Contacts of the helix formed by residues 183 - 196 (chain k) 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 183 (chain k).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38k ARG* 3.4 12.5 + - - +
182k GLU* 1.3 80.9 + - - +
184k ASP* 1.3 67.2 + - - +
185k ASP* 4.2 8.7 - - - -
186k LEU* 2.9 26.6 + - - +
187k THR 3.0 11.6 + - - -
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Residues in contact with ASP 184 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38k ARG* 3.8 13.0 + - - +
39k ASP* 4.9 6.3 - - - +
40k ILE* 4.1 27.6 + - + +
183k THR* 1.3 72.6 - - - +
185k ASP* 1.3 57.7 + - - +
186k LEU 3.0 5.9 + - - -
187k THR* 3.1 3.7 + - - -
188k ILE* 3.0 29.3 + - - +
212k ARG* 4.9 9.2 - - - +
228k TYR* 6.0 0.2 - - - +
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Residues in contact with ASP 185 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183k THR* 4.2 8.3 - - - -
184k ASP* 1.3 78.1 - - - +
186k LEU* 1.3 57.3 + - + +
188k ILE* 4.8 1.1 - - - -
189k LYS* 3.2 24.4 + - - +
228k TYR* 4.2 34.8 + - + +
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Residues in contact with LEU 186 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179k GLU 3.2 25.6 - - - +
180k ALA* 4.0 8.8 - - + +
181k ILE 3.8 11.5 + - - +
182k GLU* 4.1 9.6 - - + +
183k THR* 2.9 22.4 + - - +
185k ASP* 1.3 79.7 - - - +
187k THR* 1.3 60.6 + - - +
188k ILE 3.4 0.2 - - - -
189k LYS* 3.3 12.0 - - + +
190k LEU* 2.9 24.9 + - - +
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Residues in contact with THR 187 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35k VAL* 4.1 14.9 - - - +
37k GLY* 5.0 4.5 - - - -
38k ARG* 3.9 13.5 - - - -
40k ILE* 5.4 5.4 - - - -
42k VAL* 5.5 4.0 - - - -
181k ILE* 3.7 30.4 - - - +
183k THR 3.0 5.7 + - - -
184k ASP* 3.9 4.7 - - - -
186k LEU* 1.3 73.6 - - - +
188k ILE* 1.4 61.7 + - - +
190k LEU* 2.9 22.6 + - - +
191k VAL* 3.0 17.8 + - - +
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Residues in contact with ILE 188 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42k VAL* 4.6 11.1 - - + +
184k ASP 3.0 17.3 + - - +
185k ASP* 4.5 4.9 - - - +
187k THR* 1.4 74.4 - - - +
189k LYS* 1.3 63.0 + - - +
191k VAL* 3.1 11.6 + - - +
192k ILE* 3.0 24.7 + - - +
210k VAL* 5.1 9.9 - - + -
220k LEU* 6.1 2.9 - - + -
228k TYR* 5.1 20.4 - - + -
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Residues in contact with LYS 189 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185k ASP 3.2 21.9 + - - +
186k LEU* 3.3 17.5 - - + +
188k ILE* 1.3 79.9 - - - +
190k LEU* 1.3 56.0 + - - +
192k ILE* 3.4 5.7 + - - +
193k LYS* 2.9 30.5 + - - +
228k TYR* 5.5 11.6 - - + +
232k ILE* 5.5 10.0 - - + +
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Residues in contact with LEU 190 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35k VAL* 4.2 11.7 - - + -
171k PHE* 4.1 13.0 - - + -
172k LEU* 4.1 20.0 - - + -
175k ASN* 4.0 28.3 - - + +
176k TYR* 4.0 36.3 - - + -
180k ALA* 5.0 12.6 - - + -
181k ILE* 5.8 2.9 - - + -
186k LEU 2.9 12.7 + - - +
187k THR* 2.9 14.6 + - - +
189k LYS* 1.3 72.7 - - - +
191k VAL* 1.3 59.8 + - - +
193k LYS* 3.3 5.2 + - + +
194k ALA* 2.9 25.5 + - - +
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Residues in contact with VAL 191 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33k VAL* 3.7 23.3 - - + +
35k VAL* 3.6 31.2 - - + -
42k VAL* 3.7 22.4 - - + +
43k LEU 4.7 2.2 - - - -
44k GLY* 4.1 19.1 - - - +
187k THR 3.0 13.1 + - - +
188k ILE* 3.1 8.0 + - - +
190k LEU* 1.3 76.7 - - - +
192k ILE* 1.3 59.5 + - - +
194k ALA* 3.1 7.0 + - - +
195k LEU* 2.9 30.3 + - + +
206k ILE* 6.4 1.3 - - + -
208k LEU* 5.1 9.9 - - + -
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Residues in contact with ILE 192 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188k ILE 3.0 15.0 + - - +
189k LYS* 3.9 6.3 - - - +
191k VAL* 1.3 76.6 - - - +
193k LYS* 1.3 57.5 + - - +
195k LEU* 3.4 6.2 + - - +
196k LEU* 2.9 32.4 + - - +
206k ILE* 5.5 10.1 - - + +
228k TYR* 5.6 12.3 - - + +
229k VAL* 5.6 7.4 - - + +
232k ILE* 5.6 6.1 - - + -
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Residues in contact with LYS 193 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171k PHE* 4.0 21.0 - - + -
189k LYS 2.9 18.6 + - - +
190k LEU* 3.5 10.1 - - + +
192k ILE* 1.3 77.9 - - - +
194k ALA* 1.3 60.0 + - - +
196k LEU* 3.6 12.1 + - - +
197k GLU* 3.7 11.6 + - - +
232k ILE* 5.8 6.8 - - + +
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Residues in contact with ALA 194 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33k VAL* 5.1 4.0 - - + -
168k VAL* 3.7 23.7 - - + +
171k PHE* 3.7 17.0 - - + -
172k LEU* 3.6 29.2 - - + -
190k LEU 2.9 16.8 + - - +
191k VAL* 3.5 5.4 - - - +
193k LYS* 1.3 75.8 - - - +
195k LEU* 1.3 63.6 + - - +
197k GLU* 3.2 19.6 + - - +
198k VAL 4.2 0.3 + - - -
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Residues in contact with LEU 195 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31k THR* 5.9 5.4 - - + +
33k VAL* 5.0 17.4 - - + +
44k GLY* 6.0 2.5 - - - +
45k VAL 6.1 1.1 - - - -
46k GLU* 5.7 6.2 - - + +
168k VAL* 5.3 1.3 - - - -
191k VAL* 2.9 17.8 + - + +
192k ILE* 3.9 4.9 - - - +
194k ALA* 1.3 71.1 - - - +
196k LEU* 1.3 57.2 + - - +
197k GLU 3.0 7.2 + - - -
198k VAL* 3.2 2.8 + - - +
199k VAL* 3.0 31.8 + - + +
206k ILE* 4.1 30.3 - - + -
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Residues in contact with LEU 196 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192k ILE 2.9 18.8 + - - +
193k LYS* 3.8 9.0 - - - +
194k ALA 3.3 0.2 - - - -
195k LEU* 1.3 74.9 - - - +
197k GLU* 1.3 57.6 + - - +
198k VAL 3.3 2.1 + - - -
199k VAL* 4.1 15.2 - - - +
201k SER* 5.6 4.3 + - - +
206k ILE* 5.0 3.8 - - + +
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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