Contacts of the helix formed by residues 186 - 205 (chain A) in PDB entry 5GKI
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 GLU 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LYS* 5.5 0.2 - - - +
183A ARG* 3.8 26.4 + - - -
184A ARG* 4.0 8.5 - - + +
185A ALA* 1.3 80.2 - - - +
187A LEU* 1.3 67.3 + - - +
188A HIS* 3.2 11.6 - - + +
189A ALA* 3.1 15.7 + - - +
190A VAL* 3.5 6.8 + - - +
218A THR* 3.9 20.9 - - + +
221A ALA* 3.9 10.2 - - - +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU* 1.3 73.7 - - - +
188A HIS* 1.3 64.9 + - - +
190A VAL* 2.8 18.1 + - - +
191A ARG* 2.9 44.7 + - + +
218A THR* 4.4 2.9 + - - +
220A GLY* 3.5 38.1 - - - +
221A ALA* 4.2 2.5 - - - +
223A ARG* 5.8 0.7 - - - +
224A LEU* 4.1 12.1 - - + -
161B THR* 3.6 19.1 - - + -
162B GLY* 3.8 27.8 - - - +
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Residues in contact with HIS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LYS* 4.8 8.7 - - + -
186A GLU* 4.3 8.3 - - + +
187A LEU* 1.3 78.0 - - - +
189A ALA* 1.3 59.7 + - + +
191A ARG* 3.4 20.9 + - - +
192A GLN* 3.1 53.1 + - + +
188B HIS* 4.7 26.3 + - + +
191B ARG* 5.9 0.2 - - - -
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU* 3.7 9.0 - - + +
181A LYS* 3.6 42.6 - - + +
185A ALA* 4.3 9.6 - - + -
186A GLU 3.1 13.1 + - - +
187A LEU 3.1 1.0 - - - -
188A HIS* 1.3 79.3 - - + +
190A VAL* 1.3 62.4 + - - +
192A GLN* 3.5 6.4 + - - +
193A LEU* 3.1 26.0 + - - +
212A LEU* 4.5 6.3 - - + +
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLU 3.5 9.8 + - - +
187A LEU* 2.8 7.9 + - - +
189A ALA* 1.3 75.5 - - - +
191A ARG* 1.3 60.2 + - - +
193A LEU* 3.6 4.3 - - - +
194A LYS* 2.9 30.5 + - + +
212A LEU* 3.8 24.9 - - + -
221A ALA* 3.8 24.2 - - + +
224A LEU* 3.8 30.3 - - + +
225A LEU* 3.6 28.7 - - + -
228A GLU* 6.1 0.2 - - + -
230A LEU* 4.6 6.5 - - + -
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Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 2.9 43.2 + - - +
188A HIS* 3.5 34.0 + - - +
190A VAL* 1.3 75.1 - - - +
192A GLN* 1.3 60.0 + - - +
194A LYS* 4.0 6.5 - - + +
195A SER* 2.9 32.6 + - - -
224A LEU* 4.5 10.9 - - + +
161B THR 5.6 0.2 + - - -
162B GLY* 4.7 1.8 - - - -
191B ARG* 3.7 28.2 - - + +
192B GLN* 4.1 21.4 + - - +
195B SER* 3.3 38.0 + - - +
196B TYR* 3.9 22.6 + - - -
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Residues in contact with GLN 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE 5.1 0.2 + - - -
179A GLU* 2.9 13.3 + - - +
181A LYS* 3.8 7.0 + - - +
188A HIS* 3.1 46.4 + - + +
189A ALA 3.5 9.0 - - - +
191A ARG* 1.3 73.7 - - - +
193A LEU* 1.3 65.7 + - - +
195A SER* 3.4 1.9 - - - -
196A TYR* 3.0 57.1 + - + +
301A MG 2.6 30.5 - - - -
191B ARG* 4.1 23.3 - - - +
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 4.0 21.1 - - + +
179A GLU* 4.1 17.2 - - + +
189A ALA 3.1 14.9 + - - +
190A VAL* 3.6 5.6 - - - +
192A GLN* 1.3 77.0 - - - +
194A LYS* 1.3 63.4 + - - +
196A TYR* 2.9 19.5 + - - +
197A VAL* 2.9 15.4 + - + +
210A GLY* 3.7 24.0 - - - +
211A ILE 3.7 9.9 - - - +
212A LEU* 3.5 38.6 - - + +
225A LEU* 4.2 8.1 - - + -
230A LEU* 4.0 20.2 - - + -
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Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A VAL* 2.9 21.5 + - + +
191A ARG* 4.0 6.3 - - - +
193A LEU* 1.3 72.0 - - - +
195A SER* 1.3 63.4 + - - +
197A VAL* 3.2 6.2 + - - +
198A GLU* 2.6 53.3 + - - +
224A LEU* 5.3 12.8 - - + -
227A LYS* 5.9 0.4 - - - +
228A GLU* 3.4 41.3 - - + +
230A LEU* 4.0 17.7 - - + +
194B LYS* 3.2 11.1 - - - +
195B SER* 6.0 2.7 - - - +
198B GLU* 3.0 35.5 + - - -
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Residues in contact with SER 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A THR* 4.9 1.0 + - - +
191A ARG 2.9 23.5 + - - -
192A GLN 3.4 4.5 - - - -
194A LYS* 1.3 74.8 - - - +
196A TYR* 1.3 67.9 + - - +
198A GLU* 3.3 12.2 + - - +
199A ILE* 3.2 34.2 + - - +
191B ARG* 3.1 33.4 + - - +
194B LYS* 5.2 5.6 - - - +
224B LEU* 4.7 8.4 - - - +
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Residues in contact with TYR 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.9 16.6 - - + +
161A THR 4.3 3.1 - - - -
162A GLY* 4.0 2.7 - - - -
163A ILE 3.4 35.4 + - - -
164A VAL* 3.9 26.5 - - + -
177A VAL* 4.1 13.9 - - + -
179A GLU* 3.7 22.0 - - - -
192A GLN* 3.0 50.6 + - + +
193A LEU* 2.9 14.8 + - + +
195A SER* 1.3 75.5 - - - +
197A VAL* 1.3 63.5 + - - +
199A ILE* 3.1 4.2 + - - +
200A LEU* 3.0 27.8 + - - +
191B ARG* 3.6 27.0 + - - -
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 4.4 8.3 - - + -
193A LEU* 2.9 22.6 + - + +
194A LYS* 3.2 7.8 + - - +
196A TYR* 1.3 74.8 - - - +
198A GLU* 1.3 57.3 + - - +
200A LEU* 3.4 1.4 + - - +
201A ARG* 2.8 68.3 + - - +
208A VAL* 4.1 16.9 - - + +
210A GLY* 3.6 33.7 - - - +
230A LEU* 3.7 14.1 - - + -
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Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LYS* 2.6 44.5 + - - +
195A SER* 3.6 10.4 - - - +
197A VAL* 1.3 77.7 - - - +
199A ILE* 1.3 65.4 + - + +
201A ARG* 3.0 23.3 + - - +
202A GLU* 3.2 17.7 + - - +
228A GLU* 4.4 5.9 - - - +
194B LYS* 2.4 34.4 + - - -
198B GLU* 4.2 2.4 - - - +
227B LYS* 5.8 5.1 + - - +
228B GLU* 4.5 2.7 - - - +
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Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 4.1 15.9 - - + -
160A GLY* 4.5 7.9 - - - +
161A THR* 3.1 55.9 - - + +
195A SER* 3.2 20.2 - - - +
196A TYR 3.1 6.2 + - - +
198A GLU* 1.3 79.4 - - + +
200A LEU* 1.3 57.0 + - + +
202A GLU* 3.2 32.6 + - - +
203A GLU* 3.9 6.4 + - - +
224B LEU* 5.5 2.9 - - + -
227B LYS* 5.1 15.7 - - - +
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.9 31.4 - - + -
164A VAL* 4.9 1.6 - - + -
167A LEU* 3.6 25.4 - - + -
175A ILE* 4.4 7.9 - - + -
177A VAL* 3.4 31.6 - - + -
196A TYR 3.0 15.9 + - - +
197A VAL 4.0 2.9 - - - +
199A ILE* 1.3 72.8 - - + +
201A ARG* 1.3 64.8 + - - +
202A GLU 3.1 1.6 - - - -
203A GLU* 3.6 2.8 + - + +
204A TYR* 3.1 50.6 + - + +
208A VAL* 3.7 13.3 - - + +
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Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A VAL* 2.8 39.8 + - - +
198A GLU* 3.0 16.7 + - - +
200A LEU* 1.3 76.2 - - - +
202A GLU* 1.3 58.5 + - - +
205A GLY* 2.6 44.7 + - - +
206A ASP* 3.1 37.0 + - - +
208A VAL* 3.2 29.5 + - + +
209A ARG* 5.3 0.8 - - - +
228A GLU 5.6 3.4 + - - -
229A GLY 5.3 6.1 + - - -
230A LEU* 5.7 3.2 - - - +
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Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLU 3.2 13.6 + - - +
199A ILE* 3.3 21.0 - - - +
200A LEU 3.1 1.0 - - - -
201A ARG* 1.3 78.8 - - + +
203A GLU* 1.3 63.3 + - + +
205A GLY* 5.5 0.2 - - - -
227B LYS* 3.6 34.8 + - - +
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Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ILE 3.9 6.3 + - - +
200A LEU* 3.6 4.4 + - + +
201A ARG 3.3 0.2 - - - -
202A GLU* 1.3 81.8 - - + +
204A TYR* 1.3 93.9 + - + +
205A GLY 3.4 2.8 + - - -
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Residues in contact with TYR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE* 3.4 35.7 - - + -
200A LEU* 3.1 36.3 + - + +
203A GLU* 1.3 103.3 + - + +
205A GLY* 1.3 66.1 + - - +
206A ASP 3.6 0.9 + - - -
207A LYS* 3.7 21.7 + - + +
208A VAL* 4.4 6.3 - - + -
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Residues in contact with GLY 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ARG* 2.6 44.9 + - - +
202A GLU 4.8 0.2 + - - -
203A GLU 3.4 2.6 + - - -
204A TYR* 1.3 75.5 - - - +
206A ASP* 1.3 62.8 + - - -
207A LYS 3.1 1.9 + - - -
208A VAL* 3.5 5.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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