Contacts of the helix formed by residues 145 - 158 (chain C) in PDB entry 1JJ6
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 145 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C ARG* 5.8 1.6 - - - -
143C ALA 4.4 0.2 - - - -
144C ILE* 1.3 78.8 - - - +
146C LYS* 1.3 60.5 + - - +
147C HIS* 3.1 12.5 + - - +
148C GLU* 2.5 64.3 + - - +
149C GLN* 2.9 24.3 + - - +
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Residues in contact with LYS 146 (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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145C ASN* 1.3 70.7 - - - +
147C HIS* 1.3 67.0 + - - +
149C GLN* 3.1 21.5 + - - +
150C GLU* 2.9 25.6 + - - +
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Residues in contact with HIS 147 (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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145C ASN* 3.1 10.4 + - - +
146C LYS* 1.3 78.7 - - - +
148C GLU* 1.3 59.0 + - + +
150C GLU* 3.3 10.9 + - - +
151C GLN* 3.0 28.0 + - - +
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Residues in contact with GLU 148 (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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143C ALA 3.9 4.2 - - - +
144C ILE* 2.9 23.6 - - + -
145C ASN* 2.5 67.1 + - - +
147C HIS* 1.3 70.1 - - + +
149C GLN* 1.3 60.8 + - - +
151C GLN* 3.7 12.5 - - - +
152C ILE* 2.8 37.6 + - - +
169C PHE* 4.4 21.9 - - + -
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Residues in contact with GLN 149 (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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142C ARG* 4.9 8.7 - - - +
144C ILE* 3.1 37.7 + - + +
145C ASN* 2.9 24.6 + - - +
146C LYS* 3.1 24.1 + - - +
148C GLU* 1.3 75.7 - - - +
150C GLU* 1.3 56.3 + - - +
151C GLN 3.1 0.2 + - - -
152C ILE* 3.2 1.1 + - - -
153C SER* 2.8 36.2 + - - -
179C TYR* 3.7 24.8 + - + -
180C PHE* 3.7 17.2 - - + -
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Residues in contact with GLU 150 (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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146C LYS 2.9 14.9 + - - +
147C HIS* 3.6 10.5 - - - +
149C GLN* 1.3 76.8 - - - +
151C GLN* 1.3 66.6 + - - +
153C SER* 3.4 15.6 - - - -
154C ARG* 2.4 43.8 + - - +
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Residues in contact with GLN 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 HIS 3.0 16.9 + - - +
148C GLU* 3.7 9.9 - - - +
149C GLN 3.1 0.2 - - - -
150C GLU* 1.3 73.6 - - - +
152C ILE* 1.3 69.4 + - - +
154C ARG* 2.8 38.3 + - - +
155C LEU* 3.0 32.6 + - + +
169C PHE* 4.0 23.8 - - + -
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Residues in contact with ILE 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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144C ILE* 3.8 22.9 - - + -
148C GLU 2.8 23.5 + - - +
149C GLN 3.7 2.7 - - - +
151C GLN* 1.3 73.7 - - - +
153C SER* 1.3 64.8 + - - +
155C LEU* 3.3 9.3 + - + +
156C LEU* 3.0 30.4 + - + +
165C LEU* 3.9 13.0 - - + -
169C PHE* 3.5 54.1 - - + -
176C LEU* 4.4 13.9 - - + -
180C PHE* 3.6 23.3 - - + -
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Residues in contact with SER 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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149C GLN 2.8 16.9 + - - -
150C GLU* 3.4 15.5 - - - -
151C GLN 2.8 0.6 + - - -
152C ILE* 1.3 77.8 - - - +
154C ARG* 1.3 64.9 + - - +
156C LEU* 3.1 5.2 + - - +
157C GLU* 3.0 20.9 + - - +
180C PHE* 4.1 20.9 - - - -
185C ILE* 5.7 1.2 - - - +
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Residues in contact with ARG 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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150C GLU* 2.4 46.1 + - - +
151C GLN* 2.8 29.2 + - - +
153C SER* 1.3 77.6 - - - +
155C LEU* 1.3 66.6 + - + +
157C GLU* 2.9 10.9 + - + +
158C LYS* 2.9 23.6 + - - +
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Residues in contact with LEU 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 GLN* 3.0 41.5 + - + +
152C ILE* 3.5 13.2 - - - +
154C ARG* 1.3 78.3 - - + +
156C LEU* 1.3 60.7 + - - +
158C LYS* 3.1 9.4 + - + +
160C HIS* 2.8 49.6 + - + +
165C LEU* 3.7 30.5 - - + -
169C PHE* 4.4 9.4 - - + -
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Residues in contact with LEU 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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152C ILE* 3.0 34.3 + - + +
153C SER* 3.6 6.3 - - - +
155C LEU* 1.3 71.5 - - - +
157C GLU* 1.3 58.3 + - - +
158C LYS 3.0 5.2 - - - -
159C GLY* 3.0 17.5 + - - -
160C HIS 2.9 29.8 + - - +
162C ARG* 3.6 34.8 - - + +
165C LEU* 3.4 16.4 - - + -
176C LEU* 5.5 1.6 - - + -
180C PHE* 3.9 28.3 - - + -
185C ILE* 4.1 22.8 - - + +
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Residues in contact with GLU 157 (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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153C SER* 3.0 11.9 + - - +
154C ARG* 2.9 13.5 + - - +
156C LEU* 1.3 77.5 - - - +
158C LYS* 1.3 58.2 + - - +
159C GLY 3.1 1.4 + - - -
185C ILE* 3.9 19.5 - - + +
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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
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154C ARG 2.9 10.8 + - - +
155C LEU* 3.4 12.3 - - + +
156C LEU 3.0 0.6 - - - -
157C GLU* 1.3 76.2 - - - +
159C GLY* 1.3 59.1 + - - +
160C HIS* 3.6 17.7 + - + +
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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