Contacts of the helix formed by residues 206 - 216 (chain D) in PDB entry 6M04
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 206 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D LYS 4.2 6.0 + - - -
203D CYS* 4.1 5.8 + - - -
204D PHE 3.3 4.9 - - - +
205D GLU* 1.3 77.9 - - - +
207D PRO* 1.3 59.8 - - - +
208D TRP* 3.2 18.7 + - - +
209D THR* 2.6 41.0 + - - +
280D ASP* 4.0 9.3 + - - +
283D GLN* 6.3 1.6 - - - -
284D ALA* 4.0 19.5 + - - +
287D LEU* 5.5 4.5 - - - -
437D PHE* 5.0 4.0 - - - -
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Residues in contact with PRO 207 (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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205D GLU 3.6 9.9 - - - +
206D SER* 1.3 80.4 - - - +
208D TRP* 1.3 59.4 + - - +
209D THR 3.2 0.4 - - - -
210D THR* 3.2 19.2 - - + +
211D LYS* 3.0 27.2 + - - +
277D ASP* 6.1 0.7 - - - +
280D ASP* 3.3 26.9 - - + +
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Residues in contact with TRP 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 SER* 3.2 9.3 - - - +
207D PRO* 1.3 78.8 - - - +
209D THR* 1.3 71.6 + - + +
211D LYS* 3.5 31.9 - - - +
212D ALA* 2.8 43.9 + - + +
280D ASP* 3.2 27.1 + - + +
284D ALA* 4.8 0.9 - - + -
288D PHE* 4.2 9.6 - + - -
436D VAL* 5.5 4.5 - - + -
437D PHE* 4.3 17.5 - + - -
442D SER* 3.1 40.4 - - - -
445D LYS* 4.6 9.7 - - + +
446D LEU* 3.5 50.1 - - + +
449D ILE* 5.5 6.7 - - + +
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Residues in contact with THR 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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203D CYS 4.4 8.5 + - - +
204D PHE 5.1 1.6 + - - -
206D SER* 2.6 28.6 + - - +
208D TRP* 1.3 89.8 - - + +
210D THR* 1.3 61.8 + - - +
212D ALA* 3.4 2.2 + - - +
213D LEU* 2.9 38.5 + - - +
433D ARG* 3.9 30.1 - - - +
436D VAL* 5.7 3.8 - - + -
437D PHE* 3.7 35.2 - - + +
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Residues in contact with THR 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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207D PRO* 3.2 26.7 - - + +
209D THR* 1.3 80.6 + - - +
211D LYS* 1.3 61.0 + - - +
213D LEU* 3.8 7.0 - - - +
214D SER* 2.9 27.7 + - - -
433D ARG* 6.1 1.3 - - - -
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Residues in contact with LYS 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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207D PRO 3.0 19.0 + - - +
208D TRP* 3.2 31.7 + - - +
210D THR* 1.3 77.9 - - - +
212D ALA* 1.3 57.3 + - - +
214D SER* 2.3 28.0 + - - +
215D GLU* 2.9 13.6 + - + +
277D ASP* 3.5 33.7 + - - +
280D ASP* 5.4 2.2 + - - -
449D ILE* 4.9 14.2 - - - +
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Residues in contact with ALA 212 (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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208D TRP* 2.8 47.7 + - + +
209D THR* 3.9 4.0 - - - +
211D LYS* 1.3 74.8 - - - +
213D LEU* 1.3 56.4 + - + +
215D GLU* 3.6 11.6 - - - +
216D THR* 2.6 37.6 + - - +
409D ILE* 5.4 0.4 - - + +
436D VAL* 5.5 3.6 - - + -
442D SER* 5.0 3.6 - - - +
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Residues in contact with LEU 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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209D THR* 2.9 28.5 + - - +
210D THR* 3.9 7.9 - - - +
212D ALA* 1.3 77.3 - - + +
214D SER* 1.3 63.0 + - - +
215D GLU 3.2 0.6 - - - -
216D THR* 3.4 28.6 + - - +
407D SER 6.1 0.9 - - - +
409D ILE* 5.8 0.7 - - + -
432D LYS* 5.5 9.6 - - + -
433D ARG* 5.6 8.1 - - + -
436D VAL* 3.7 42.0 - - + -
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Residues in contact with SER 214 (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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210D THR 2.9 15.0 + - - -
211D LYS* 2.3 34.0 + - - +
213D LEU* 1.3 76.2 - - - +
215D GLU* 1.3 61.4 + - - +
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Residues in contact with GLU 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 LYS* 2.9 11.8 + - - +
212D ALA* 3.6 13.5 - - - +
213D LEU 3.2 0.6 - - - -
214D SER* 1.3 79.5 + - - +
216D THR* 1.3 68.4 + - - +
445D LYS* 6.0 2.5 - - - -
449D ILE* 5.9 2.9 - - - +
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Residues in contact with THR 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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212D ALA 2.6 25.3 + - - +
213D LEU* 3.4 33.2 - - - +
215D GLU* 1.3 86.1 + - - +
407D SER 4.8 1.8 - - - +
408D ASP* 3.6 31.6 - - + +
409D ILE* 3.4 36.4 - - + +
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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