Contacts of the helix formed by residues 170 - 188 (chain G) in PDB entry 4GEK
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 170 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLU 4.1 2.4 - - - +
225A HIS* 2.9 39.7 + - - +
226A SER 4.8 2.4 + - - +
227A GLU* 6.1 0.7 - - - +
168G PHE* 3.3 4.8 - - + +
169G GLU* 1.3 77.0 - - - +
171G ALA* 1.3 58.8 + - - +
172G LYS* 2.9 16.5 + - - +
173G VAL* 3.1 24.2 + - + +
174G GLY* 2.8 25.8 + - - -
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Residues in contact with ALA 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G PHE 5.1 2.0 - - - -
169G GLU 3.2 7.9 + - - +
170G ASP* 1.3 73.8 + - - +
172G LYS* 1.3 56.8 + - - +
174G GLY* 3.7 2.5 - - - +
175G GLU* 2.9 29.5 + - - +
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Residues in contact with LYS 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 5.8 5.7 - - - -
225A HIS* 3.7 38.6 - - + +
241A LEU* 4.3 17.1 - - + +
243A ALA* 6.2 1.8 - - - +
244A GLU* 3.8 29.8 + - - +
170G ASP* 2.9 8.8 + - - +
171G ALA* 1.3 74.1 - - - +
173G VAL* 1.3 62.1 + - - +
175G GLU* 3.5 25.8 + - - +
176G LEU* 3.0 26.9 + - - +
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Residues in contact with VAL 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A HIS* 4.1 13.2 - - + -
226A SER 3.9 22.2 - - - +
227A GLU* 3.7 29.6 - - + +
239A VAL* 5.9 2.7 - - + +
241A LEU* 5.2 5.6 - - + -
168G PHE* 4.1 9.9 - - + -
170G ASP* 3.1 30.4 + - + +
172G LYS* 1.3 73.6 - - - +
174G GLY* 1.3 65.7 + - - +
176G LEU* 3.1 10.7 + - + +
177G LEU* 2.9 40.5 + - + +
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Residues in contact with GLY 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G PHE* 4.1 23.1 - - - +
170G ASP 2.8 14.7 + - - -
171G ALA* 3.3 4.7 + - - -
172G LYS 3.3 0.2 - - - -
173G VAL* 1.3 75.7 - - - +
175G GLU* 1.3 55.5 + - - +
177G LEU* 3.4 1.6 + - - +
178G PHE* 2.8 30.9 + - - +
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Residues in contact with GLU 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G ALA 2.9 16.8 + - - +
172G LYS* 3.7 32.0 + - - +
173G VAL 3.2 0.2 - - - -
174G GLY* 1.3 74.3 - - - +
176G LEU* 1.3 66.4 + - - +
178G PHE* 3.3 9.8 + - + +
179G ASN* 2.9 38.4 + - - +
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Residues in contact with LEU 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.8 11.9 - - + -
52A ARG* 5.7 1.1 - - - -
53A PHE* 3.6 31.4 - - + -
229A TRP* 5.0 1.8 - - + -
239A VAL* 3.8 37.9 - - + -
241A LEU* 4.1 21.1 - - + -
172G LYS 3.0 14.6 + - - +
173G VAL* 3.5 11.7 - - + +
175G GLU* 1.3 77.9 - - - +
177G LEU* 1.3 68.6 + - + +
179G ASN* 3.1 9.1 + - + +
180G MET* 2.8 40.9 + - + +
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Residues in contact with LEU 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU* 5.0 3.1 - - + -
229A TRP* 4.1 21.8 - - + -
239A VAL* 5.2 1.3 - - + -
168G PHE* 3.6 39.5 - - + -
173G VAL* 2.9 30.4 + - + +
174G GLY* 4.0 3.4 - - - +
176G LEU* 1.3 87.1 - - + +
178G PHE* 1.3 59.8 + - - +
180G MET* 3.3 3.6 + - + +
181G HIS* 2.9 30.7 + - - +
231G GLN* 4.6 3.1 - - - +
233G PHE* 3.8 33.0 - - + +
234G ASN* 3.9 20.5 - - + +
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Residues in contact with PHE 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G LYS* 6.3 0.9 - - - -
174G GLY 2.8 18.1 + - - +
175G GLU* 3.4 10.1 - - + +
177G LEU* 1.3 76.2 - - - +
179G ASN* 1.3 72.8 + - - +
181G HIS* 3.3 10.3 + - - +
182G HIS* 2.9 39.7 + + + +
185G LYS* 5.9 4.9 - - - -
204G ASN* 5.5 6.7 - - - -
234G ASN* 4.7 7.5 - - - +
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Residues in contact with ASN 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 3.7 38.1 + - - +
175G GLU* 2.9 35.7 + - - +
176G LEU* 3.5 10.3 - - + +
178G PHE* 1.3 91.6 - - - +
180G MET* 1.3 59.4 + - + +
182G HIS* 3.3 7.0 - - - +
183G ASP* 2.8 36.7 + - - +
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Residues in contact with MET 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A MET* 3.5 36.0 - - + +
49A LEU* 4.2 11.4 - - + -
52A ARG* 3.8 29.2 - - - -
229A TRP* 4.2 11.9 - - + -
176G LEU* 2.8 40.1 + - + +
177G LEU* 3.7 4.0 - - - +
179G ASN* 1.3 76.6 - - - +
181G HIS* 1.3 56.5 + - - +
183G ASP* 3.1 11.1 + - - +
184G PHE* 2.8 29.6 + - - +
233G PHE* 3.4 46.0 - - + -
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Residues in contact with HIS 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G SER* 2.7 27.2 + - - -
37G PRO* 3.9 11.9 - - + -
165G LYS* 4.5 3.5 + - - -
177G LEU 2.9 17.6 + - - +
178G PHE* 3.6 8.7 - - - +
180G MET* 1.3 72.9 - - - +
182G HIS* 1.3 65.3 + - - +
184G PHE* 3.2 6.2 + + - +
185G LYS* 2.9 51.4 + - + +
203G GLU* 3.5 25.8 - - - -
233G PHE* 4.7 4.0 - - - -
234G ASN* 3.5 24.7 + - - +
235G PHE* 3.5 19.6 - + - -
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Residues in contact with HIS 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 3.8 9.0 + - - -
178G PHE* 2.9 25.8 + + + +
179G ASN* 3.3 12.8 - - - +
181G HIS* 1.3 77.7 - - - +
183G ASP* 1.3 75.0 + - - +
185G LYS* 3.3 15.9 + - - +
186G ARG* 3.0 67.8 + - + +
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Residues in contact with ASP 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A MET* 3.8 19.5 - - + +
51A GLU* 5.9 1.0 - - - +
52A ARG* 2.7 49.0 + - - +
179G ASN 2.8 16.3 + - - +
180G MET* 3.1 12.3 + - - +
182G HIS* 1.3 85.3 + - - +
184G PHE* 1.3 59.0 + - - +
186G ARG* 3.3 19.5 + - - +
187G ALA* 2.9 30.8 + - - +
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Residues in contact with PHE 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A MET* 3.6 14.0 - - + +
33G GLN 3.9 12.6 - - - -
34G ARG 3.6 27.1 - - - -
35G SER 4.2 0.7 - - - -
36G VAL 4.4 0.4 - - - -
37G PRO* 3.6 50.5 - - + -
38G GLY 4.9 2.9 - - - -
180G MET 2.8 13.2 + - - +
181G HIS* 3.4 12.6 - + - +
183G ASP* 1.3 73.1 - - - +
185G LYS* 1.3 70.7 + - + +
187G ALA* 3.2 4.1 + - - -
188G ASN* 2.9 50.8 + - - +
232G CYS* 5.9 1.3 - - - -
233G PHE* 4.5 10.5 - + + -
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Residues in contact with LYS 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G ARG 3.6 21.5 - - - +
35G SER* 4.2 4.0 - - - -
178G PHE* 5.9 4.9 - - - -
181G HIS* 2.9 61.5 + - + +
182G HIS* 3.7 13.0 - - - +
184G PHE* 1.3 76.6 - - + +
186G ARG* 1.3 62.4 + - - +
188G ASN 3.2 6.4 + - - -
190G TYR* 3.0 62.7 + - + -
191G SER 5.6 0.2 - - - -
200G SER* 4.6 11.7 + - - -
203G GLU* 5.2 4.7 + - - +
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Residues in contact with ARG 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG* 4.8 3.0 - - - +
182G HIS* 3.0 49.9 + - + +
183G ASP* 3.6 23.0 + - - +
185G LYS* 1.3 75.5 - - - +
187G ALA* 1.3 64.4 + - - +
188G ASN 3.1 1.2 + - - -
189G GLY* 3.2 12.2 + - - -
190G TYR 5.2 0.2 - - - +
191G SER 6.2 0.2 - - - +
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Residues in contact with ALA 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A MET* 5.9 3.8 - - + -
183G ASP 2.9 16.6 + - - +
184G PHE* 3.2 7.2 + - - +
186G ARG* 1.3 78.6 - - - +
188G ASN* 1.3 63.3 + - - +
189G GLY 3.4 1.4 + - - -
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Residues in contact with ASN 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G GLN* 4.9 6.0 - - - +
34G ARG* 3.2 40.4 + - + +
184G PHE* 2.9 56.9 + - - +
185G LYS 3.2 2.9 + - - +
186G ARG 3.1 1.2 - - - -
187G ALA* 1.3 83.8 - - - +
189G GLY* 1.3 64.5 + - - +
190G TYR 3.3 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
------------------------------------------------------------
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