Contacts of the helix formed by residues 191 - 205 (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 SER 191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153C ILE* 4.4 12.5 - - - +
157C THR* 4.7 1.2 + - - -
187C ALA 4.1 9.0 + - - -
188C ILE 3.4 9.3 + - - +
189C MET 3.4 3.2 - - - -
190C ARG* 1.3 79.7 - - - +
192C PRO* 1.3 66.4 - - - +
193C GLN* 2.9 20.5 + - - +
194C MET* 2.7 33.2 + - - +
195C VAL* 3.4 7.8 + - - +
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Residues in contact with PRO 192 (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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189C MET 4.9 0.9 - - - +
190C ARG 3.2 12.6 - - - +
191C SER* 1.3 82.2 - - - +
193C GLN* 1.3 72.2 + - - +
195C VAL* 4.6 8.7 - - + +
196C SER* 2.8 37.0 + - - -
230C ALA* 6.4 0.4 - - + -
234C SER* 5.5 3.5 - - - -
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Residues in contact with GLN 193 (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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157C THR* 3.5 21.7 - - + +
161C ASN* 5.0 0.7 - - - +
191C SER* 2.8 22.6 + - - +
192C PRO* 1.3 93.9 - - - +
194C MET* 1.3 56.1 + - - +
196C SER* 4.0 4.1 - - - -
197C ALA* 3.1 25.5 + - - +
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Residues in contact with MET 194 (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 ILE* 4.1 23.6 - - + +
156C LEU* 3.9 12.3 - - + -
157C THR* 3.4 52.2 + - - +
160C LEU* 4.0 19.1 - - + -
175C VAL* 4.1 21.8 - - + -
188C ILE* 4.1 24.5 - - + +
191C SER* 2.7 20.7 + - - +
193C GLN* 1.3 71.0 - - - +
195C VAL* 1.3 54.7 + - - +
196C SER 3.1 1.3 - - - -
197C ALA* 2.9 3.9 + - - +
198C ILE* 2.6 52.5 + - + +
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Residues in contact with VAL 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ILE* 3.8 15.3 - - + +
189C MET* 3.6 29.6 - - - +
191C SER 3.4 5.7 + - - +
192C PRO* 4.2 6.7 - - + +
194C MET* 1.3 75.3 - - - +
196C SER* 1.3 58.2 + - - +
198C ILE* 3.1 12.1 + - + +
199C VAL* 2.8 40.1 + - + +
218C LEU* 6.5 0.9 - - + -
221C LEU* 4.5 10.8 - - + -
230C ALA* 4.0 7.2 - - + -
231C ILE* 4.1 24.5 - - + +
234C SER* 3.7 22.0 - - - +
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Residues in contact with SER 196 (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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192C PRO* 2.8 22.7 + - - -
193C GLN* 4.0 5.6 - - - -
195C VAL* 1.3 77.1 - - - +
197C ALA* 1.3 57.1 + - - +
199C VAL* 3.3 3.4 + - - +
200C ARG* 2.9 32.9 + - - +
234C SER* 4.4 23.9 + - - -
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Residues in contact with ALA 197 (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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157C THR* 4.3 4.7 - - + +
160C LEU* 3.5 29.4 - - + -
161C ASN* 3.9 16.4 - - - +
193C GLN 3.1 14.5 + - - +
194C MET* 2.9 11.8 + - - +
196C SER* 1.3 77.0 - - - +
198C ILE* 1.3 65.7 + - - +
200C ARG* 3.5 4.9 + - - +
201C THR* 2.9 29.5 + - - -
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Residues in contact with ILE 198 (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* 3.9 14.8 - - + -
175C VAL* 4.3 8.5 - - + -
188C ILE* 4.1 11.2 - - + -
194C MET* 2.6 41.2 + - + +
195C VAL* 3.4 13.5 - - + +
197C ALA* 1.3 74.5 - - - +
199C VAL* 1.3 64.1 + - + +
201C THR* 3.8 2.4 - - - -
202C MET* 3.1 21.8 + - - +
214C THR* 3.5 36.3 - - + +
217C THR* 3.5 26.7 - - + -
218C LEU* 4.4 13.5 - - + -
221C LEU* 4.7 4.7 - - + -
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Residues in contact with VAL 199 (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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195C VAL* 2.8 37.7 + - + +
196C SER* 3.7 3.8 - - - +
198C ILE* 1.3 73.3 - - + +
200C ARG* 1.3 63.9 + - - +
201C THR 3.2 0.2 + - - -
202C MET* 3.3 6.4 + - - +
203C GLN* 3.1 25.4 + - - +
218C LEU* 4.4 16.6 - - + -
231C ILE* 5.0 1.3 - - - +
234C SER* 4.1 13.5 - - - +
235C GLY 3.5 29.2 - - - +
236C GLY* 3.9 15.5 - - - +
239C ALA* 3.7 16.0 - - + +
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Residues in contact with ARG 200 (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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196C SER 2.9 20.9 + - - +
197C ALA* 4.0 4.5 - - - +
199C VAL* 1.3 74.0 - - - +
201C THR* 1.3 58.1 + - - +
203C GLN* 3.7 7.2 + - - +
204C ASN* 2.9 42.4 + - - +
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Residues in contact with THR 201 (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* 3.6 24.2 + - + +
165C GLN* 5.9 1.6 - - - +
168C VAL* 4.3 15.9 - - + +
172C ALA* 5.2 2.5 - - + -
197C ALA 2.9 20.2 + - - -
198C ILE* 3.8 3.8 - - - -
200C ARG* 1.3 75.3 - - - +
202C MET* 1.3 61.2 + - - +
203C GLN 3.1 2.0 - - - -
204C ASN* 2.9 4.4 + - - +
205C THR* 2.6 39.4 + - - +
210C THR* 3.9 27.4 - - + -
214C THR* 4.4 8.3 - - + -
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Residues in contact with MET 202 (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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198C ILE 3.1 12.4 + - - +
199C VAL* 3.3 4.5 + - - +
201C THR* 1.3 78.5 - - - +
203C GLN* 1.3 59.7 + - - +
205C THR* 3.3 17.6 - - - +
211C ALA* 4.9 5.6 - - - +
214C THR* 3.4 23.8 + - - +
215C ALA* 3.5 31.2 - - + +
218C LEU* 3.1 35.9 - - + -
239C ALA* 4.3 10.5 - - - +
240C LEU* 3.9 13.2 - - + -
243C MET* 3.0 55.5 - - - +
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Residues in contact with GLN 203 (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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199C VAL* 3.1 17.5 + - - +
200C ARG* 4.0 8.1 - - - +
201C THR 3.1 0.6 - - - -
202C MET* 1.3 79.3 - - - +
204C ASN* 1.3 66.1 + - - +
205C THR 5.0 0.6 - - - +
235C GLY 5.3 1.4 + - - +
238C PRO* 4.2 9.7 + - - +
239C ALA* 3.7 35.8 - - + +
242C LYS* 4.2 27.4 - - + +
243C MET* 3.9 8.5 - - - -
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Residues in contact with ASN 204 (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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200C ARG* 2.9 27.4 + - - +
201C THR* 2.9 5.3 + - - +
203C GLN* 1.3 90.1 - - - +
205C THR* 1.3 71.7 + - - +
206C ASN* 4.4 3.6 - - - +
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Residues in contact with THR 205 (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* 5.1 11.8 + - - -
169C ASN* 4.6 0.3 + - - -
201C THR* 2.6 28.0 + - - +
202C MET* 3.3 22.1 - - - +
203C GLN 5.0 0.3 - - - +
204C ASN* 1.3 82.5 - - - +
206C ASN* 1.3 63.5 + - - +
207C ASP* 2.8 19.3 + - - +
210C THR* 3.1 36.4 + - + +
211C ALA* 4.4 10.3 - - + +
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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