Contacts of the helix formed by residues 207 - 221 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199D ASN* 3.4 29.5 + - - +
200D PHE* 3.9 13.5 - - + -
204D SER* 4.0 3.1 + - - -
205D SER* 3.1 28.4 + - - +
206D LYS* 1.3 74.8 - - - +
208D PRO* 1.3 66.4 - - - +
209D LYS* 3.0 4.3 - - + -
210D LEU* 2.8 53.5 + - + +
259D LEU* 3.7 9.2 - - - +
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Residues in contact with PRO 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D LYS* 3.4 15.5 - - + +
207D GLN* 1.3 88.9 - - - +
209D LYS* 1.3 55.8 + - - +
210D LEU 3.1 0.7 - - - -
211D LEU* 3.0 8.3 + - - +
212D HIS* 2.8 51.0 + - + +
232D GLU* 3.6 50.0 - - + +
259D LEU* 4.8 0.4 - - + -
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Residues in contact with LYS 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D GLN* 2.9 3.4 + - + -
208D PRO* 1.3 76.9 - - - +
210D LEU* 1.3 59.8 + - - +
211D LEU 3.2 0.4 - - - -
212D HIS* 3.7 15.7 - - + -
213D ARG* 2.9 73.3 + - - +
216D GLU* 4.2 21.1 + - - +
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Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D ASP* 5.8 0.4 - - - +
173D TYR* 2.3 41.3 + - + +
195D LEU* 3.9 1.9 - - - +
197D HIS* 4.2 32.3 - - + +
199D ASN* 5.7 0.9 - - + -
200D PHE* 3.4 38.4 - - + +
207D GLN* 2.8 42.4 + - + +
209D LYS* 1.3 80.9 - - - +
211D LEU* 1.3 56.9 + - - +
213D ARG* 5.9 2.2 - - - +
214D VAL* 3.3 9.2 + - - +
259D LEU* 4.0 10.5 - - + -
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Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LEU* 4.2 11.9 - - + -
207D GLN 4.0 0.2 + - - -
208D PRO 3.0 8.9 + - - +
210D LEU* 1.3 80.4 - - - +
212D HIS* 1.3 56.9 + - + +
213D ARG 3.3 0.7 - - - -
214D VAL* 3.3 3.7 + - + +
215D VAL* 2.7 48.5 + - + +
231D GLY 4.1 8.7 - - - +
232D GLU 4.0 7.6 - - - +
233D THR 3.5 34.1 - - - +
234D LYS 3.9 1.6 - - - +
235D PHE* 3.8 16.2 - - + +
257D ILE* 3.3 35.7 - - + +
259D LEU* 3.9 18.8 - - + +
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Residues in contact with HIS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D PRO* 2.8 44.9 + - + +
209D LYS* 4.0 13.9 - - + -
211D LEU* 1.3 79.7 - - + +
213D ARG* 1.3 58.4 + - - +
215D VAL* 3.9 8.3 - - + +
216D GLU* 2.8 55.9 + - + +
230D LYS* 3.7 42.8 + - + +
231D GLY 3.1 28.0 + - - -
232D GLU* 4.6 2.4 - - - +
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Residues in contact with ARG 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D LEU* 3.1 62.6 + - + +
170D ASP* 3.7 23.0 + - - +
173D TYR* 3.9 18.4 + - - +
209D LYS* 2.9 44.3 + - - +
210D LEU* 5.9 1.9 - - - +
212D HIS* 1.3 76.4 - - - +
214D VAL* 1.3 61.6 + - - +
216D GLU* 4.3 4.0 - - - +
217D GLN* 3.4 15.6 + - - +
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Residues in contact with VAL 214 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D VAL* 5.8 0.7 - - + -
165D GLU* 6.0 0.4 - - + +
166D VAL* 3.8 25.1 - - + -
169D LEU* 3.8 9.4 - - + -
173D TYR* 3.4 28.3 - - + +
195D LEU* 3.6 21.1 - - + -
210D LEU 3.3 18.6 - - - +
211D LEU 3.3 8.0 + - - +
212D HIS 3.2 0.2 - - - -
213D ARG* 1.3 73.9 - - - +
215D VAL* 1.3 65.7 + - + +
217D GLN* 3.6 1.9 + - - +
218D LEU* 3.2 37.7 + - + +
257D ILE* 4.9 9.4 - - + -
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Residues in contact with VAL 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D LEU* 2.7 45.7 + - + +
212D HIS* 3.0 12.1 + - - +
214D VAL* 1.3 78.7 - - + +
216D GLU* 1.3 56.3 + - + +
218D LEU* 3.3 5.8 + - - +
219D GLN* 2.8 44.7 + - - +
224D ILE* 3.9 11.7 - - + +
230D LYS* 5.1 9.0 - - + -
235D PHE* 3.6 41.5 - - + -
257D ILE* 4.9 5.4 - - + -
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Residues in contact with GLU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D LYS* 4.2 19.0 + - - +
212D HIS* 2.8 41.5 + - + +
213D ARG* 4.5 2.9 - - - +
215D VAL* 1.3 73.2 - - + +
217D GLN* 1.3 60.3 + - - +
219D GLN* 3.2 22.2 - - - +
220D LYS* 3.1 36.4 + - - +
230D LYS* 5.4 6.6 + - + +
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Residues in contact with GLN 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D GLU* 3.4 37.2 + - + +
169D LEU* 3.7 28.5 - - + +
213D ARG 3.4 17.7 + - - +
214D VAL 3.8 3.8 - - - +
215D VAL 3.2 0.2 - - - -
216D GLU* 1.3 74.8 - - - +
218D LEU* 1.3 57.9 + - - +
219D GLN 2.9 4.3 - - - -
220D LYS* 2.8 61.2 + - - +
221D VAL* 3.0 23.2 + - - +
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Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ILE* 4.6 1.1 - - + +
162D VAL* 4.2 24.2 - - + +
165D GLU* 4.1 27.8 - - + -
166D VAL* 5.7 0.2 - - + -
214D VAL* 3.2 27.6 + - + +
215D VAL 3.3 0.4 + - - +
217D GLN* 1.3 76.3 - - - +
219D GLN* 1.3 58.7 + - - +
221D VAL* 3.6 5.8 - - + +
222D ARG 3.6 0.9 + - - -
223D PHE* 2.9 53.3 + - + -
224D ILE* 3.1 38.4 + - + -
255D ILE* 5.3 0.7 - - + -
257D ILE* 4.0 21.1 - - + -
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Residues in contact with GLN 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D VAL* 2.8 34.0 - - + +
216D GLU* 3.2 28.8 + - - +
217D GLN 2.9 0.4 - - - -
218D LEU* 1.3 77.9 - - - +
220D LYS* 1.3 68.6 + - - +
222D ARG* 3.0 15.8 + - - +
224D ILE* 4.2 26.7 + - + +
225D THR 6.0 0.8 + - - -
226D ASP* 6.0 0.8 - - - +
227D THR* 4.3 15.9 + - - -
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Residues in contact with LYS 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D LEU* 5.7 1.2 - - - +
216D GLU* 3.1 22.8 + - - +
217D GLN* 2.8 42.5 + - - +
219D GLN* 1.3 76.3 - - - +
221D VAL* 1.3 54.9 + - + +
222D ARG* 2.7 24.8 + - - +
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Residues in contact with VAL 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D ILE* 4.7 6.2 - - + +
165D GLU* 3.4 42.4 - - + +
168D LYS* 5.9 0.4 - - - +
217D GLN* 3.0 24.4 + - - +
218D LEU* 3.6 17.9 - - + +
220D LYS* 1.3 72.8 - - + +
222D ARG* 1.3 68.6 + - - +
223D PHE* 3.3 12.2 + - + +
242D PRO* 5.7 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