Contacts of the helix formed by residues 211 - 219 (chain D) in PDB entry 6DWM
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 HIS 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205D ARG* 4.4 11.2 + - - -
207D TYR* 3.7 35.4 - + + -
208D ASP* 3.0 28.0 + - + +
209D HIS 3.7 0.2 - - - -
210D ASN* 1.3 75.4 - - - +
212D GLN* 1.3 60.5 + - - +
213D GLU* 3.5 46.0 + - + +
214D LEU* 3.4 8.2 + - + +
215D LEU* 3.0 26.9 + - - +
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Residues in contact with GLN 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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210D ASN 3.1 7.3 + - - +
211D HIS* 1.3 71.8 - - - +
213D GLU* 1.3 57.8 + - - +
215D LEU* 3.7 32.8 - - - +
216D SER* 2.6 50.0 + - - +
220D LEU* 5.5 7.7 - - - +
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Residues in contact with GLU 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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205D ARG* 5.3 1.4 + - - -
207D TYR* 4.1 14.0 + - + -
211D HIS* 3.4 27.0 + - + -
212D GLN* 1.3 81.1 - - - +
214D LEU* 1.3 62.6 + - - +
216D SER* 3.4 6.8 + - - -
217D LEU* 3.3 19.0 + - + +
257D LYS* 5.0 1.0 + - - -
261D PHE* 4.2 21.0 - - + -
264D LYS* 2.6 39.2 + - - +
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Residues in contact with LEU 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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192D VAL* 3.6 41.7 - - + -
195D THR* 3.6 26.5 - - + -
196D ASN* 4.1 4.7 - - - +
207D TYR* 3.7 48.6 - - + -
208D ASP 4.8 1.6 - - - +
211D HIS* 3.4 10.1 + - + +
212D GLN 3.2 0.4 - - - -
213D GLU* 1.3 76.4 - - - +
215D LEU* 1.3 56.2 + - + +
217D LEU* 2.6 37.4 + - + +
218D VAL* 2.9 26.0 + - + +
261D PHE* 5.8 1.8 - - + -
315D PHE* 4.9 2.2 - - + -
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Residues in contact with LEU 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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188D ARG* 3.4 51.8 - - - +
192D VAL* 3.6 23.1 - - + -
208D ASP 5.8 0.2 - - - +
209D HIS 3.9 7.4 - - - +
210D ASN* 4.1 8.3 - - - +
211D HIS 3.0 20.9 + - - +
212D GLN* 3.7 29.4 - - - +
214D LEU* 1.3 76.2 - - + +
216D SER* 1.3 57.5 + - - +
218D VAL* 4.4 4.9 - - + -
219D ASN* 3.1 46.2 + - + +
220D LEU* 3.6 1.2 - - - +
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Residues in contact with SER 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 GLN* 2.6 32.8 + - - +
213D GLU* 3.5 8.1 - - - -
215D LEU* 1.3 72.7 - - - +
217D LEU* 1.3 53.4 + - - +
220D LEU* 3.5 37.1 - - - +
257D LYS* 2.7 36.3 + - - -
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Residues in contact with LEU 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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213D GLU* 3.3 10.4 + - + +
214D LEU* 2.6 25.7 + - + +
216D SER* 1.3 73.6 - - - +
218D VAL* 1.3 59.3 + - + +
219D ASN 3.7 0.9 - - - -
222D ASN* 3.2 19.6 + - - +
254D LEU* 5.0 0.5 - - - +
257D LYS* 3.3 23.7 + - + +
258D PHE* 3.5 46.4 - - + -
261D PHE* 3.8 48.7 - - + -
315D PHE* 3.9 23.6 - - + -
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Residues in contact with VAL 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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187D TYR* 4.2 8.1 + - - -
191D VAL* 3.7 36.3 - - + +
192D VAL* 4.9 2.5 - - + -
195D THR* 3.7 28.9 - - + +
214D LEU* 2.9 35.3 + - + +
215D LEU* 4.4 4.3 - - - -
217D LEU* 1.3 85.7 - - + +
219D ASN* 1.3 61.9 + - + +
222D ASN* 2.8 16.6 + - - +
315D PHE* 4.9 1.3 - - + -
319D PHE* 3.6 31.9 - - + -
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Residues in contact with ASN 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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187D TYR* 3.7 24.0 - - - -
188D ARG* 3.8 34.6 + - - +
191D VAL* 4.4 11.7 - - + -
215D LEU* 3.1 23.1 + - + +
218D VAL* 1.3 82.9 - - + +
220D LEU* 1.3 60.6 + - - +
221D ASN 4.2 0.7 - - - -
222D ASN* 3.8 1.3 - - - +
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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