Contacts of the strand formed by residues 212 - 219 (chain D) in PDB entry 1M6X
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 GLY 212 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207D GLN* 3.5 6.2 + - - +
208D ASN 3.0 27.4 + - - +
211D LEU* 1.3 75.6 - - - +
213D VAL* 1.3 68.9 + - - +
381D ILE* 3.7 19.5 - - - +
384D TRP* 4.0 22.7 - - - -
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Residues in contact with VAL 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 LEU* 4.5 16.2 - - + -
206D VAL 3.3 15.7 - - - +
207D GLN* 4.3 10.3 - - + +
208D ASN 4.5 0.4 - - - +
211D LEU* 3.1 10.5 + - - +
212D GLY* 1.3 83.3 - - - +
214D ILE* 1.3 73.6 + - - +
233D PHE* 5.0 2.6 - - - +
234D SER 5.5 1.0 + - - -
384D TRP* 3.4 51.9 - - + +
414D TYR* 3.8 32.7 + - + +
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Residues in contact with ILE 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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205D LEU* 3.5 4.5 - - - -
206D VAL* 2.9 45.9 + - + +
207D GLN 5.3 1.1 - - - +
208D ASN* 4.1 18.2 - - + +
211D LEU* 4.0 17.7 - - + -
213D VAL* 1.3 82.5 - - - +
215D ILE* 1.3 62.6 + - - +
216D GLN 3.7 0.2 + - - -
231D TYR* 3.4 32.8 - - + -
232D PHE 3.8 9.6 - - - +
233D PHE* 3.6 22.2 - - + +
355D PHE* 3.8 27.4 - - + -
414D TYR* 5.6 1.3 - - - -
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Residues in contact with ILE 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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203D PHE* 3.4 35.2 - - + -
204D LYS 3.4 10.1 - - - +
205D LEU* 4.1 14.8 - - + -
214D ILE* 1.3 74.1 - - - +
216D GLN* 1.3 61.9 + - - +
217D CYS 4.4 0.2 - - - -
231D TYR* 3.2 8.5 - - - +
232D PHE* 2.8 42.7 + - + +
242D LEU* 3.7 17.7 - - + -
245D LEU* 3.6 26.0 - - + -
411D VAL* 4.1 17.3 - - + -
414D TYR* 4.2 17.5 - - + -
415D LEU* 4.5 7.0 - - + -
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Residues in contact with GLN 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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202D SER 3.3 4.5 - - - +
203D PHE* 3.5 0.6 - - - -
204D LYS* 2.8 54.3 + - - +
206D VAL* 3.6 35.5 - - + +
214D ILE 3.7 0.4 + - - -
215D ILE* 1.3 76.2 - - - +
217D CYS* 1.3 64.2 + - - +
229D HIS* 3.4 50.2 + - + +
230D ILE 3.4 3.4 - - - -
231D TYR* 3.5 31.4 + - + -
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Residues in contact with CYS 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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198D VAL* 3.4 26.0 - - + -
202D SER* 3.7 9.2 - - - +
203D PHE* 4.0 25.6 - - + -
216D GLN* 1.3 75.3 - - - +
218D LEU* 1.3 60.5 + - - +
229D HIS* 3.1 14.1 + - - +
230D ILE* 2.8 62.4 + - - -
232D PHE* 3.9 15.5 - - - -
274D LEU* 5.8 0.2 - - - -
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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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198D VAL* 3.6 2.0 - - - -
199D ASP* 3.0 31.0 + - + +
202D SER* 2.9 26.1 + - - +
217D CYS* 1.3 76.9 - - - +
219D VAL* 1.3 73.6 + - - +
220D THR* 4.0 14.4 + - - +
227D SER* 4.3 11.7 - - - -
228D ARG* 3.5 19.3 - - - +
229D HIS* 3.7 25.4 - - + +
347D ILE* 5.1 6.3 - - + -
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Residues in contact with VAL 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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193D SER 4.1 1.8 - - - +
194D ASP 3.0 33.7 - - - +
197D ASN* 3.6 30.7 - - + +
198D VAL* 3.7 4.5 - - + -
218D LEU* 1.3 76.4 - - - +
220D THR* 1.3 63.5 + - - +
221D GLU 4.5 1.6 - - - +
222D THR* 4.0 19.8 - - + +
227D SER* 3.2 6.6 - - - -
228D ARG* 2.8 37.0 + - + +
230D ILE* 3.4 26.9 - - + -
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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