Contacts of the helix formed by residues 185 - 201 (chain j) in PDB entry 5GJQ
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 THR 185 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39j ALA* 3.8 4.5 - - - -
41j ASP* 3.6 13.2 - - - +
183j GLU 4.7 6.1 - - - +
184j MET* 1.3 79.2 - - - +
186j LEU* 1.3 54.6 + - - +
187j LYS* 3.6 7.7 + - - +
188j SER* 2.7 45.6 + - - +
189j ALA* 2.8 23.6 + - - +
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Residues in contact with LEU 186 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39j ALA* 4.6 2.0 - - + -
41j ASP* 2.9 25.8 + - - +
42j GLY* 4.7 12.6 - - - -
43j VAL 4.7 4.7 - - - +
44j LEU* 4.9 10.5 - - + -
185j THR* 1.3 73.4 - - - +
187j LYS* 1.3 58.1 + - - +
189j ALA* 3.9 4.2 - - + +
190j LEU* 3.0 38.3 + - + +
215j THR* 3.8 32.3 - - + +
217j THR* 3.8 28.0 - - + -
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Residues in contact with LYS 187 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185j THR* 3.2 8.4 + - - +
186j LEU* 1.3 78.1 - - - +
188j SER* 1.3 65.1 + - - +
190j LEU* 3.2 21.2 + - + +
191j ALA* 3.0 21.0 + - - +
236j LEU* 5.2 16.1 - - - +
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Residues in contact with SER 188 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180j LYS* 2.6 32.1 + - - -
183j GLU 4.7 2.1 + - - -
184j MET* 4.1 0.3 - - - -
185j THR* 2.7 32.2 + - - +
187j LYS* 1.3 78.9 - - - +
189j ALA* 1.3 54.2 + - - +
191j ALA* 3.1 11.2 + - - +
192j LEU* 2.9 28.4 + - - +
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Residues in contact with ALA 189 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37j ILE* 4.3 11.3 - - + +
38j LEU 5.0 2.7 - - - +
39j ALA* 4.7 9.6 - - + -
44j LEU* 3.8 25.7 - - + +
180j LYS* 3.7 10.7 - - - +
185j THR 2.8 24.1 + - - +
186j LEU* 3.9 6.3 - - + +
188j SER* 1.3 72.2 + - - +
190j LEU* 1.3 57.6 + - - +
192j LEU* 3.3 7.6 + - - +
193j ALA* 2.8 29.2 + - - +
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Residues in contact with LEU 190 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44j LEU* 4.8 9.0 - - + -
186j LEU* 3.0 33.3 + - + +
187j LYS* 3.2 19.5 + - + +
189j ALA* 1.3 74.7 - - - +
191j ALA* 1.3 65.8 + - - +
193j ALA* 3.2 7.3 + - + +
194j ILE* 3.0 23.6 + - - +
213j ILE* 4.0 36.1 - - + +
215j THR* 5.1 5.8 - - + -
228j LEU* 4.0 20.0 - - + -
236j LEU* 3.9 30.3 - - + +
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Residues in contact with ALA 191 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187j LYS 3.0 12.2 + - - +
188j SER* 3.2 13.2 - - - +
190j LEU* 1.3 75.6 - - - +
192j LEU* 1.3 63.3 + - - +
194j ILE* 3.2 8.7 + - - +
195j LYS* 3.0 22.4 + - - +
236j LEU* 4.4 6.8 - - + +
240j HIS* 4.8 3.3 + - - +
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Residues in contact with LEU 192 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37j ILE* 5.3 5.6 - - + -
174j MET 4.9 0.9 - - - +
175j LEU* 3.6 23.6 - - + -
178j ASP* 3.9 37.7 - - + +
179j TYR* 4.4 10.5 - - + -
180j LYS* 4.0 26.0 - - + -
188j SER 2.9 12.8 + - - +
189j ALA* 3.5 10.1 - - - +
191j ALA* 1.3 76.0 - - - +
193j ALA* 1.3 56.3 + - - +
195j LYS* 3.2 10.4 + - + +
196j VAL* 2.9 49.6 + - + +
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Residues in contact with ALA 193 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35j LEU* 4.8 15.5 - - + +
37j ILE* 5.8 2.0 - - + +
44j LEU* 4.1 24.0 - - + -
46j ALA* 4.7 11.0 - - + -
189j ALA 2.8 18.7 + - - +
190j LEU* 3.2 11.9 + - + +
192j LEU* 1.3 75.5 - - - +
194j ILE* 1.3 56.5 + - - +
196j VAL* 4.0 1.2 - - - +
197j LEU* 2.9 35.3 + - - +
213j ILE* 4.9 6.3 - - + -
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Residues in contact with ILE 194 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190j LEU 3.0 12.2 + - - +
191j ALA* 3.6 10.1 - - - +
193j ALA* 1.3 75.3 - - - +
195j LYS* 1.3 57.3 + - - +
197j LEU* 3.9 4.6 - - - +
198j ASN* 3.0 31.2 + - - +
206j LEU* 4.3 7.7 - - + +
213j ILE* 5.6 4.8 - - + +
236j LEU* 4.4 22.7 - - + +
237j ILE* 5.2 3.1 - - + +
240j HIS* 4.3 21.8 - - + -
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Residues in contact with LYS 195 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174j MET* 4.1 20.0 - - + -
178j ASP* 2.6 41.9 + - - +
191j ALA 3.0 13.4 + - - +
192j LEU* 3.3 15.7 - - + +
193j ALA 3.2 0.2 - - - -
194j ILE* 1.3 73.1 - - - +
196j VAL* 1.3 67.6 + - - +
198j ASN* 3.0 14.2 + - - +
199j LYS* 3.0 14.4 + - + +
240j HIS* 3.6 26.8 + - + +
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Residues in contact with VAL 196 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35j LEU* 4.1 18.4 - - + -
171j ALA* 3.6 36.8 - - + +
174j MET* 3.9 26.9 - - + -
175j LEU* 4.1 14.4 - - + -
192j LEU* 2.9 42.7 + - + +
193j ALA* 4.2 2.7 - - - +
195j LYS* 1.3 73.9 - - + +
197j LEU* 1.3 54.0 + - - +
199j LYS* 3.2 1.0 + - - -
200j THR* 2.8 42.0 + - + +
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Residues in contact with LEU 197 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35j LEU* 4.5 11.8 - - + +
46j ALA* 5.9 5.2 - - + -
193j ALA 2.9 20.9 + - - +
194j ILE* 3.9 4.9 - - - +
196j VAL* 1.3 76.1 - - - +
198j ASN* 1.3 62.8 + - - +
200j THR* 3.5 6.5 + - - -
201j MET* 3.1 30.5 + - - +
206j LEU* 3.9 14.4 - - + +
211j VAL* 4.8 11.7 - - + -
213j ILE* 6.5 0.9 - - + -
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Residues in contact with ASN 198 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194j ILE 3.0 18.8 + - - +
195j LYS 3.0 6.5 + - - +
197j LEU* 1.3 79.5 - - - +
199j LYS* 1.3 63.6 + - - +
201j MET* 3.9 10.6 - - - +
204j SER* 4.6 12.4 + - - -
205j LYS* 4.2 16.5 + - - +
206j LEU* 4.0 28.7 - - + +
240j HIS* 3.7 27.4 + - + +
244j GLU* 4.5 9.1 + - - -
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Residues in contact with LYS 199 (chain j).
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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424I GLU* 3.5 33.0 + - - -
170j ALA* 6.0 5.2 - - + -
174j MET* 3.5 40.2 - - + +
195j LYS* 3.0 12.3 + - + +
196j VAL 4.0 0.2 - - - +
198j ASN* 1.3 82.3 - - - +
200j THR* 1.3 63.0 + - + +
201j MET 3.7 4.5 + - - +
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Residues in contact with THR 200 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33j THR* 4.3 21.3 + - - +
35j LEU* 5.0 0.5 - - - +
166j ASN* 5.1 0.3 + - - -
167j ASN* 3.0 42.0 + - - +
170j ALA* 4.2 9.6 - - + -
171j ALA* 3.8 37.2 - - + +
174j MET* 4.7 3.1 - - + -
196j VAL* 2.8 32.2 + - + +
197j LEU* 3.5 6.8 + - - -
199j LYS* 1.3 77.1 - - - +
201j MET* 1.3 66.8 + - - +
202j ASP* 3.3 0.7 + - - -
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Residues in contact with MET 201 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33j THR* 5.5 1.3 - - - -
48j GLU* 5.0 21.1 - - + +
197j LEU 3.1 21.1 + - - +
198j ASN 3.9 7.9 - - - +
199j LYS 3.5 7.3 - - - +
200j THR* 1.3 78.7 + - - +
202j ASP* 1.3 66.2 + - - +
203j VAL* 3.5 11.2 + - + +
204j SER* 4.4 1.0 + - - -
206j LEU* 3.8 20.6 - - + -
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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