Contacts of the helix formed by residues 146 - 166 (chain C) in PDB entry 1HJV
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 146 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C SER* 2.5 35.1 + - - +
139C TRP* 3.7 18.8 + - + -
141C TYR 5.1 0.5 - - - +
142C PRO* 3.7 21.9 - - + +
143C GLY* 3.2 18.6 + - - +
144C ARG 3.0 1.4 - - - -
145C ARG* 1.3 97.9 + - - +
147C LYS* 1.3 71.3 + - - +
148C GLN 3.5 1.6 - - - -
149C HIS* 3.9 13.2 - - - -
150C PHE* 2.9 23.0 + - - +
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Residues in contact with LYS 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C GLY 3.9 3.0 + - - -
144C ARG* 3.4 13.8 + - - +
146C ASP* 1.3 79.6 - - - +
148C GLN* 1.3 78.3 + - - +
150C PHE* 3.1 5.2 + - - +
151C THR* 3.1 18.9 + - - -
186C ASP 4.0 13.6 + - - +
187C SER 5.0 1.3 - - - +
188C SER* 3.9 29.8 - - - +
189C TYR 3.7 31.4 + - - +
190C ASP* 3.8 21.6 + - + +
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Residues in contact with GLN 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ASP 3.5 0.2 - - - -
147C LYS* 1.3 87.2 - - - +
149C HIS* 1.3 76.7 + - + +
151C THR* 2.8 16.2 + - + +
152C THR* 2.8 28.8 + - - +
190C ASP* 4.1 17.6 + - - -
193C LYS* 5.5 3.4 - - - +
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Residues in contact with HIS 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C SER 5.1 0.2 - - - -
110C ALA* 4.2 8.7 - - + +
111C SER* 3.3 45.2 + - - -
116C ARG* 4.5 6.5 + - - +
139C TRP* 4.6 10.8 - - + -
145C ARG* 4.0 20.0 + - - -
146C ASP* 3.6 17.4 - - - +
147C LYS 3.3 0.6 - - - -
148C GLN* 1.3 78.8 + - + +
150C PHE* 1.3 55.0 + - - +
152C THR* 3.0 8.1 + - - -
153C LEU* 2.7 35.8 + - - +
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Residues in contact with PHE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU* 4.6 14.6 - - + -
139C TRP* 3.3 47.9 - + + -
142C PRO* 4.3 9.0 - - + -
146C ASP 2.9 13.7 + - - +
147C LYS* 3.2 10.8 - - - +
149C HIS* 1.3 75.8 - - - +
151C THR* 1.3 63.9 + - - +
153C LEU* 3.1 7.3 + - + +
154C ILE* 2.9 56.6 + - + +
176C ALA* 4.8 4.5 - - + -
178C LEU* 3.9 20.4 - - + -
188C SER 4.2 6.3 - - - -
189C TYR* 3.8 33.4 - + - -
194C ILE* 4.4 11.7 - - + -
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Residues in contact with THR 151 (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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147C LYS 3.1 8.5 + - - -
148C GLN* 2.8 24.0 + - + +
150C PHE* 1.3 75.4 - - - +
152C THR* 1.3 58.5 - - - +
154C ILE* 3.5 3.3 + - - +
155C LYS* 2.9 33.2 + - + +
190C ASP* 3.4 24.5 + - - +
193C LYS* 4.1 33.9 - - + -
194C ILE* 3.8 17.4 - - + +
197C HIS* 5.1 4.5 - - + +
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Residues in contact with THR 152 (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 28.9 - - - +
148C GLN* 2.8 21.7 + - - +
149C HIS* 3.2 9.1 - - - -
151C THR* 1.3 72.1 - - - +
153C LEU* 1.3 57.8 + - - +
155C LYS* 2.6 42.9 + - - +
156C GLU* 2.7 38.2 + - + +
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Residues in contact with LEU 153 (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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106C PHE* 4.5 11.7 - - + -
110C ALA* 4.1 16.8 - - + -
116C ARG* 4.4 16.3 - - + +
119C PHE* 4.5 11.7 - - + -
120C ILE* 4.3 13.4 - - + +
137C LEU* 4.1 20.2 - - + -
139C TRP* 3.9 30.1 - - + -
149C HIS 2.7 16.5 + - - +
150C PHE* 3.4 10.3 - - + +
152C THR* 1.3 73.3 - - - +
154C ILE* 1.3 50.3 - - - +
156C GLU* 5.0 0.9 - - - -
157C MET* 2.7 60.8 + - + +
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Residues in contact with ILE 154 (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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137C LEU* 4.1 18.2 - - + -
150C PHE* 2.9 47.0 + - + +
151C THR* 3.8 4.9 - - - +
153C LEU* 1.3 73.5 - - - +
155C LYS* 1.3 69.0 + - - +
157C MET* 3.6 5.6 - - - +
158C LYS* 3.0 20.3 + - - +
174C LEU* 3.8 8.0 - - + +
176C ALA* 4.7 3.1 - - + -
194C ILE* 3.9 22.0 - - + +
197C HIS* 3.6 19.5 - - + +
198C LEU* 3.3 39.7 - - + -
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Residues in contact with LYS 155 (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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151C THR* 2.9 19.8 + - + +
152C THR* 2.6 30.7 + - - +
154C ILE* 1.3 67.2 - - - +
156C GLU* 1.3 86.9 + - - +
158C LYS* 2.9 16.1 + - - +
159C ALA* 3.1 10.2 + - - +
197C HIS* 3.7 38.3 + - + +
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Residues in contact with GLU 156 (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* 3.1 28.8 + - - -
120C ILE* 3.5 22.0 - - + +
152C THR* 2.7 41.2 + - + +
155C LYS* 1.3 85.5 - - - +
157C MET* 1.3 63.1 + - - +
159C ALA* 3.1 24.2 + - + +
160C GLU* 3.2 6.1 + - - +
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Residues in contact with MET 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C PHE* 3.8 20.4 - - + -
120C ILE* 3.9 32.5 - - + +
123C VAL* 3.7 18.4 - - + -
135C LEU* 3.5 22.0 - - + -
137C LEU* 5.0 3.8 - - + -
153C LEU* 2.7 31.8 + - + +
154C ILE* 3.6 5.4 - - - +
156C GLU* 1.3 79.1 - - - +
158C LYS* 1.3 60.4 + - - +
160C GLU* 3.5 2.3 + - - +
161C PHE* 3.0 55.3 + - + -
174C LEU* 3.7 24.2 - - + -
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Residues in contact with LYS 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ILE 3.0 13.9 + - - +
155C LYS 2.9 5.7 + - - +
157C MET* 1.3 74.3 - - - +
159C ALA* 1.3 68.5 + - - +
161C PHE* 3.0 20.5 + - + +
162C ILE* 3.2 25.4 + - + +
171C GLN* 4.7 15.3 - - - +
172C LEU 6.1 1.6 - - - +
174C LEU* 4.0 13.2 - - + +
196C GLN 4.2 7.5 + - - +
197C HIS* 2.8 48.0 + - + +
198C LEU 4.8 2.0 + - - -
199C ASP* 3.8 24.9 + - - +
253C LYS* 5.3 2.2 - - - +
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Residues in contact with ALA 159 (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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155C LYS* 3.1 7.9 + - + +
156C GLU* 3.1 20.1 + - - +
158C LYS* 1.3 75.8 - - - +
160C GLU* 1.3 64.3 + - - +
162C ILE* 3.1 23.1 + - - +
163C LYS* 3.3 11.5 + - - +
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Residues in contact with GLU 160 (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* 3.5 31.2 + - - +
120C ILE* 3.5 39.0 - - + +
121C LYS* 3.8 15.5 - - - +
124C PRO* 4.1 14.8 - - + -
156C GLU 3.2 2.6 + - - +
157C MET 3.8 3.8 - - - +
158C LYS 3.2 0.2 - - - -
159C ALA* 1.3 78.7 - - - +
161C PHE* 1.3 64.7 + - + +
163C LYS* 2.9 36.2 + - - +
164C GLU* 3.0 27.1 + - + +
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Residues in contact with PHE 161 (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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123C VAL* 4.2 9.9 - - + -
124C PRO* 4.2 19.5 - - + -
127C LEU* 4.7 0.7 - - + -
134C GLY* 4.6 0.4 - - - -
135C LEU* 3.7 26.5 - - + -
157C MET* 3.0 44.9 - - + -
158C LYS* 3.0 16.8 + - + +
160C GLU* 1.3 79.1 - - + +
162C ILE* 1.3 59.8 + - - +
164C GLU* 4.2 4.6 - - - +
165C ALA* 3.3 22.5 + - - +
171C GLN* 3.7 9.3 + - - +
172C LEU* 3.0 53.0 + - + +
173C LEU 3.1 23.3 - - - -
174C LEU* 4.3 9.6 - - + -
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Residues in contact with ILE 162 (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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158C LYS* 3.2 29.4 - - + +
159C ALA* 3.6 11.7 - - - +
160C GLU 3.1 0.4 - - - -
161C PHE* 1.3 74.8 - - - +
163C LYS* 1.3 61.7 + - - +
165C ALA* 2.9 3.8 + - + -
166C GLN* 2.8 32.3 + - + +
171C GLN* 3.1 24.7 - - - +
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Residues in contact with LYS 163 (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* 4.0 19.8 - - - +
121C LYS* 6.1 1.0 - - - +
159C ALA 3.3 7.3 + - - +
160C GLU* 2.9 28.3 + - - +
162C ILE* 1.3 77.5 - - - +
164C GLU* 1.3 67.7 + - - +
166C GLN* 2.9 42.4 + - - +
167C PRO* 3.9 0.9 - - - +
1387C SO4 5.7 1.0 + - - -
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Residues in contact with GLU 164 (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* 3.8 19.3 - - + +
125C PRO* 5.7 1.1 - - + -
128C ARG* 2.9 43.2 + - + +
160C GLU* 3.0 14.9 + - - +
161C PHE 4.3 2.9 - - - +
163C LYS* 1.3 83.5 - - + +
165C ALA* 1.3 58.8 + - - +
167C PRO* 3.1 8.5 - - - +
169C LYS* 2.8 32.6 - - + +
172C LEU* 3.1 22.2 - - - +
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Residues in contact with ALA 165 (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 ARG* 4.6 0.2 - - - +
161C PHE 3.3 18.2 + - - +
162C ILE* 2.9 7.1 + - + +
164C GLU* 1.3 86.2 + - - +
166C GLN* 1.3 59.4 + - - +
167C PRO* 3.0 7.5 - - - -
168C GLY* 3.6 6.1 + - - -
169C LYS* 3.5 23.4 - - + +
171C GLN* 3.8 31.9 - - + +
172C LEU 5.0 0.2 - - - +
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Residues in contact with GLN 166 (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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162C ILE* 2.8 12.1 + - + +
163C LYS* 2.9 39.0 + - - +
165C ALA* 1.3 73.6 - - - +
167C PRO* 1.4 75.8 - - + +
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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
------------------------------------------------------------
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