Contacts of the helix formed by residues 167 - 183 (chain C) in PDB entry 1JPM
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 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C ASP* 1.3 82.0 - - - +
168C ILE* 1.3 65.3 + - - +
169C ALA* 4.0 7.4 - - + +
170C THR* 3.1 27.4 + - - +
171C ASP* 3.1 20.4 + - - -
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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
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166C ASP 3.7 1.5 + - - +
167C ASP* 1.3 72.4 - - - +
169C ALA* 1.3 58.1 + - - +
171C ASP* 3.1 11.1 + - + +
172C ILE* 2.9 44.6 + - + +
196C TRP* 4.2 15.3 - - + +
200C GLU* 3.7 43.1 - - + +
203C THR* 5.0 8.3 - - + -
204C ALA* 3.7 29.8 - - + +
207C LYS* 4.2 9.6 - - + -
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Residues in contact with ALA 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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167C ASP* 3.1 7.7 - - + +
168C ILE* 1.3 81.2 - - - +
170C THR* 1.3 57.3 + - - +
172C ILE* 3.3 9.0 + - - +
173C ALA* 2.8 32.2 + - - +
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Residues in contact with THR 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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141C PRO* 6.1 1.6 - - + -
166C ASP* 4.2 7.0 - - + -
167C ASP* 3.1 35.7 + - - +
169C ALA* 1.3 77.1 - - - +
171C ASP* 1.3 64.4 + - - +
173C ALA* 3.8 5.6 - - + +
174C ARG* 3.1 57.8 + - + +
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Residues in contact with ASP 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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162C LYS 4.3 0.7 - - - +
163C VAL* 3.4 35.6 - - + +
164C GLY* 3.0 23.4 + - - -
166C ASP 4.3 6.2 + - - +
167C ASP 3.1 15.4 + - - +
168C ILE* 3.4 10.8 - - + +
170C THR* 1.3 77.3 - - - +
172C ILE* 1.3 58.9 + - + +
174C ARG* 3.2 25.7 + - - +
175C ILE* 2.8 37.5 + - + +
196C TRP* 3.8 13.2 + - + -
208C MET* 6.0 1.8 - - - -
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Residues in contact with ILE 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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168C ILE* 2.9 29.1 + - + +
169C ALA* 3.7 7.4 - - - +
171C ASP* 1.3 74.1 - - + +
173C ALA* 1.3 57.7 + - - +
175C ILE* 3.9 6.0 - - - +
176C GLN* 2.7 53.9 + - - +
204C ALA* 4.4 1.1 - - + +
207C LYS* 3.3 44.6 - - + -
208C MET* 3.8 20.4 - - + -
211C ALA* 5.1 4.0 - - + -
213C LEU* 4.5 9.2 - - + -
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Residues in contact with ALA 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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141C PRO* 3.7 14.3 - - + +
169C ALA 2.8 21.6 + - - +
170C THR* 3.8 7.0 - - - +
172C ILE* 1.3 73.6 - - - +
174C ARG* 1.3 63.3 + - + +
176C GLN* 4.0 4.0 - - - +
177C GLU* 3.1 25.3 + - - +
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Residues in contact with ARG 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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138C VAL* 3.1 28.9 - - - +
139C ASN 2.9 25.4 + - - -
141C PRO* 3.6 31.6 - - + +
144C MET* 3.4 21.0 - - + -
161C ILE* 6.0 2.2 - - + +
162C LYS 5.1 3.6 + - - -
166C ASP* 2.7 31.3 + - - +
170C THR* 3.1 35.4 + - + +
171C ASP* 3.3 26.5 + - - +
173C ALA* 1.3 76.8 - - + +
175C ILE* 1.3 61.1 + - + +
177C GLU* 3.6 2.8 + - - +
178C ILE* 3.0 30.9 + - - +
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Residues in contact with ILE 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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161C ILE* 4.4 15.3 - - + -
163C VAL* 4.1 12.1 - - + -
171C ASP* 2.8 22.4 + - + +
172C ILE 3.9 2.9 - - - +
174C ARG* 1.3 76.2 - - + +
176C GLN* 1.3 61.9 + - - +
178C ILE* 3.0 8.6 + - - +
179C ARG* 2.8 27.1 + - + +
188C LEU* 4.4 11.2 - - + -
190C LEU* 3.5 42.2 - - + -
208C MET* 3.7 13.7 - - - -
213C LEU* 3.7 21.8 - - + -
215C ILE* 3.9 16.4 - - + -
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Residues in contact with GLN 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 ILE* 2.7 33.9 + - - +
173C ALA* 4.0 4.2 - - - +
175C ILE* 1.3 72.8 - - - +
177C GLU* 1.3 61.2 + - - +
179C ARG* 4.0 0.3 - - - +
180C LYS* 3.0 28.5 + - + +
211C ALA* 3.6 33.8 - - - +
213C LEU* 3.4 21.9 - - + +
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Residues in contact with GLU 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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141C PRO* 3.1 32.7 - - + +
142C GLU* 2.5 35.2 + - - +
145C ALA* 3.5 9.2 - - + -
173C ALA 3.1 18.4 + - - +
174C ARG 3.8 2.5 - - - +
175C ILE 3.2 0.2 - - - -
176C GLN* 1.3 77.5 - - - +
178C ILE* 1.3 58.3 + - - +
180C LYS* 4.2 4.8 - - - +
181C ARG* 3.2 34.5 + - - +
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Residues in contact with ILE 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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136C VAL* 4.6 5.4 - - + -
141C PRO 5.1 0.2 - - - +
144C MET* 4.0 25.1 - - + +
145C ALA* 4.0 23.6 - - + +
148C ALA* 3.8 20.4 - - + -
159C LEU* 5.0 0.7 - - + -
161C ILE* 3.3 29.4 - - + -
174C ARG 3.0 19.7 - - - +
175C ILE* 3.0 6.6 + - - +
177C GLU* 1.3 76.2 - - - +
179C ARG* 1.3 61.4 + - - +
181C ARG* 3.1 2.4 + - - +
182C VAL* 2.9 39.4 + - + +
188C LEU* 4.0 23.8 - - + -
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Residues in contact with ARG 179 (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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175C ILE 2.8 18.6 + - - +
176C GLN 4.0 2.7 - - - +
178C ILE* 1.3 72.5 - - - +
180C LYS* 1.3 65.0 + - - +
182C VAL* 4.2 4.0 - - - +
183C GLY* 2.9 45.9 + - - -
184C SER* 3.7 22.4 + - - +
186C VAL 3.3 25.1 + - - -
188C LEU* 3.5 36.1 - - + +
212C GLY 4.3 6.3 + - - +
213C LEU* 2.5 45.7 + - + +
214C GLY* 2.6 32.1 + - - -
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Residues in contact with LYS 180 (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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176C GLN* 3.0 21.1 + - + +
177C GLU* 4.3 5.8 - - - +
179C ARG* 1.3 80.3 - - - +
181C ARG* 1.3 60.3 + - - +
183C GLY* 4.1 4.3 + - - -
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Residues in contact with ARG 181 (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 GLU* 4.7 12.7 + - - +
145C ALA* 3.6 46.7 + - + +
146C ALA* 3.8 8.7 - - - +
149C GLU* 3.7 33.6 + - + +
152C LEU* 5.8 0.2 - - - +
177C GLU* 3.2 31.7 + - - +
178C ILE 3.1 5.0 + - - +
180C LYS* 1.3 80.9 - - - +
182C VAL* 1.3 61.8 + - + +
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Residues in contact with VAL 182 (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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148C ALA* 4.0 28.9 - - + +
149C GLU* 4.0 17.3 - - - +
152C LEU* 4.3 19.7 - - + +
159C LEU* 5.0 3.8 - - + -
178C ILE* 2.9 32.5 + - + +
179C ARG* 4.0 6.5 - - - +
181C ARG* 1.3 78.2 - - + +
183C GLY* 1.3 71.4 + - - +
186C VAL* 4.1 34.0 - - + +
188C LEU* 5.2 1.6 - - + -
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Residues in contact with GLY 183 (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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179C ARG* 2.9 36.0 + - - +
180C LYS 4.1 3.7 + - - -
181C ARG 3.5 2.2 - - - -
182C VAL* 1.3 83.8 - - - +
184C SER* 1.3 61.8 + - - -
185C ALA* 3.4 4.2 + - - -
186C VAL 3.9 4.3 + - - -
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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