Contacts of the helix formed by residues 202 - 210 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510B SER* 5.1 4.7 - - - -
192C GLU* 4.5 7.6 - - - +
195C ASP* 5.8 0.2 - - - +
200C GLY 3.3 4.3 + - - +
201C LEU* 1.3 77.8 - - - +
203C VAL* 1.3 59.7 + - - +
204C PHE* 3.2 37.3 + + + -
205C ARG* 3.1 54.5 + - + +
206C ILE* 3.3 23.1 + - - +
424C GLN* 3.1 28.2 + - - -
425C LEU* 4.0 12.2 - - + +
428C GLN* 3.7 5.3 + - - -
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Residues in contact with VAL 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C LEU* 3.0 16.8 + - + +
202C HIS* 1.3 71.8 - - - +
204C PHE* 1.3 68.9 + - + +
206C ILE* 3.2 10.7 + - - +
207C ALA* 2.8 26.9 + - - +
214C PRO* 4.5 2.6 - - + +
218C ILE* 4.0 23.6 - - + -
260C ILE* 3.8 26.9 - - + +
263C ALA* 4.2 5.4 - - + -
264C ASP* 4.4 16.4 - - + +
267C GLN* 6.5 0.2 - - + -
425C LEU* 4.7 4.5 - - + +
429C TRP* 4.0 26.0 - - + +
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Residues in contact with PHE 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C HIS* 3.2 16.2 + + + -
203C VAL* 1.3 75.4 - - + +
205C ARG* 1.3 65.4 + - - +
207C ALA* 3.2 18.4 - - - +
208C GLU* 3.3 14.9 + - - +
260C ILE* 4.0 13.5 - - + -
425C LEU* 3.8 13.5 - - + -
428C GLN* 3.4 46.9 - - + +
429C TRP* 3.5 54.3 - + - -
432C ARG* 3.1 41.7 - - - -
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Residues in contact with ARG 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B SER* 3.7 33.5 + - - -
188C VAL* 5.7 3.4 - - - -
192C GLU* 3.0 29.7 + - - +
202C HIS* 3.1 51.0 + - + +
204C PHE* 1.3 72.5 - - - +
206C ILE* 1.3 67.1 + - - +
208C GLU* 3.0 17.9 + - - +
209C LEU* 2.9 42.2 + - + +
424C GLN* 4.5 3.2 - - - +
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Residues in contact with ILE 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LEU* 4.0 11.1 - - + +
192C GLU* 3.7 24.9 - - + -
193C LEU* 3.8 30.7 - - + -
201C LEU* 3.6 39.9 - - + -
202C HIS 3.3 12.8 - - - +
203C VAL* 3.2 9.1 + - - +
205C ARG* 1.3 76.8 - - - +
207C ALA* 1.3 53.6 + - - +
209C LEU* 4.0 7.6 - - - -
210C SER* 2.8 34.7 + - - -
214C PRO* 4.5 6.3 - - + -
217C VAL* 4.5 6.3 - - + -
218C ILE* 4.3 14.8 - - + -
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Residues in contact with ALA 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C VAL 2.8 13.2 + - - +
204C PHE* 3.2 15.7 - - - +
205C ARG 3.0 0.2 - - - -
206C ILE* 1.3 77.8 - - - +
208C GLU* 1.3 54.5 + - + +
210C SER* 3.0 9.0 + - - -
212C ASN* 2.8 36.9 + - - +
214C PRO* 3.9 23.6 - - + -
260C ILE* 4.2 20.9 - - + -
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Residues in contact with GLU 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C PHE 3.3 13.5 + - - +
205C ARG* 3.0 16.1 + - - +
207C ALA* 1.3 74.4 - - + +
209C LEU* 1.3 58.0 + - + +
210C SER 2.8 5.5 + - - -
211C GLY* 2.8 26.0 + - - -
212C ASN 4.8 1.1 - - - +
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Residues in contact with LEU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C GLN* 4.2 39.4 - - + +
186C GLU* 5.8 1.9 - - - +
188C VAL* 4.0 12.3 - - + -
189C LEU* 3.6 42.0 - - + +
192C GLU* 3.8 29.4 - - + -
205C ARG* 2.9 36.6 + - + +
206C ILE* 4.6 1.3 - - - +
208C GLU* 1.3 73.4 - - + +
210C SER* 1.3 57.9 + - - +
211C GLY 3.5 0.4 + - - -
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Residues in contact with SER 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LEU* 3.9 8.1 - - - -
206C ILE 2.8 21.5 + - - -
207C ALA 3.0 3.3 + - - -
208C GLU 2.8 1.8 + - - -
209C LEU* 1.3 77.4 - - - +
211C GLY* 1.3 62.6 + - - +
213C ARG* 2.9 39.0 + - - +
214C PRO 3.4 0.3 - - - -
217C VAL* 3.7 28.5 - - - -
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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