Contacts of the helix formed by residues 202 - 210 (chain K) in PDB entry 1MKD
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 202 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192K GLU* 4.5 7.9 - - - +
195K ASP* 5.8 0.2 - - - +
200K GLY 3.3 3.6 + - - +
201K LEU* 1.3 76.3 - - - +
203K VAL* 1.3 59.6 - - - +
204K PHE* 3.2 37.1 + + + -
205K ARG* 3.1 54.6 + - + +
206K ILE* 3.3 22.7 + - - +
424K GLN* 3.1 29.0 + - - -
425K LEU* 4.0 12.0 - - + +
428K GLN* 3.8 5.1 + - - -
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Residues in contact with VAL 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201K LEU* 2.9 16.3 + - + +
202K HIS* 1.3 72.0 + - - +
204K PHE* 1.3 69.4 + - + +
206K ILE* 3.3 11.3 + - - +
207K ALA* 2.8 26.5 + - - +
214K PRO* 4.5 2.6 - - + +
218K ILE* 4.0 23.1 - - + -
260K ILE* 3.8 27.1 - - + +
263K ALA* 4.2 6.1 - - + -
264K ASP* 4.4 16.2 - - + +
267K GLN* 6.5 0.2 - - + -
425K LEU* 4.8 4.0 - - + -
429K TRP* 4.0 26.0 - - + +
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Residues in contact with PHE 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202K HIS* 3.2 12.2 + + + -
203K VAL* 1.3 75.5 - - + +
205K ARG* 1.3 67.1 + - - +
207K ALA* 3.2 18.2 - - - +
208K GLU* 3.3 14.1 + - - +
260K ILE* 4.0 21.1 - - + -
425K LEU* 3.8 20.6 - - + -
428K GLN* 3.4 45.3 - - + +
429K TRP* 3.5 43.7 - + - -
432K ARG* 3.1 42.2 - - - -
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Residues in contact with ARG 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K VAL* 5.7 3.1 - - - -
192K GLU* 3.0 30.4 + - - +
202K HIS* 3.1 50.5 + - + +
204K PHE* 1.3 74.8 - - - +
206K ILE* 1.3 65.1 + - - +
208K GLU* 2.9 17.9 + - - +
209K LEU* 2.9 43.4 + - + +
424K GLN* 4.5 8.3 + - - +
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Residues in contact with ILE 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K LEU* 3.9 16.1 - - + +
192K GLU* 3.7 24.7 - - + -
193K LEU* 3.8 31.0 - - + -
201K LEU* 3.6 39.0 - - + -
202K HIS 3.3 13.5 - - - +
203K VAL* 3.3 8.7 + - - +
205K ARG* 1.3 76.3 - - - +
207K ALA* 1.3 53.3 + - - +
209K LEU* 4.5 2.4 - - - +
210K SER* 2.8 35.0 + - - -
214K PRO* 4.5 6.5 - - + -
217K VAL* 4.5 6.1 - - + -
218K ILE* 4.3 15.5 - - + -
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Residues in contact with ALA 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203K VAL 2.8 13.0 + - - +
204K PHE* 3.2 16.4 - - - +
205K ARG 3.0 0.2 - - - -
206K ILE* 1.3 78.0 - - - +
208K GLU* 1.3 55.5 + - + +
210K SER* 3.1 8.9 + - - -
212K ASN* 2.7 36.6 + - - +
214K PRO* 3.9 22.0 - - + -
260K ILE* 4.2 20.6 - - + -
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Residues in contact with GLU 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204K PHE 3.3 13.7 + - - +
205K ARG* 2.9 17.4 + - - +
207K ALA* 1.3 73.6 - - + +
209K LEU* 1.3 57.7 + - + +
210K SER 2.8 5.5 + - - -
211K GLY* 2.7 26.6 + - - -
212K ASN 4.8 0.7 - - - +
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Residues in contact with LEU 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K GLN* 4.2 39.4 - - + +
186K GLU* 5.7 2.4 - - - +
188K VAL* 4.0 13.7 - - + -
189K LEU* 3.6 41.5 - - + +
192K GLU* 3.8 29.4 - - + -
205K ARG* 2.9 37.8 + - + +
206K ILE* 4.6 1.3 - - - +
208K GLU* 1.3 74.0 - - + +
210K SER* 1.3 56.8 + - - +
211K GLY 3.5 0.2 - - - -
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Residues in contact with SER 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K LEU* 3.9 8.5 - - - -
206K ILE 2.8 22.0 + - - -
207K ALA 3.1 3.8 + - - -
208K GLU 2.9 1.4 - - - -
209K LEU* 1.3 77.4 - - - +
211K GLY* 1.3 63.8 + - - +
213K ARG* 2.9 38.8 + - - +
214K PRO 3.4 0.3 - - - -
217K VAL* 3.7 28.7 - - - +
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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