Contacts of the helix formed by residues 112 - 130 (chain C) in PDB entry 1HJX
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 ASN 112 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C LYS 3.6 16.8 + - - +
109C ILE 3.5 0.2 - - - +
110C ALA 3.4 0.8 - - - -
111C SER* 1.3 77.8 - - - +
113C THR* 1.3 65.3 + - - +
114C GLN* 3.0 23.8 + - - +
115C SER* 2.9 38.3 + - - +
116C ARG* 2.9 25.3 + - - +
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Residues in contact with THR 113 (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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111C SER 4.0 1.7 + - - -
112C ASN* 1.3 71.2 + - - +
114C GLN* 1.3 79.5 + - - +
116C ARG* 3.3 31.7 + - - +
117C ARG* 3.1 24.0 + - + +
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Residues in contact with GLN 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ASN* 3.0 22.4 + - - +
113C THR* 1.3 92.1 - - - +
115C SER* 1.3 66.4 + - - +
117C ARG* 3.2 6.1 + - - +
118C THR* 2.9 28.2 + - - +
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Residues in contact with SER 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ASP* 3.5 36.7 + - - +
108C LYS 4.7 1.0 + - - -
109C ILE* 3.4 24.4 - - - +
112C ASN* 2.9 24.3 + - - +
114C GLN* 1.3 73.0 - - - +
116C ARG* 1.3 62.6 + - - +
118C THR* 3.2 3.8 + - - -
119C PHE* 2.9 24.9 + - - +
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Residues in contact with ARG 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ILE* 3.2 12.7 + - - +
110C ALA* 2.8 34.8 + - - +
111C SER* 4.0 5.3 + - - +
112C ASN 2.9 17.6 + - - +
113C THR* 3.3 45.7 + - - +
115C SER* 1.3 78.7 - - - +
117C ARG* 1.3 62.4 + - - +
119C PHE* 3.2 5.2 + - - +
120C ILE* 3.0 34.7 + - + +
149C HIS* 5.5 3.4 - - - -
152C THR* 3.9 18.5 - - - +
153C LEU* 4.2 22.2 - - + +
156C GLU* 2.7 37.6 + - - +
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Residues in contact with ARG 117 (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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113C THR* 3.1 18.1 + - + +
114C GLN* 3.6 6.3 - - - +
116C ARG* 1.3 80.8 - - - +
118C THR* 1.3 58.3 + - - +
120C ILE* 3.3 17.2 + - - +
121C LYS* 2.8 60.0 + - + +
156C GLU* 5.8 0.7 - - - -
160C GLU* 3.0 30.3 + - - +
163C LYS* 4.1 15.2 - - - +
1387C SO4 2.9 43.5 + - - +
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Residues in contact with THR 118 (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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63C ASN 4.3 0.2 - - - +
64C ASP* 3.3 21.6 + - + +
65C HIS* 3.3 36.1 - - + +
114C GLN* 2.9 15.1 + - - +
115C SER* 3.5 7.5 - - - -
117C ARG* 1.3 77.7 - - - +
119C PHE* 1.3 63.2 + - - +
121C LYS* 3.7 7.2 - - - +
122C SER* 3.0 23.0 + - - -
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Residues in contact with PHE 119 (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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61C ILE* 3.5 40.4 - - + -
64C ASP 2.9 17.0 + - - +
66C ILE* 4.0 18.4 - - + -
96C VAL* 4.3 20.4 - - + -
106C PHE* 4.7 6.1 - + - -
109C ILE* 4.2 15.5 - - + -
115C SER 2.9 16.4 + - - +
116C ARG* 3.7 2.7 - - - +
118C THR* 1.3 75.5 - - - +
120C ILE* 1.3 61.5 + - + +
122C SER* 2.6 26.0 + - - -
123C VAL* 3.2 21.1 - - + +
135C LEU* 4.7 1.3 - - + -
137C LEU* 4.7 7.2 - - + -
153C LEU* 4.3 18.6 - - + -
157C MET* 3.3 27.8 - - + -
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Residues in contact with ILE 120 (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* 3.0 37.3 + - + +
117C ARG* 3.9 12.8 - - - +
119C PHE* 1.3 76.1 - - + +
121C LYS* 1.3 64.1 + - - +
123C VAL* 3.2 11.1 + - - +
124C PRO* 3.2 13.0 - - - +
153C LEU* 4.0 11.0 - - + -
156C GLU* 3.7 33.7 - - + +
157C MET* 3.7 39.0 - - + +
160C GLU* 3.4 33.7 - - + +
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Residues in contact with LYS 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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117C ARG* 2.8 41.0 + - + +
118C THR* 3.7 6.7 - - - +
120C ILE* 1.3 78.1 - - - +
122C SER* 1.3 61.8 + - - +
123C VAL 3.3 0.9 + - - -
124C PRO* 3.6 2.7 - - - +
125C PRO* 3.5 18.4 - - - +
160C GLU* 4.8 8.4 - - - +
1387C SO4 2.7 43.2 + - - +
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Residues in contact with SER 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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65C HIS* 3.5 31.3 - - - -
66C ILE* 3.0 26.1 + - - +
118C THR 3.0 14.8 + - - -
119C PHE 2.6 18.9 + - - -
121C LYS* 1.3 79.5 - - - +
123C VAL* 1.3 61.4 + - - +
125C PRO* 3.3 15.4 - - - +
126C PHE* 3.6 13.5 - - - +
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 4.2 12.1 - - + +
119C PHE* 3.2 39.5 - - + +
120C ILE 3.2 5.3 + - - +
122C SER* 1.3 77.6 - - - +
124C PRO* 1.4 73.2 - - + +
126C PHE* 3.3 3.6 + - - +
127C LEU* 3.1 37.7 + - + +
135C LEU* 4.0 13.7 - - + -
157C MET* 3.7 16.8 - - + -
161C PHE* 3.7 23.6 - - + -
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Residues in contact with PRO 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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120C ILE 3.2 19.5 - - - +
121C LYS 3.6 3.6 - - - +
123C VAL* 1.4 85.6 - - + +
125C PRO* 1.3 73.9 - - + +
127C LEU* 3.2 4.3 + - - +
128C ARG* 2.9 28.3 + - - +
160C GLU* 4.0 18.4 - - + +
161C PHE* 4.0 21.3 - - + -
164C GLU* 3.6 34.3 - - + +
172C LEU* 3.7 12.6 - - + -
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Residues in contact with PRO 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 LYS 3.5 15.7 - - - +
122C SER* 3.3 16.6 - - - +
124C PRO* 1.3 94.9 - - + +
126C PHE* 1.3 54.6 + - - +
128C ARG* 3.2 8.6 + - + +
129C THR* 2.8 37.9 + - - +
164C GLU* 5.8 0.2 - - + -
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Residues in contact with PHE 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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66C ILE* 3.5 37.9 - - + -
67C ASP* 3.8 23.6 - - - -
68C THR* 4.0 18.4 - - + -
77C TYR* 3.9 18.4 - + - -
94C LEU* 3.8 29.8 - - + -
122C SER 3.6 6.7 - - - +
123C VAL 3.3 2.4 + - - +
124C PRO 3.3 0.6 - - - -
125C PRO* 1.3 80.5 - - - +
127C LEU* 1.3 65.3 + - + +
129C THR* 3.8 3.8 - - - -
130C HIS* 3.2 60.2 + + + +
132C PHE* 5.3 0.4 - + - -
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Residues in contact with LEU 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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66C ILE* 5.0 1.3 - - + -
94C LEU* 3.9 24.2 - - + -
123C VAL* 3.1 35.7 + - + +
124C PRO 3.6 5.6 - - - +
126C PHE* 1.3 80.9 - - + +
128C ARG* 1.3 62.3 + - - +
130C HIS 3.3 1.6 + - - -
131C GLY 3.1 4.5 + - - -
132C PHE* 2.9 59.3 + - + +
134C GLY* 3.7 31.6 - - - +
135C LEU* 3.9 10.5 - - + +
161C PHE* 4.3 1.3 - - + -
172C LEU* 3.8 22.0 - - + -
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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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124C PRO 2.9 20.8 + - - +
125C PRO* 3.6 8.3 - - + +
127C LEU* 1.3 74.1 - - - +
129C THR* 1.3 63.8 + - - +
130C HIS 3.1 1.4 + - - -
131C GLY* 3.1 12.4 + - - -
132C PHE 4.9 3.3 + - - -
164C GLU* 2.5 42.7 + - - +
165C ALA* 4.4 3.4 - - - +
169C LYS* 3.9 29.3 - - - +
170C LYS* 3.1 29.5 + - - +
172C LEU* 3.7 30.1 - - - +
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Residues in contact with THR 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 PRO* 2.8 22.3 + - - +
126C PHE* 3.8 5.8 - - - -
128C ARG* 1.3 76.7 - - - +
130C HIS* 1.3 78.2 + - + +
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Residues in contact with HIS 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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68C THR* 5.2 1.0 - - - +
74C VAL* 4.1 33.7 - - + +
77C TYR* 3.6 27.6 - + + +
81C ASN* 2.6 29.8 + - - -
126C PHE* 3.2 61.4 + + - +
128C ARG 3.1 0.8 - - - -
129C THR* 1.3 93.5 + - + +
131C GLY* 1.3 51.8 + - - +
132C PHE* 3.5 13.2 + - + -
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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
------------------------------------------------------------
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