Contacts of the helix formed by residues 207 - 221 (chain E) in PDB entry 3K75
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 GLN 207 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199E ASN* 3.2 31.7 + - - +
200E PHE* 3.8 12.3 - - + +
204E SER* 3.8 7.4 + - - -
205E SER* 3.4 21.4 + - - +
206E LYS* 1.3 80.0 - - - +
208E PRO* 1.3 69.0 - - - +
209E LYS* 2.9 6.0 + - + -
210E LEU* 2.9 51.1 + - + +
259E LEU* 3.9 8.8 - - - +
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Residues in contact with PRO 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E LYS* 3.6 10.5 - - + +
207E GLN* 1.3 89.4 - - - +
209E LYS* 1.3 56.0 + - - +
211E LEU* 2.9 9.9 + - + +
212E HIS* 2.8 51.1 + - + +
232E GLU* 3.8 45.1 - - + +
259E LEU* 5.1 1.1 - - + -
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Residues in contact with LYS 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E GLN* 2.9 3.6 + - + -
208E PRO* 1.3 80.8 - - + +
210E LEU* 1.3 57.3 + - + +
211E LEU 3.2 0.2 - - - -
212E HIS* 3.8 13.8 - - + -
213E ARG* 3.0 63.9 + - + +
216E GLU* 3.4 31.0 + - - -
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Residues in contact with LEU 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E ASP* 5.7 0.2 - - - +
173E TYR* 2.5 39.5 + - + +
195E LEU* 3.8 2.7 - - - +
197E HIS* 4.0 35.4 - - + +
199E ASN* 5.9 0.2 - - + -
200E PHE* 3.6 25.4 - - + +
207E GLN* 2.9 52.7 + - + +
209E LYS* 1.3 79.4 - - - +
211E LEU* 1.3 59.2 + - - +
213E ARG* 5.9 2.7 - - - +
214E VAL* 3.6 7.4 + - - +
259E LEU* 4.2 12.1 - - + -
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Residues in contact with LEU 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E LEU* 4.4 9.4 - - + -
207E GLN 4.1 0.4 + - - -
208E PRO 2.9 7.7 + - - +
210E LEU* 1.3 77.8 - - - +
212E HIS* 1.3 66.7 + - + +
213E ARG 3.2 1.3 - - - -
214E VAL* 2.9 7.2 + - + +
215E VAL* 2.8 43.1 + - + +
231E GLY 4.0 5.6 - - - +
232E GLU 3.3 24.7 - - - +
233E THR 3.4 23.3 - - - +
234E LYS 3.8 13.2 - - - +
235E PHE* 4.0 3.6 - - + +
257E ILE* 3.4 38.4 - - + +
259E LEU* 4.3 15.2 - - + +
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Residues in contact with HIS 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E PRO* 2.8 48.4 + - + +
209E LYS* 3.9 22.2 - - + +
211E LEU* 1.3 75.7 - - + +
213E ARG* 1.3 55.1 + - - +
215E VAL* 3.6 6.9 - - - +
216E GLU* 2.6 48.4 + - + +
230E LYS* 3.8 42.1 - - + +
231E GLY 3.2 26.1 + - - -
232E GLU* 4.4 5.0 - - - +
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Residues in contact with ARG 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E LEU* 2.9 51.0 + - + +
170E ASP* 4.1 20.2 + - - +
173E TYR* 4.2 18.1 + - - +
209E LYS* 3.0 39.6 + - - +
210E LEU* 5.9 2.4 - - - +
212E HIS* 1.3 78.3 - - - +
214E VAL* 1.3 57.7 + - - +
216E GLU* 3.3 4.6 + - - +
217E GLN* 2.9 30.3 + - - +
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Residues in contact with VAL 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E VAL* 5.6 0.7 - - + -
165E GLU* 6.1 0.9 - - + -
166E VAL* 3.9 27.8 - - + -
169E LEU* 3.8 12.8 - - + -
173E TYR* 3.5 41.5 - - + +
195E LEU* 3.7 17.7 - - + -
210E LEU 3.6 4.0 - - - +
211E LEU 2.9 8.5 + - - +
213E ARG* 1.3 75.6 - - - +
215E VAL* 1.3 63.4 + - + +
217E GLN* 3.5 1.7 + - - +
218E LEU* 3.1 35.9 + - + +
257E ILE* 5.1 9.0 - - + -
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Residues in contact with VAL 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E LEU* 2.8 41.9 + - + +
212E HIS* 3.6 9.4 - - - +
214E VAL* 1.3 77.7 - - + +
216E GLU* 1.3 60.0 + - + +
218E LEU* 3.4 6.1 + - - +
219E GLN* 2.9 34.5 + - - +
224E ILE* 3.8 8.5 - - + +
230E LYS* 5.1 8.7 - - + -
235E PHE* 3.6 50.5 - - + -
257E ILE* 4.1 9.9 - - + -
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Residues in contact with GLU 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E LYS* 3.4 27.7 + - - -
212E HIS* 2.6 28.8 + - + +
213E ARG* 3.7 4.0 - - - +
215E VAL* 1.3 73.8 - - + +
217E GLN* 1.3 63.8 + - - +
219E GLN* 3.0 33.9 + - - +
220E LYS* 3.2 17.7 + - - +
230E LYS* 5.0 11.3 + - + +
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Residues in contact with GLN 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E GLU* 2.8 35.6 + - + +
169E LEU* 3.8 35.1 - - + +
213E ARG 2.9 16.2 + - - +
214E VAL 3.9 3.1 - - - +
216E GLU* 1.3 73.3 - - - +
218E LEU* 1.3 59.7 + - - +
219E GLN 3.0 5.8 + - - -
220E LYS* 3.2 40.1 + - - +
221E VAL* 3.2 21.8 + - - +
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Residues in contact with LEU 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E ILE* 4.3 4.3 - - + +
162E VAL* 3.9 39.9 - - + +
165E GLU* 4.0 21.5 - - + -
214E VAL* 3.1 31.8 + - + +
215E VAL 3.7 0.2 - - - +
216E GLU 3.3 0.4 - - - -
217E GLN* 1.3 75.8 - - - +
219E GLN* 1.3 58.0 + - - +
221E VAL* 3.7 5.2 - - + +
223E PHE* 2.9 44.0 + - + +
224E ILE* 3.1 28.4 + - + -
255E ILE* 5.1 1.1 - - + -
257E ILE* 4.0 26.5 - - + -
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Residues in contact with GLN 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E VAL* 2.9 26.7 - - - +
216E GLU* 3.2 23.5 + - - +
217E GLN 3.0 0.2 - - - -
218E LEU* 1.3 77.3 - - - +
220E LYS* 1.3 57.9 + - - +
221E VAL 3.1 1.6 - - - -
222E ARG* 2.5 30.8 + - - +
224E ILE* 4.2 30.3 + - + +
225E THR 5.9 1.0 - - - -
226E ASP* 5.7 1.2 - - - +
227E THR* 4.2 17.3 + - - +
230E LYS* 6.2 0.3 - - - +
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Residues in contact with LYS 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E GLU* 3.2 16.7 + - - +
217E GLN* 3.6 33.9 + - - +
219E GLN* 1.3 79.1 - - - +
221E VAL* 1.3 58.2 + - + +
222E ARG* 3.1 16.8 + - - +
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Residues in contact with VAL 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E ILE* 4.6 7.4 - - + -
165E GLU* 3.5 27.8 - - + +
217E GLN* 3.2 35.2 + - - +
218E LEU* 3.7 16.6 - - - +
220E LYS* 1.3 73.4 - - + +
222E ARG* 1.3 70.7 + - - +
223E PHE* 3.3 11.1 + - + +
242E PRO* 5.8 3.6 - - - +
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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