Contacts of the helix formed by residues 202 - 210 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192I GLU* 4.5 10.5 - - - +
195I ASP* 5.8 0.2 - - - +
200I GLY 3.3 4.2 + - - +
201I LEU* 1.3 78.2 - - - +
203I VAL* 1.3 60.8 + - - +
204I PHE* 3.2 38.2 + + + -
205I ARG* 3.1 50.7 + - + +
206I ILE* 3.3 22.2 + - - +
424I GLN* 3.1 28.0 + - - -
425I LEU* 4.0 12.4 - - + +
428I GLN* 3.8 5.1 + - - -
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Residues in contact with VAL 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201I LEU* 2.9 19.8 + - + +
202I HIS* 1.3 70.6 + - - +
204I PHE* 1.3 72.2 + - + +
206I ILE* 3.3 10.6 + - - +
207I ALA* 2.8 27.4 + - - +
214I PRO* 4.5 2.5 - - + -
218I ILE* 4.0 21.5 - - + -
260I ILE* 3.8 26.2 - - + +
263I ALA* 4.2 6.3 - - + -
264I ASP* 4.4 17.0 - - - +
425I LEU* 4.8 4.0 - - + -
429I TRP* 4.0 25.8 - - + +
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Residues in contact with PHE 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202I HIS* 3.2 12.6 + - + -
203I VAL* 1.3 76.3 - - + +
205I ARG* 1.3 66.2 + - - +
207I ALA* 3.2 18.2 - - - +
208I GLU* 3.3 13.9 + - - +
260I ILE* 4.0 13.7 - - + -
425I LEU* 3.8 21.5 - - + -
428I GLN* 3.4 44.4 - - + +
429I TRP* 3.5 52.9 - + - -
432I ARG* 3.0 42.0 - - - -
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Residues in contact with ARG 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188I VAL* 5.7 3.4 - - - -
192I GLU* 3.1 29.2 + - - +
202I HIS* 3.1 50.9 + - + +
204I PHE* 1.3 72.9 - - - +
206I ILE* 1.3 68.6 + - - +
208I GLU* 2.9 18.3 + - - +
209I LEU* 2.9 42.6 + - + +
424I GLN* 4.5 7.7 + - - +
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Residues in contact with ILE 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I LEU* 3.9 11.7 - - + +
192I GLU* 3.7 24.7 - - + -
193I LEU* 3.8 31.0 - - + -
201I LEU* 3.6 38.8 - - + -
202I HIS 3.3 14.3 + - - +
203I VAL* 3.5 9.0 - - - +
205I ARG* 1.3 76.8 - - - +
207I ALA* 1.3 53.3 + - - +
209I LEU* 4.5 7.0 - - - -
210I SER* 2.7 35.2 + - - +
214I PRO* 4.5 8.5 - - + -
217I VAL* 4.5 4.0 - - + -
218I ILE* 4.3 15.7 - - + -
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Residues in contact with ALA 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203I VAL 2.8 13.8 + - - +
204I PHE* 3.2 15.5 - - + +
205I ARG 3.0 0.2 - - - -
206I ILE* 1.3 77.8 - - - +
208I GLU* 1.3 55.8 + - + +
210I SER* 3.0 9.1 + - - -
212I ASN* 2.7 37.4 + - - +
214I PRO* 3.9 22.4 - - + -
260I ILE* 4.2 21.1 - - + -
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Residues in contact with GLU 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204I PHE 3.7 12.8 - - - +
205I ARG* 2.9 18.6 + - - +
207I ALA* 1.3 74.1 - - + +
209I LEU* 1.3 59.7 - - + +
210I SER 2.9 4.7 - - - -
211I GLY* 2.8 22.5 + - - -
212I ASN 4.8 0.9 - - - +
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Residues in contact with LEU 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I GLN* 4.2 38.2 - - + +
186I GLU* 5.7 2.6 - - - +
188I VAL* 4.0 13.9 - - + -
189I LEU* 3.5 48.9 - - + +
192I GLU* 3.8 20.9 - - + -
205I ARG* 2.9 37.5 + - + +
206I ILE* 4.6 1.1 - - - +
208I GLU* 1.3 74.1 - - + +
210I SER* 1.3 57.1 + - - +
211I GLY 3.5 0.4 - - - -
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Residues in contact with SER 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I LEU* 3.9 8.3 - - - -
206I ILE 2.7 21.8 + - - -
207I ALA 3.0 3.5 + - - -
208I GLU 2.8 2.0 + - - -
209I LEU* 1.3 78.6 - - - +
211I GLY* 1.3 63.6 + - - +
212I ASN 3.4 0.2 + - - -
213I ARG* 2.9 38.4 + - - +
214I PRO 3.3 0.3 - - - -
217I VAL* 3.7 28.3 - - - -
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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