Contacts of the helix formed by residues 191 - 206 (chain X) in PDB entry 5JPQ
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 191 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189X THR 3.9 0.6 + - - -
190X LYS* 1.3 73.1 - - - +
192X PRO* 1.3 66.6 - - - +
193X LYS* 4.3 2.0 - - + +
194X GLU* 3.0 24.2 + - + +
195X ILE* 3.2 11.0 + - - +
51d ALA* 4.1 14.8 - - + +
53d VAL* 3.1 36.2 - - + +
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Residues in contact with PRO 192 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183X ALA* 3.7 29.4 - - + +
190X LYS 3.6 3.6 - - - +
191X ASP* 1.3 70.5 - - - +
193X LYS* 1.3 56.5 + - - +
195X ILE* 3.2 6.3 + - + +
196X TYR* 3.1 26.3 + - - +
222X ASP* 4.5 17.5 - - + -
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Residues in contact with LYS 193 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191X ASP* 3.1 1.6 - - + +
192X PRO* 1.3 77.4 - - - +
194X GLU* 1.3 62.9 + - - +
196X TYR* 3.8 7.7 + - - +
197X LYS* 3.6 19.2 + - - +
51d ALA* 4.5 26.7 - - + +
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Residues in contact with GLU 194 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190X LYS* 5.5 4.0 - - + -
191X ASP* 3.0 22.9 + - + +
193X LYS* 1.3 75.0 - - - +
195X ILE* 1.3 65.2 + - - +
197X LYS* 3.4 7.3 + - - +
198X THR* 3.2 23.2 + - - -
51d ALA 5.4 0.4 + - - -
53d VAL* 4.9 14.1 - - + +
54d PRO 5.5 2.9 - - - +
55d PRO 6.0 1.1 - - - +
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Residues in contact with ILE 195 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181X ILE* 6.1 1.1 - - + -
183X ALA* 4.7 18.4 - - + +
186X ILE* 5.4 8.1 - - + -
187X ASP* 6.5 0.4 - - + -
190X LYS* 5.4 8.2 - - + +
191X ASP 3.2 11.2 + - - +
192X PRO* 3.2 12.1 + - + +
194X GLU* 1.3 74.2 - - - +
196X TYR* 1.3 66.1 + - - +
198X THR* 3.1 5.6 + - - -
199X GLU* 3.0 27.1 + - - +
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Residues in contact with TYR 196 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181X ILE* 5.2 10.3 - - + -
192X PRO 3.1 14.2 + - - +
193X LYS* 4.1 8.7 - - - +
194X GLU 3.4 0.2 - - - -
195X ILE* 1.3 76.2 - - - +
197X LYS* 1.3 62.3 + - - +
199X GLU* 4.2 3.8 - - - +
200X VAL* 3.2 25.1 + - - +
224X ALA* 4.7 19.5 - - + -
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Residues in contact with LYS 197 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193X LYS 3.6 9.9 + - - +
194X GLU* 3.4 11.3 + - - +
195X ILE 3.1 0.4 - - - -
196X TYR* 1.3 81.1 - - - +
198X THR* 1.3 61.2 + - - +
200X VAL* 3.6 4.6 + - - +
201X GLU* 3.2 21.3 + - - +
141d HIS* 6.4 2.2 - - + -
143d ILE* 6.3 2.2 - - + -
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Residues in contact with THR 198 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194X GLU 3.2 14.2 + - - -
195X ILE* 3.1 6.4 + - - -
197X LYS* 1.3 74.3 - - - +
199X GLU* 1.3 63.7 + - - +
201X GLU* 3.6 9.1 - - - +
202X LYS* 3.4 16.6 + - - +
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Residues in contact with GLU 199 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160X THR* 4.6 19.0 - - - -
181X ILE* 5.2 11.9 - - + -
195X ILE 3.0 16.8 + - - +
196X TYR* 4.3 3.6 - - - +
198X THR* 1.3 75.4 - - - +
200X VAL* 1.3 66.4 + - - +
202X LYS* 2.9 24.6 + - - +
203X LEU* 3.3 4.9 + - - +
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Residues in contact with VAL 200 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196X TYR 3.2 17.6 + - - +
197X LYS* 3.9 5.6 - - - +
199X GLU* 1.3 76.5 - - - +
201X GLU* 1.3 57.8 + - - +
203X LEU* 2.9 25.9 + - - +
204X GLU* 3.0 13.2 + - - +
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Residues in contact with GLU 201 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197X LYS 3.2 11.4 + - - +
198X THR* 3.6 13.0 - - - +
199X GLU 3.2 0.4 - - - -
200X VAL* 1.3 78.3 - - - +
202X LYS* 1.3 51.6 + - - +
204X GLU* 3.8 7.9 - - - +
205X ASN* 2.7 37.9 + - - +
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Residues in contact with LYS 202 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160X THR* 4.8 13.7 - - - -
161X ASP 6.1 0.4 - - - +
198X THR 3.4 7.4 + - - +
199X GLU* 2.9 17.0 + - - +
201X GLU* 1.3 77.2 - - - +
203X LEU* 1.3 57.3 + - - +
205X ASN* 3.9 5.1 - - - +
206X SER* 3.0 26.3 + - - -
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Residues in contact with LEU 203 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199X GLU 3.3 3.9 + - - +
200X VAL* 2.9 14.6 + - - +
202X LYS* 1.3 77.2 - - - +
204X GLU* 1.3 62.6 + - - +
206X SER* 3.4 13.2 + - - -
208X PHE* 2.9 42.9 + - + +
228X SER* 5.6 4.5 - - - -
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Residues in contact with GLU 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200X VAL 3.0 13.7 + - - +
201X GLU* 3.8 8.3 - - - +
203X LEU* 1.3 78.2 - - - +
205X ASN* 1.3 56.4 + - - +
206X SER 2.8 14.9 - - - +
207X ASN* 4.2 2.9 - - - +
208X PHE 3.7 14.7 + - - +
210X THR* 6.2 3.6 - - - +
122d THR* 5.7 7.4 - - - +
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Residues in contact with ASN 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201X GLU 2.7 22.4 + - - +
202X LYS* 4.2 4.7 - - - +
204X GLU* 1.3 68.6 - - - +
206X SER* 1.3 65.3 + - - +
122d THR* 5.7 11.2 - - - -
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Residues in contact with SER 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164X ILE* 5.2 14.4 - - - -
202X LYS 3.0 14.2 + - - -
203X LEU* 3.4 11.9 - - - -
204X GLU 2.8 8.8 - - - +
205X ASN* 1.3 82.3 - - - +
207X ASN* 1.3 66.8 + - - +
208X PHE* 4.7 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