Contacts of the helix formed by residues 120 - 131 (chain C) in PDB entry 1HQ3
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 MET 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C THR* 4.7 0.5 - - - +
116C ARG* 3.3 39.5 - - - +
118C THR* 3.8 8.5 - - + +
119C ILE* 1.3 80.9 - - - +
121C PRO* 1.3 77.4 - - + +
122C LYS* 3.2 18.2 - - + +
123C ASP* 2.7 22.7 + - - +
124C ILE* 3.5 6.8 + - - +
607C CL 3.9 19.7 - - + -
47D SER* 4.2 11.0 - - - +
49D LEU* 6.5 0.9 - - + -
50D ILE* 3.8 6.1 - - - -
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Residues in contact with PRO 121 (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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120C MET* 1.3 87.1 - - + +
122C LYS* 1.3 63.9 + - - +
124C ILE* 2.9 18.2 + - + +
125C GLN* 2.9 24.3 + - - +
607C CL 3.7 12.3 - - + -
47D SER* 4.4 2.2 - - - +
49D LEU* 3.6 47.6 - - + +
50D ILE* 4.1 5.2 - - + +
53D GLU* 3.7 32.3 - - + +
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Residues in contact with LYS 122 (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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116C ARG* 4.0 14.4 - - - +
120C MET* 4.0 22.4 - - + +
121C PRO* 1.3 77.5 - - - +
123C ASP* 1.3 65.6 + - - +
125C GLN* 3.8 19.2 + - - +
126C LEU* 3.0 24.3 + - - +
607C CL 3.3 22.2 - - + +
113G HIS* 3.7 31.4 + - + +
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Residues in contact with ASP 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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107C THR* 3.6 25.8 - - + +
110C CYS* 3.5 11.1 - - + +
111C ALA* 3.5 10.1 - - - +
116C ARG* 2.3 37.6 + - - -
119C ILE* 3.3 5.5 - - - -
120C MET 2.7 21.7 + - - +
122C LYS* 1.3 77.1 - - - +
124C ILE* 1.3 64.4 + - - +
126C LEU* 3.4 2.3 + - - +
127C ALA* 3.1 23.2 + - - +
113G HIS* 2.9 28.5 + - - -
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Residues in contact with ILE 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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103C LEU* 4.2 15.3 - - + -
104C PHE* 4.8 5.6 - - + -
107C THR* 3.6 28.7 - - + +
119C ILE* 5.7 0.2 - - + -
120C MET 4.2 4.3 - - - +
121C PRO* 2.9 8.8 + - + +
123C ASP* 1.3 76.6 - - - +
125C GLN* 1.3 58.6 + - - +
127C ALA* 3.4 2.9 + - - +
128C ARG* 2.9 48.8 + - - +
619C CL 4.7 3.1 - - + -
50D ILE* 4.2 20.4 - - + -
53D GLU* 4.1 23.3 - - + -
54D THR* 4.0 22.4 - - - +
57D VAL* 4.3 10.3 - - + -
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Residues in contact with GLN 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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121C PRO* 2.9 28.8 + - - +
122C LYS* 3.8 15.8 - - - +
124C ILE* 1.3 75.4 - - + +
126C LEU* 1.3 58.8 + - - +
129C ARG* 2.9 30.3 + - - +
134C ARG* 3.0 29.1 + - - +
619C CL 3.6 18.8 - - + -
53D GLU* 3.7 19.6 - - - +
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Residues in contact with LEU 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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110C CYS* 3.8 17.9 - - + -
122C LYS 3.0 18.5 + - - +
123C ASP 3.8 4.0 - - - +
125C GLN* 1.3 72.7 - - - +
127C ALA* 1.3 66.9 + - - +
129C ARG* 3.2 4.6 + - + +
130C ILE* 3.0 44.4 + - + +
109G LEU* 3.9 32.3 - - + +
110G CYS* 4.5 11.7 - - - -
113G HIS* 3.4 43.5 - - + +
126G LEU* 4.8 2.2 - - + -
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Residues in contact with ALA 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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103C LEU* 4.0 13.7 - - + -
106C ASP* 3.8 29.8 - - + -
107C THR* 4.2 6.7 - - - +
110C CYS* 4.1 9.8 - - - -
123C ASP 3.1 15.1 + - - +
124C ILE 3.7 3.8 - - - +
126C LEU* 1.3 79.0 - - - +
128C ARG* 1.3 57.0 - - - +
130C ILE* 3.4 2.1 + - - +
131C ARG* 2.8 34.7 + - - +
130G ILE* 3.9 7.8 - - - +
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Residues in contact with ARG 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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99C TYR* 3.8 5.1 + - - -
103C LEU* 4.0 17.3 - - + -
124C ILE* 2.9 22.1 + - - +
125C GLN 3.9 2.5 - - - +
126C LEU 3.2 0.2 - - - -
127C ALA* 1.3 73.5 - - - +
129C ARG* 1.3 63.4 + - - +
131C ARG* 3.4 5.1 + - - -
132C GLY 3.2 2.6 + - - -
133C GLU* 2.9 72.6 + - - +
134C ARG* 3.6 26.6 + - + +
619C CL 3.0 29.5 - - + +
57D VAL* 3.8 32.6 + - - +
60D VAL* 4.3 23.4 - - - +
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Residues in contact with ARG 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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112A GLN* 4.1 15.8 + - - +
125C GLN 2.9 18.7 + - - +
126C LEU* 3.2 7.4 + - + +
128C ARG* 1.3 76.3 - - - +
130C ILE* 1.3 62.3 + - - +
132C GLY* 3.1 14.7 + - - -
134C ARG* 3.4 47.0 - - - +
135C ALA* 5.7 2.9 - - - +
106G ASP* 5.2 2.6 - - - +
109G LEU* 3.8 44.8 - - + +
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Residues in contact with ILE 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 LEU* 3.0 34.5 + - + +
127C ALA 3.8 2.5 - - - +
129C ARG* 1.3 75.4 - - + +
131C ARG* 1.3 60.5 + - - +
132C GLY* 3.0 6.8 + - - -
106G ASP* 3.8 40.3 - - + +
109G LEU* 5.0 3.1 - - + -
110G CYS* 3.6 31.4 - - - -
127G ALA* 3.9 20.9 - - - +
130G ILE* 3.7 26.7 - - + -
131G ARG* 4.0 12.8 - - + +
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Residues in contact with ARG 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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99C TYR* 3.4 23.8 + - - -
102C GLY* 3.8 16.0 + - - -
103C LEU* 3.8 23.8 - - - +
106C ASP* 2.6 38.4 + - - -
127C ALA 2.8 27.9 + - - +
128C ARG* 3.9 5.2 - - - +
129C ARG 3.3 0.4 - - - -
130C ILE* 1.3 76.0 - - - +
132C GLY* 1.3 60.4 + - - +
133C GLU* 2.9 40.5 + - + +
95D ARG* 5.4 2.0 - - - +
130G ILE* 3.7 22.4 - - + +
131G ARG* 5.8 0.9 - - - +
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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