Contacts of the helix formed by residues 212 - 223 (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 LYS 212 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204K MET* 4.1 22.8 - - + +
205K TYR* 3.7 26.5 - - - +
206K GLY 4.2 1.3 - - - -
207K PRO 3.3 26.2 + - - -
208K PRO* 4.6 0.4 - - - +
209K GLY 4.7 0.4 - - - +
210K CYS* 4.9 2.5 - - - +
211K GLY* 1.3 71.4 - - - -
213K THR* 1.3 67.0 + - - +
214K MET 3.2 1.6 - - - -
215K LEU* 3.3 15.5 - - - +
216K ALA* 3.3 7.3 + - - +
263K PHE* 4.9 1.9 - - - -
310K ALA* 4.6 10.4 - - + +
311K THR* 4.1 4.9 - - - +
312K ASN* 3.7 27.1 + - - +
333K PHE* 2.8 33.7 - - + -
501K ADP 2.1 44.1 + - - +
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Residues in contact with THR 213 (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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212K LYS* 1.3 66.2 - - - +
214K MET* 1.3 61.5 + - + +
216K ALA* 3.5 4.3 + - - +
217K LYS* 3.2 40.9 + - - +
263K PHE* 5.1 1.6 - - - -
265K ASP* 3.5 24.1 + - - +
310K ALA* 5.4 1.6 - - - +
501K ADP 2.1 55.1 + - - -
265L ASP* 5.8 3.6 - - - -
266L GLY* 3.9 26.7 - - - +
267L PHE* 3.4 8.4 - - + -
291L ARG* 6.3 0.2 - - - -
294L ARG* 5.6 0.2 + - - -
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Residues in contact with MET 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162K VAL* 2.6 38.4 - - + -
166K ASP* 2.5 31.9 - - - +
167K ILE* 2.8 38.1 - - + +
211K GLY* 4.6 8.7 - - - +
212K LYS 3.2 0.2 - - - -
213K THR* 1.3 77.6 - - + +
215K LEU* 1.3 59.9 + - - +
217K LYS* 2.9 16.3 + - + +
218K ALA* 2.8 30.3 + - - +
501K ADP 3.1 56.6 + - + +
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Residues in contact with LEU 215 (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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164K TYR* 5.9 3.1 - - + +
167K ILE* 4.8 9.1 - - + +
170K MET* 5.8 2.2 - - + -
173K GLN* 4.4 8.5 - - + +
174K LYS* 4.2 30.7 - - + +
177K VAL* 3.4 26.0 - - + -
204K MET* 3.4 14.8 - - + -
211K GLY 3.8 9.5 + - - +
212K LYS 3.3 13.0 + - - +
214K MET* 1.3 78.7 - - - +
216K ALA* 1.3 55.7 + - - +
218K ALA* 3.5 9.2 + - + +
219K VAL* 2.9 34.2 + - + +
333K PHE* 2.8 35.9 - - + -
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Residues in contact with ALA 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204K MET* 4.7 3.7 - - + +
212K LYS 3.3 4.7 + - - +
213K THR 3.5 4.9 + - - +
214K MET 3.1 0.4 - - - -
215K LEU* 1.3 76.3 - - - +
217K LYS* 1.3 61.4 + - - +
219K VAL* 3.3 4.4 + - - -
220K ALA* 2.9 30.3 + - - +
227K PHE* 3.6 9.5 - - + -
263K PHE* 2.9 47.8 - - + -
308K ILE* 5.9 0.9 - - - -
267L PHE* 3.6 13.0 - - + -
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Residues in contact with LYS 217 (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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160K PRO* 2.9 45.2 - - + +
162K VAL* 3.5 33.4 - - + +
213K THR* 3.2 21.1 + - - +
214K MET* 2.9 16.3 + - + +
216K ALA* 1.3 78.4 - - - +
218K ALA* 1.3 63.9 + - - +
221K HIS* 3.0 15.6 + - - +
265L ASP* 4.6 5.9 + - - -
266L GLY 2.8 28.8 + - - -
267L PHE* 3.3 34.9 + - + +
269L THR* 6.2 1.2 - - - -
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Residues in contact with ALA 218 (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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162K VAL 3.5 10.3 + - - +
164K TYR* 4.0 24.9 - - + +
167K ILE* 2.9 31.9 - - + -
214K MET 2.8 8.0 + - - +
215K LEU* 3.7 10.8 - - + +
217K LYS* 1.3 78.2 - - - +
219K VAL* 1.3 61.3 + - + +
221K HIS* 3.1 3.4 + - - +
222K HIS* 3.1 28.9 + - - +
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Residues in contact with VAL 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164K TYR* 5.6 6.5 - - + +
177K VAL* 4.0 26.5 - - + -
181K VAL* 5.3 2.7 - - + -
182K GLU* 6.0 7.0 - - + +
204K MET* 6.0 0.7 - - + -
215K LEU* 2.9 22.3 + - + +
216K ALA* 3.7 6.3 - - - +
217K LYS 3.3 0.2 - - - -
218K ALA* 1.3 73.4 - - + +
220K ALA* 1.3 50.7 + - - +
221K HIS 3.0 4.3 - - - -
222K HIS* 5.4 0.9 - - - -
223K THR* 2.3 46.8 + - - +
227K PHE* 4.0 6.7 - - + -
261K ILE* 3.4 32.5 - - + -
308K ILE* 5.0 5.6 - - + -
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Residues in contact with ALA 220 (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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154K LEU* 4.7 3.1 - - + -
159K LYS* 3.2 19.8 - - - -
160K PRO* 2.5 37.4 - - + +
216K ALA 2.9 12.5 + - - +
218K ALA 3.4 0.2 - - - -
219K VAL* 1.3 76.4 - - - +
221K HIS* 1.3 56.6 + - - +
223K THR* 3.2 20.6 - - - +
227K PHE* 3.6 30.4 - - + +
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Residues in contact with HIS 221 (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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159K LYS* 4.2 20.8 + - + +
160K PRO* 4.2 5.8 - - + -
161K ASP* 2.7 23.4 + - - +
162K VAL 3.8 2.9 - - - +
163K MET* 2.5 53.2 - - + -
217K LYS 3.0 17.2 + - - +
218K ALA* 3.3 5.6 - - - +
219K VAL 3.0 2.0 - - - -
220K ALA* 1.3 79.0 - - - +
222K HIS* 1.3 75.9 + + + +
223K THR* 3.1 4.1 + - - +
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Residues in contact with HIS 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163K MET* 5.3 2.0 - - + -
164K TYR* 2.6 66.6 + + + +
182K GLU* 5.8 5.8 - - - +
218K ALA 3.1 8.4 + - - +
219K VAL* 4.8 0.9 - - - +
221K HIS* 1.3 87.9 - + + +
223K THR* 1.3 73.1 - - - +
224K THR* 3.8 5.7 - - - +
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Residues in contact with THR 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159K LYS* 4.7 8.6 + - - +
185K LEU* 5.8 0.9 - - - +
219K VAL* 2.3 37.8 + - - +
220K ALA* 3.2 25.1 - - - +
221K HIS 4.1 3.3 - - - +
222K HIS* 1.3 90.9 - - - +
224K THR* 1.3 76.7 + - - +
225K ALA* 3.6 19.5 + - - +
227K PHE* 4.8 7.3 - - + +
261K ILE* 4.0 18.1 - - - +
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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