Contacts of the helix formed by residues 210 - 222 (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 SER 210 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167G SER* 3.2 26.4 + - - -
168G PHE* 5.3 0.9 - - - -
169G GLU* 4.8 18.3 + - - +
209G ASP* 1.3 74.2 - - - +
211G VAL* 1.3 66.1 + - - +
212G GLU* 3.5 18.8 + - - +
213G THR* 3.0 29.5 + - - -
214G HIS* 3.0 25.8 + - - -
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Residues in contact with VAL 211 (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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166G PHE* 3.6 40.3 - - + -
167G SER 4.4 1.8 + - - -
168G PHE* 5.3 7.9 - - + -
209G ASP 4.1 0.2 + - - -
210G SER* 1.3 72.3 - - - +
212G GLU* 1.3 67.4 + - + +
214G HIS* 3.2 9.2 + - - +
215G LYS* 2.9 53.6 + - - +
228G LEU* 4.3 26.5 - - + -
231G GLN* 5.0 3.4 - - - +
238G LEU* 4.4 4.9 - - + -
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Residues in contact with GLU 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU* 6.2 0.4 - - - -
169G GLU* 4.3 16.9 - - - +
210G SER* 3.2 12.5 - - - +
211G VAL* 1.3 91.9 + - + +
213G THR* 1.3 57.3 + - - +
215G LYS* 3.4 10.1 + - + +
216G ALA* 3.0 29.1 + - - +
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Residues in contact with THR 213 (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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169G GLU* 5.7 0.5 + - - -
209G ASP* 3.7 29.2 - - + +
210G SER* 3.0 22.5 + - - -
212G GLU* 1.3 77.1 - - - +
214G HIS* 1.3 61.8 + - - +
216G ALA* 3.2 7.6 + - + +
217G ARG* 3.0 37.8 + - + +
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Residues in contact with HIS 214 (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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135G LEU* 4.3 8.8 - - + +
147G LEU* 5.9 0.4 - - - +
162G LEU* 3.9 17.8 - - + +
164G GLU* 3.6 37.7 + - + +
165G LYS 4.9 0.2 + - - -
166G PHE* 3.7 24.7 - + - -
209G ASP* 3.5 36.5 + - + +
210G SER 3.0 24.3 + - - -
211G VAL 3.5 6.1 - - - +
213G THR* 1.3 77.9 - - - +
215G LYS* 1.3 61.3 + - - +
217G ARG* 3.2 15.8 + - - +
218G LEU* 3.0 27.4 + - - +
238G LEU* 4.1 17.0 - - + -
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Residues in contact with LYS 215 (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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212A GLU* 5.7 3.0 + - - -
211G VAL* 2.9 39.3 + - + +
212G GLU* 3.7 8.7 - - + +
213G THR 3.3 0.2 - - - -
214G HIS* 1.3 75.8 - - - +
216G ALA* 1.3 58.4 + - - +
218G LEU* 3.3 9.6 + - - +
219G HIS* 2.9 30.4 + - - +
226G SER* 5.1 13.5 + - - +
227G GLU* 3.4 30.0 + - - +
228G LEU* 4.2 11.6 - - - +
238G LEU* 3.8 13.0 - - + -
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Residues in contact with ALA 216 (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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212G GLU 3.0 16.8 + - - +
213G THR* 3.6 7.6 - - - +
214G HIS 3.2 0.2 - - - -
215G LYS* 1.3 78.6 - - - +
217G ARG* 1.4 57.7 + - + +
219G HIS* 3.4 6.3 + - - +
220G LYS* 2.9 29.7 + - - +
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Residues in contact with ARG 217 (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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135G LEU* 4.5 2.8 - - - +
140G PRO* 4.2 14.8 + - - +
143G ARG* 3.9 28.4 - - - +
144G GLN* 3.1 49.5 + - - +
147G LEU* 3.6 21.3 - - + -
209G ASP* 2.9 44.7 + - - -
213G THR* 3.0 27.5 + - + +
214G HIS* 3.7 21.4 + - - +
216G ALA* 1.4 76.4 - - - +
218G LEU* 1.3 58.6 + - - +
220G LYS* 3.3 1.1 + - - -
221G ALA* 2.9 26.0 + - - +
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Residues in contact with LEU 218 (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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147G LEU* 4.2 14.8 - - + -
160G LEU* 3.6 31.0 - - + -
162G LEU* 4.3 18.4 - - + -
214G HIS 3.0 22.6 + - - +
215G LYS* 3.3 7.2 + - - +
217G ARG* 1.3 75.0 - - - +
219G HIS* 1.3 62.7 + - - +
221G ALA* 3.2 7.9 + - - -
222G GLY 3.3 0.5 + - - -
223G PHE* 3.1 42.7 + - + -
226G SER* 3.7 29.4 - - - +
238G LEU* 4.3 19.1 - - + -
240G ALA* 4.0 8.7 - - + -
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Residues in contact with HIS 219 (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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215G LYS 2.9 16.9 + - - +
216G ALA* 3.7 7.2 - - - +
218G LEU* 1.3 75.9 - - - +
220G LYS* 1.3 58.9 + - - +
222G GLY* 3.0 22.0 + - - -
223G PHE 4.0 17.5 - - - -
224G GLU* 5.6 3.4 - - - -
226G SER* 5.0 1.4 + - - -
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Residues in contact with LYS 220 (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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144G GLN* 3.9 31.2 - - - +
148G ASP* 4.3 4.0 - - - +
216G ALA 2.9 17.7 + - - +
217G ARG* 3.3 4.7 + - - +
219G HIS* 1.3 79.6 + - - +
221G ALA* 1.3 61.8 + - - +
222G GLY* 3.2 1.0 + - - -
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Residues in contact with ALA 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G GLN* 3.5 2.9 - - - +
147G LEU* 3.7 28.0 - - + +
148G ASP* 3.2 25.7 - - - +
151G TYR* 3.3 21.6 - - + +
152G GLN* 4.8 2.3 - - - +
217G ARG 2.9 17.4 + - - +
218G LEU 3.5 6.1 - - - +
219G HIS 3.2 0.4 - - - -
220G LYS* 1.3 77.2 - - - +
222G GLY* 1.3 58.4 + - - +
223G PHE* 3.8 9.2 - - + -
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Residues in contact with GLY 222 (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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151G TYR* 3.1 24.8 - - - -
219G HIS 3.0 12.9 + - - -
220G LYS 3.1 0.9 - - - -
221G ALA* 1.3 79.0 - - - +
223G PHE* 1.3 67.0 + - - +
224G GLU* 3.1 15.2 + - - +
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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