Contacts of the helix formed by residues 167 - 186 (chain f) 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 SER 167 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20f PHE* 4.0 1.8 - - - -
165f PRO 3.4 5.8 + - - -
166f LEU* 1.3 75.2 - - - +
168f LEU* 1.3 64.7 + - - +
169f ASP* 3.5 8.8 + - - +
170f ARG* 3.3 25.0 + - - +
171f ALA* 3.0 23.2 + - - +
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Residues in contact with LEU 168 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19f ASP* 6.1 0.2 - - - +
20f PHE* 3.7 40.8 - - + -
22f ILE* 4.1 8.5 - - + -
167f SER* 1.3 72.4 - - - +
169f ASP* 1.3 64.1 + - - +
171f ALA* 3.4 1.4 + - - +
172f MET* 2.9 35.6 + - + +
197f ILE* 3.8 19.7 - - + -
199f THR* 5.0 10.5 - - + -
204f ARG* 3.9 22.0 - - - +
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Residues in contact with ASP 169 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167f SER* 3.2 8.4 + - - +
168f LEU* 1.3 80.5 - - - +
170f ARG* 1.3 63.0 + - - +
172f MET* 3.1 9.4 + - - +
173f ARG* 2.4 53.7 + - - +
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Residues in contact with ARG 170 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152f GLN* 3.0 54.9 + - - +
153f VAL* 4.9 5.9 - - - +
155f PHE* 4.6 14.4 - - - -
164f VAL 5.9 0.2 + - - -
166f LEU* 5.4 13.7 - - + +
167f SER* 3.3 21.0 + - - +
169f ASP* 1.3 75.6 - - - +
171f ALA* 1.3 61.4 + - - +
173f ARG* 3.3 27.9 - - + +
174f LEU* 2.9 37.8 + - + +
202p TYR* 4.7 6.8 - - - +
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Residues in contact with ALA 171 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15f ILE* 4.4 13.6 - - + +
20f PHE* 3.9 15.5 - - + -
22f ILE* 3.7 19.5 - - + -
166f LEU* 5.0 7.8 - - + +
167f SER 3.0 17.5 + - - +
168f LEU 3.5 4.9 - - - +
170f ARG* 1.3 76.3 - - - +
172f MET* 1.3 63.3 + - - +
174f LEU* 3.2 10.4 - - - +
175f VAL* 3.0 27.4 + - - +
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Residues in contact with MET 172 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22f ILE* 3.6 22.9 - - + -
168f LEU* 2.9 27.3 + - + +
169f ASP* 3.1 11.4 + - - +
171f ALA* 1.3 77.3 - - - +
173f ARG* 1.3 62.3 + - - +
175f VAL* 3.2 5.5 + - - +
176f LYS* 3.0 36.1 + - - +
195f ILE* 3.9 29.2 - - + -
197f ILE* 3.7 20.9 - - + -
204f ARG* 4.9 5.6 - - - +
206f GLU* 3.0 35.2 - - - +
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Residues in contact with ARG 173 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169f ASP* 2.4 44.3 + - - +
170f ARG* 3.3 44.1 - - + +
172f MET* 1.3 77.3 - - - +
174f LEU* 1.3 61.3 + - - +
176f LYS* 3.6 2.1 + - - +
177f ASP* 3.0 32.3 + - - +
199p LEU* 3.9 48.2 + - + +
200p GLY* 4.4 7.4 - - - -
202p TYR* 5.8 1.8 - - + +
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Residues in contact with LEU 174 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15f ILE* 4.1 9.0 - - + -
148f LEU* 4.6 4.5 - - + -
149f LEU* 4.1 17.7 - - + -
152f GLN* 4.2 13.9 - - + -
153f VAL* 3.4 33.7 - - + -
170f ARG* 2.9 22.5 + - + +
171f ALA* 3.2 13.0 - - - +
173f ARG* 1.3 75.5 - - - +
175f VAL* 1.3 67.5 + - - +
177f ASP* 3.1 1.7 + - - +
178f VAL* 2.9 39.4 + - + +
202p TYR* 3.5 36.8 - - + +
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Residues in contact with VAL 175 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13f LEU* 3.9 10.5 - - + -
15f ILE* 3.7 23.3 - - + -
22f ILE* 4.0 19.5 - - + -
24f ALA* 3.8 27.6 - - + -
171f ALA 3.0 14.3 + - - +
172f MET* 3.2 8.7 + - - +
174f LEU* 1.3 79.1 - - - +
176f LYS* 1.3 65.3 + - - +
178f VAL* 3.2 10.2 - - - +
179f PHE* 3.0 32.0 + - + -
193f LEU* 4.9 1.1 - - + -
195f ILE* 3.9 19.3 - - + -
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Residues in contact with LYS 176 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172f MET* 3.0 25.7 + - - +
173f ARG 3.8 4.7 - - - +
175f VAL* 1.3 77.5 - - - +
177f ASP* 1.3 55.9 + - - +
179f PHE* 3.5 1.7 + - - +
180f ILE* 3.0 39.3 + - + +
193f LEU* 4.4 9.0 - - + +
195f ILE* 4.1 16.2 - - + -
206f GLU* 2.4 34.7 + - - -
208f VAL* 3.8 26.1 - - + +
199p LEU* 3.8 32.7 - - + +
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Residues in contact with ASP 177 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148f LEU* 5.7 1.3 - - + -
173f ARG 3.0 19.7 + - - +
174f LEU 3.1 2.0 + - - +
176f LYS* 1.3 75.7 - - - +
178f VAL* 1.3 63.6 + - + +
180f ILE* 3.1 8.3 + - - +
181f SER* 3.0 26.9 + - - -
197p THR 4.0 3.8 - - - +
198p ARG* 4.1 10.1 - - - +
199p LEU* 3.2 31.1 + - - +
200p GLY* 3.2 20.8 + - - -
202p TYR* 2.6 34.1 + - + +
152q SER* 5.4 1.3 - - - +
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Residues in contact with VAL 178 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13f LEU* 3.4 29.4 - - + -
145f LEU* 3.4 21.4 - - + +
148f LEU* 3.5 38.8 - - + -
149f LEU* 4.4 15.3 - - + -
174f LEU* 2.9 21.6 + - + +
175f VAL* 3.2 12.3 - - - +
177f ASP* 1.3 75.5 - - - +
179f PHE* 1.3 63.4 - - + +
181f SER* 3.5 7.1 + - - -
182f ALA* 2.9 29.8 + - - +
152q SER* 5.0 0.4 - - - +
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Residues in contact with PHE 179 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11f THR* 4.2 27.4 - - + -
13f LEU* 3.6 33.0 - - + -
24f ALA* 3.9 27.1 - - + -
25f SER* 3.9 5.2 - - - -
26f ASP* 3.6 23.1 - - + -
145f LEU* 4.4 3.6 - - + -
175f VAL* 3.0 27.0 + - + +
176f LYS 4.0 1.1 - - - +
178f VAL* 1.3 83.9 - - + +
180f ILE* 1.3 57.2 + - - +
182f ALA* 3.8 4.0 - - + +
183f ALA* 2.9 31.0 + - - +
189f THR* 4.3 16.1 - - + +
193f LEU* 3.7 31.6 - - + -
210f LEU* 4.2 12.2 - - + +
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Residues in contact with ILE 180 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176f LYS* 3.0 28.7 + - + +
177f ASP* 3.1 6.9 + - - +
179f PHE* 1.3 76.3 - - - +
181f SER* 1.3 65.1 + - - +
183f ALA* 3.5 3.9 + - - +
184f GLU* 3.4 24.6 + - + +
193f LEU* 6.2 0.2 - - + -
208f VAL* 5.5 9.6 - - + -
209f SER 5.3 2.7 - - - +
210f LEU* 4.2 18.6 - - + -
211f ARG* 5.5 0.2 - - - -
195p LYS* 5.2 8.3 - - + +
196p GLY* 3.8 40.6 - - - +
197p THR* 4.4 4.7 - - - +
199p LEU* 4.3 18.4 - - + -
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Residues in contact with SER 181 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145f LEU* 6.1 0.4 - - - -
177f ASP* 3.0 11.5 + - - +
178f VAL* 3.7 7.2 - - - -
180f ILE* 1.3 75.2 - - - +
182f ALA* 1.3 66.1 + - - +
184f GLU* 3.0 26.0 + - - +
185f ARG* 3.3 10.7 + - - +
195p LYS* 5.2 4.5 + - - +
198p ARG* 5.7 0.9 + - - -
148q GLY* 5.1 2.9 - - - -
151q GLU* 3.5 28.0 + - - +
152q SER* 3.2 26.7 + - - -
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Residues in contact with ALA 182 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11f THR* 5.5 0.2 - - + -
141f ALA* 3.9 19.7 - - + -
144f MET* 4.5 11.9 - - - -
145f LEU* 3.7 19.7 - - + +
178f VAL 2.9 18.5 + - - +
179f PHE* 3.8 7.0 - - + +
181f SER* 1.3 77.0 - - - +
183f ALA* 1.3 58.9 + - - +
185f ARG 3.1 0.2 + - - -
186f ASP* 2.7 36.9 + - - +
189f THR* 4.3 8.7 - - + -
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Residues in contact with ALA 183 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179f PHE 2.9 18.6 + - - +
180f ILE* 3.8 6.1 - - - +
181f SER 3.2 0.2 - - - -
182f ALA* 1.3 77.3 - - - +
184f GLU* 1.3 60.0 + - - +
186f ASP 3.8 8.9 - - - +
189f THR* 3.6 28.4 - - + +
190f GLY* 4.5 0.7 - - - -
210f LEU* 4.4 17.7 - - + -
211f ARG* 4.1 27.7 + - + +
213f ASP* 4.8 5.4 - - - +
19p ARG* 5.1 4.7 + - - -
26p VAL* 5.8 0.2 - - - +
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Residues in contact with GLU 184 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180f ILE* 3.4 16.6 + - + +
181f SER* 3.0 14.0 + - - +
183f ALA* 1.3 79.0 - - - +
185f ARG* 1.3 62.5 + - + +
211f ARG* 2.6 50.0 + - - +
19p ARG* 4.9 3.5 + - - -
26p VAL* 3.5 22.9 - - - +
29p LYS* 3.6 27.8 + - - +
194p LYS 4.5 0.2 - - - +
195p LYS* 4.2 29.3 - - + +
196p GLY 4.8 1.6 + - - -
151q GLU* 3.9 21.1 - - - +
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Residues in contact with ARG 185 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144f MET* 3.6 25.7 - - + +
181f SER 3.3 4.7 + - - +
182f ALA 3.1 1.8 + - - -
184f GLU* 1.3 81.5 - - - +
186f ASP* 1.3 61.1 + - - +
25p VAL* 3.5 5.2 - - + -
26p VAL* 2.6 51.2 + - - +
27p ALA 3.3 26.5 + - - -
29p LYS* 3.1 25.7 - - - +
135q ASP* 3.9 9.3 + - - -
136q PHE* 3.1 26.9 + - - -
147q TYR* 3.6 24.8 - - + +
148q GLY* 5.9 0.2 - - - -
151q GLU* 2.4 49.9 + - + +
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Residues in contact with ASP 186 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140f SER* 3.0 27.2 + - - -
141f ALA* 3.3 21.4 + - + -
144f MET* 4.1 11.0 - - + -
182f ALA 2.7 21.1 + - - +
183f ALA 3.8 6.7 - - - +
185f ARG* 1.3 73.7 - - - +
187f VAL* 1.3 78.1 + - - +
188f TYR* 2.8 25.2 + - - +
189f THR* 3.0 37.0 + - - +
213f ASP 5.7 0.3 - - - +
19p ARG* 6.0 0.2 + - - -
24p MET 3.9 8.9 - - - +
26p VAL* 4.9 1.3 - - - -
144q GLU* 5.2 1.1 - - - -
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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