Contacts of the helix formed by residues 158 - 178 (chain C) in PDB entry 3J8B
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 GLU 158 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157C GLY* 1.3 68.1 - - - -
159C GLY* 1.3 61.2 + - - +
161C ILE* 3.1 9.1 + - - +
162C VAL* 2.9 30.9 + - - +
209C PHE* 6.4 1.6 - - + -
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Residues in contact with GLY 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C GLY 3.5 0.4 - - - -
158C GLU* 1.3 78.5 - - - +
160C VAL* 1.3 56.7 + - - +
162C VAL* 4.0 5.3 - - - +
163C LYS* 2.9 34.1 + - - +
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C VAL* 5.4 10.8 - - + -
148C VAL 6.0 0.4 - - - -
150C ILE* 5.6 1.3 - - + -
155C ASN 3.4 22.0 - - - +
156C LEU 5.0 0.2 - - - -
157C GLY* 3.3 14.9 + - - +
158C GLU 3.1 0.2 - - - -
159C GLY* 1.3 76.9 - - - +
161C ILE* 1.3 56.8 + - - +
163C LYS* 4.3 2.8 - - - +
164C ILE* 2.9 31.6 + - - +
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Residues in contact with ILE 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C VAL 5.3 7.0 - - - +
157C GLY 3.2 8.2 + - - +
158C GLU* 3.1 13.1 + - - +
160C VAL* 1.3 79.0 - - - +
162C VAL* 1.3 57.8 + - - +
164C ILE* 3.2 6.1 + - - +
165C LYS* 2.9 31.1 + - - +
201C ILE* 5.6 10.3 - - + -
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Residues in contact with VAL 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C GLU 2.9 15.4 + - - +
159C GLY* 4.0 6.1 - - - +
161C ILE* 1.3 76.8 - - - +
163C LYS* 1.3 57.6 + - - +
165C LYS* 3.3 5.2 + - - +
166C PHE* 2.9 31.5 + - - +
198C LEU* 6.3 1.3 - - - -
201C ILE* 6.2 3.8 - - + +
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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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123C LEU* 6.0 2.1 - - - +
159C GLY 2.9 18.4 + - - +
160C VAL* 4.3 2.9 - - - +
162C VAL* 1.3 75.1 - - - +
164C ILE* 1.3 62.8 + - - +
166C PHE* 4.0 7.5 - - - +
167C ASN* 3.8 16.6 + - - +
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Residues in contact with ILE 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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123C LEU* 6.4 2.5 - - - -
144C LEU* 5.7 2.4 - - - +
148C VAL* 4.6 25.6 - - + +
160C VAL 2.9 21.5 + - - +
161C ILE* 3.4 7.0 - - - +
163C LYS* 1.3 76.4 - - - +
165C LYS* 1.3 61.1 + - - +
167C ASN* 3.4 5.4 + - - +
168C ILE* 2.9 27.3 + - - +
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Residues in contact with LYS 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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161C ILE 2.9 16.0 + - - +
162C VAL* 3.9 4.9 - - - +
164C ILE* 1.3 75.7 - - - +
166C PHE* 1.3 57.4 + - - +
168C ILE* 2.7 26.2 + - - -
169C ILE* 3.0 17.8 + - - +
194C CYS* 5.4 5.4 - - + +
198C LEU* 4.2 26.2 - - + +
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Residues in contact with PHE 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 VAL 2.9 17.8 + - - +
163C LYS* 4.1 9.9 - - - +
164C ILE 3.2 0.2 - - - -
165C LYS* 1.3 77.6 - - - +
167C ASN* 1.3 58.4 + - - +
169C ILE* 4.6 3.9 + - - +
170C ALA* 4.7 9.4 + - - +
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Residues in contact with ASN 167 (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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127C LEU* 5.9 7.0 - - + -
163C LYS 3.8 9.2 + - - +
164C ILE 3.4 7.1 + - - +
165C LYS 3.1 0.4 - - - -
166C PHE* 1.3 78.1 - - - +
168C ILE* 1.3 58.6 + - - +
169C ILE 3.6 0.4 - - - -
170C ALA* 4.6 2.6 - - - +
171C SER* 3.1 24.9 + - - -
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Residues in contact with ILE 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 4.9 17.3 - - + -
164C ILE 2.9 17.4 + - - +
165C LYS* 2.7 14.6 + - - +
167C ASN* 1.3 78.2 - - - +
169C ILE* 1.3 65.0 + - - +
171C SER* 3.2 18.1 - - - -
172C LEU* 3.2 9.9 + - - +
194C CYS* 6.0 5.2 - - + -
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Residues in contact with ILE 169 (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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165C LYS 3.0 12.5 + - - +
166C PHE* 5.1 3.4 - - - +
167C ASN 3.6 0.2 - - - -
168C ILE* 1.3 76.1 - - - +
170C ALA* 1.3 63.3 + - - +
172C LEU* 3.0 17.5 + - - +
173C TYR* 3.1 12.0 + - - +
191C CYS* 5.9 5.1 - - + +
194C CYS* 5.5 13.6 - - + +
195C ILE* 5.9 6.3 - - + +
237C LEU* 5.0 16.6 - - + -
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Residues in contact with ALA 170 (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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166C PHE 4.7 9.0 + - - +
167C ASN* 4.4 4.5 + - - +
168C ILE 3.5 0.2 - - - -
169C ILE* 1.3 78.6 - - - +
171C SER* 1.3 57.4 + - - +
173C TYR* 3.7 8.9 - - - +
174C ASP* 2.8 34.5 + - - +
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Residues in contact with SER 171 (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 ARG* 5.5 1.4 - - - +
140C GLN* 5.9 4.0 - - - -
141C ILE* 5.8 12.1 - - - +
144C LEU* 6.1 3.1 - - - -
167C ASN 3.1 21.4 + - - -
168C ILE* 3.2 12.8 + - - -
170C ALA* 1.3 80.5 - - - +
172C LEU* 1.3 59.7 + - - +
174C ASP* 4.1 4.4 - - - +
175C TYR* 3.6 17.8 + - - +
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Residues in contact with LEU 172 (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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141C ILE* 5.8 8.0 - - + +
168C ILE 3.2 6.3 + - - +
169C ILE* 3.0 11.0 + - - +
171C SER* 1.3 77.4 - - - +
173C TYR* 1.3 67.7 + - - +
175C TYR* 3.1 15.5 + - - +
176C ASN* 3.5 10.0 + - - +
191C CYS* 4.9 16.6 - - + -
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Residues in contact with TYR 173 (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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169C ILE 3.1 10.5 + - - +
170C ALA* 3.8 11.2 - - - +
172C LEU* 1.3 80.7 - - - +
174C ASP* 1.3 62.9 + - - +
176C ASN* 3.5 14.5 + - - +
177C PRO* 3.5 11.3 - - - +
240C ARG* 5.1 15.7 - - + -
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Residues in contact with ASP 174 (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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170C ALA 2.8 19.3 + - - +
171C SER* 4.1 5.6 - - - +
173C TYR* 1.3 75.6 - - - +
175C TYR* 1.3 64.5 + - - +
177C PRO* 3.2 17.5 - - - +
178C ASN* 3.3 12.8 + - - +
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Residues in contact with TYR 175 (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 ARG* 3.5 33.0 - - + +
171C SER 3.6 10.0 + - - +
172C LEU* 3.1 11.5 + - - +
174C ASP* 1.3 78.9 - - - +
176C ASN* 1.3 64.1 + - - +
177C PRO 3.4 0.2 - - - -
178C ASN* 3.5 6.6 + - - +
179C LEU* 3.4 20.1 + - - +
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Residues in contact with ASN 176 (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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172C LEU 3.5 5.6 + - - +
173C TYR* 3.5 10.4 + - - +
174C ASP 3.2 0.4 - - - -
175C TYR* 1.3 80.3 - - - +
177C PRO* 1.3 58.1 - - - +
179C LEU* 2.9 28.9 + - - +
180C ALA 4.7 1.7 - - - +
181C THR* 5.2 2.6 + - - -
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Residues in contact with PRO 177 (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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173C TYR 3.5 8.5 - - - +
174C ASP* 3.2 14.1 - - - +
176C ASN* 1.3 79.4 - - - +
178C ASN* 1.3 62.6 + - - +
179C LEU 3.1 7.6 - - - +
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Residues in contact with ASN 178 (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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174C ASP 3.3 8.4 + - - +
175C TYR* 3.8 9.4 - - - +
176C ASN 3.3 0.2 - - - -
177C PRO* 1.3 80.1 - - - +
179C LEU* 1.3 61.3 + - - +
180C ALA 3.9 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
------------------------------------------------------------
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