Contacts of the helix formed by residues 164 - 179 (chain C) in PDB entry 1JPW
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 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C ASP* 2.6 16.6 + - - +
163C GLU* 1.3 77.0 - - - +
165C GLN* 1.3 59.5 + - - +
166C VAL* 2.8 22.9 + - - +
167C VAL* 3.1 29.3 + - + +
168C VAL* 3.2 13.9 + - - +
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Residues in contact with GLN 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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162C ASP 5.1 2.4 + - - -
163C GLU 3.0 17.5 + - - +
164C ASP* 1.3 70.3 - - - +
166C VAL* 1.3 61.4 + - + +
168C VAL* 4.0 27.3 - - - +
169C ASN* 3.3 29.8 + - - +
201C THR* 5.9 0.9 - - - +
205C THR* 5.1 12.5 + - - -
206C ASN 5.5 1.2 + - - -
210C THR* 5.9 0.5 - - - +
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Residues in contact with VAL 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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164C ASP* 2.8 16.9 + - - +
165C GLN* 1.3 79.6 - - + +
167C VAL* 1.3 68.1 + - + +
168C VAL 3.1 1.1 - - - -
169C ASN* 3.0 14.1 + - + +
170C LYS* 3.1 26.7 + - + +
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Residues in contact with VAL 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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159C LEU* 3.6 34.8 - - + -
162C ASP* 4.0 19.3 - - + +
164C ASP* 3.1 24.8 + - + +
166C VAL* 1.3 78.0 - - + +
168C VAL* 1.3 57.5 + - - +
170C LYS* 4.4 22.8 - - + +
171C ALA* 3.1 26.3 + - - +
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Residues in contact with VAL 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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159C LEU 3.3 18.6 - - - +
160C LEU* 2.9 25.7 - - + +
162C ASP* 3.6 25.1 - - + +
164C ASP 3.3 16.2 - - - +
165C GLN* 4.1 26.0 - - - +
166C VAL 3.1 0.8 - - - -
167C VAL* 1.3 75.9 - - - +
169C ASN* 1.3 60.0 + - - +
171C ALA* 3.9 1.5 - - - +
172C ALA* 3.1 27.4 + - - +
201C THR* 4.3 20.6 - - + -
210C THR* 5.3 1.3 - - + -
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Residues in contact with ASN 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 GLN* 3.3 23.5 + - - +
166C VAL* 3.0 7.2 + - + +
168C VAL* 1.3 75.7 - - - +
170C LYS* 1.3 66.9 + - - +
171C ALA 3.1 1.3 - - - -
172C ALA* 3.1 7.1 + - - +
173C VAL* 3.0 27.7 + - - +
205C THR* 4.6 0.5 + - - -
207C ASP* 2.9 32.9 + - - +
209C GLU* 5.0 3.4 - - - +
210C THR* 2.3 31.5 + - - +
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Residues in contact with LYS 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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159C LEU* 6.2 2.7 - - + -
166C VAL* 3.1 17.8 + - + +
167C VAL* 4.4 28.6 - - + +
169C ASN* 1.3 78.6 - - - +
171C ALA* 1.3 65.6 - - + +
173C VAL* 3.3 10.6 + - - +
174C MET* 3.0 45.4 + - + +
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Residues in contact with ALA 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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156C LEU* 4.1 16.3 - - + +
159C LEU* 3.9 25.8 - - + -
160C LEU* 4.3 8.5 - - + +
167C VAL 3.1 20.8 + - - +
168C VAL* 3.9 3.6 - - - +
169C ASN 3.1 0.6 - - - -
170C LYS* 1.3 80.4 - - + +
172C ALA* 1.3 66.6 + - - +
174C MET* 3.0 8.6 + - - +
175C VAL* 2.9 27.5 + - - +
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Residues in contact with ALA 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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160C LEU* 3.7 17.4 - - + +
168C VAL 3.1 17.1 + - - +
169C ASN 3.1 5.8 + - - +
171C ALA* 1.3 78.1 - - - +
173C VAL* 1.3 62.0 + - - +
175C VAL* 3.3 7.5 + - - +
176C HIS* 3.1 21.7 + - - +
201C THR* 5.2 0.7 - - + -
210C THR* 4.0 16.4 - - + +
213C CYS* 4.3 4.0 - - + +
214C THR* 3.9 25.6 + - + +
217C THR* 4.9 1.4 + - - -
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Residues in contact with VAL 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 ASN* 3.0 19.2 + - - +
170C LYS* 3.4 11.7 - - - +
172C ALA* 1.3 77.6 - - + +
174C MET* 1.3 64.5 + - + +
176C HIS* 3.1 14.3 + - - +
177C GLN* 3.2 17.3 + - + +
209C GLU* 4.6 18.4 - - + +
210C THR* 5.8 1.6 - - - -
213C CYS* 3.9 26.9 - - + -
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Residues in contact with MET 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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156C LEU* 3.5 32.1 - - + -
159C LEU* 5.2 4.7 - - + -
170C LYS* 3.0 29.1 + - + +
171C ALA* 3.0 11.3 + - + +
173C VAL* 1.3 76.8 - - + +
175C VAL* 1.3 63.4 + - - +
177C GLN* 3.3 9.3 + - - +
178C LEU* 3.1 26.4 + - + +
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Residues in contact with VAL 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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156C LEU* 3.4 34.3 - - + -
160C LEU* 4.7 5.4 - - + -
171C ALA 2.9 21.0 + - - +
172C ALA* 3.4 11.0 - - - +
173C VAL 3.2 0.2 - - - -
174C MET* 1.3 75.4 - - - +
176C HIS* 1.3 57.5 + - - +
178C LEU* 2.9 27.9 + - - +
179C SER* 3.1 6.6 + - - -
188C ILE* 3.7 24.1 - - + +
194C MET* 4.1 18.8 - - + -
198C ILE* 4.3 8.5 - - + -
217C THR* 4.3 13.9 - - + +
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Residues in contact with HIS 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 ALA 3.1 10.0 + - - +
173C VAL* 3.1 11.2 + - - +
175C VAL* 1.3 72.2 - - - +
177C GLN* 1.3 59.6 + - - +
178C LEU 2.8 4.5 - - - -
179C SER* 2.6 33.4 + - - -
180C LYS* 3.6 37.0 + - - +
212C ARG* 5.9 3.6 - - + -
213C CYS* 3.3 44.2 + - + -
216C GLY* 3.7 14.6 - - - -
217C THR* 3.2 29.8 + - - +
220C ASN* 4.4 3.6 + - - -
254C TYR* 4.5 13.0 + + - -
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Residues in contact with GLN 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 VAL* 3.2 12.1 + - + +
174C MET* 3.3 11.0 + - - +
176C HIS* 1.3 83.6 + - - +
178C LEU* 1.3 61.8 + - + +
179C SER 3.5 0.5 + - - -
180C LYS* 3.2 52.8 + - - +
181C LYS* 4.4 3.5 + - - +
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Residues in contact with LEU 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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152C ALA* 5.5 5.6 - - + -
153C ILE* 3.6 31.0 - - + -
156C LEU* 4.0 20.0 - - + -
174C MET* 3.1 14.2 + - + +
175C VAL* 2.9 14.5 + - - +
176C HIS 2.8 0.4 - - - -
177C GLN* 1.3 80.6 - - + +
179C SER* 1.3 57.7 + - - +
180C LYS 3.2 1.8 + - - -
181C LYS* 3.8 2.4 + - - -
184C SER* 3.1 46.6 - - - +
188C ILE* 4.5 9.1 - - + +
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Residues in contact with SER 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 VAL 3.1 3.9 + - - -
176C HIS* 2.6 29.1 + - - -
178C LEU* 1.3 71.2 - - - +
180C LYS* 1.3 58.0 + - - -
181C LYS 3.5 1.8 - - - -
185C ARG* 2.6 46.2 + - - +
188C ILE* 4.6 7.0 - - - -
217C THR* 3.6 32.6 - - - -
220C ASN* 3.2 23.4 + - - +
221C LEU* 5.0 1.6 - - - -
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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