0 + - + +
131C ILE* 1.3 78.4 - - + +
133C CYS* 1.3 65.3 + - - +
134C SER 3.1 0.2 + - - -
135C ARG* 3.4 12.0 + - - +
140C LEU* 4.3 20.9 - - + +
155C LEU* 5.3 1.8 - - + -
159C ILE* 4.8 8.7 - - + -
171C MET* 3.3 34.5 - - + +
174C LEU* 3.5 38.1 - - + +
175C ALA* 4.1 23.1 - - + +
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Residues in contact with CYS 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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129C ILE* 2.8 42.8 + - - +
130C GLU* 3.8 2.0 - - - +
132C ILE* 1.3 75.8 - - - +
134C SER* 1.3 59.8 + - - +
135C ARG 4.7 1.6 - - - +
171C MET* 5.2 1.3 - - - -
174C LEU* 4.0 19.3 - - - +
255C ALA* 3.7 23.1 - - - -
258C ASN* 4.2 4.0 - - + -
259C LEU* 3.8 35.2 - - - +
262C CYS* 3.9 17.8 - - - +
269C TYR* 5.2 0.2 - - - +
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Residues in contact with SER 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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130C GLU* 2.3 40.4 + - - +
133C CYS* 1.3 74.8 - - - +
135C ARG* 1.3 83.7 + - - +
139C GLU* 4.4 0.9 - - - +
262C CYS* 3.9 14.6 - - - -
266C LYS* 3.0 34.8 + - - +
269C TYR* 4.4 1.6 - - - -
270C PHE* 3.6 20.6 - - - -
295C ARG* 4.6 2.0 + - - -
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Residues in contact with ARG 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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110C ASP* 3.1 32.2 + - - +
130C GLU* 4.4 5.5 + - - -
131C ILE* 2.8 41.4 + - + +
132C ILE 3.4 3.4 + - - +
133C CYS 4.7 1.2 - - - +
134C SER* 1.3 98.9 + - - +
136C THR* 1.3 64.4 + - - +
139C GLU* 3.3 24.2 + - + +
140C LEU* 3.5 32.9 - - + +
143C ILE* 3.9 21.1 - - + -
270C PHE* 3.8 10.5 - - - -
290C ARG* 5.8 2.2 - - - +
294C SER* 3.4 25.9 + - - -
295C ARG* 3.7 15.9 - - - +
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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