Contacts of the helix formed by residues 185 - 193 (chain G) 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 GLN 185 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183G THR 5.4 0.2 - - - +
184G GLU* 1.3 95.8 - - + +
186G GLU* 1.3 79.4 + - - +
187G ASP 2.9 6.5 - - - -
188G VAL* 2.9 33.7 + - + +
189G LEU* 3.0 13.5 + - - +
209G LEU* 4.2 31.8 - - + +
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Residues in contact with GLU 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G THR* 3.1 49.3 + - + +
184G GLU 3.1 1.0 - - - -
185G GLN* 1.3 95.9 + - - +
187G ASP* 1.3 60.3 + - - +
189G LEU* 3.8 16.1 - - + +
190G ALA* 3.3 21.3 + - - +
209G LEU 5.7 2.5 - - - +
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Residues in contact with ASP 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183G THR* 2.7 29.2 + - - +
184G GLU* 2.9 11.9 - - - +
185G GLN 2.9 0.2 - - - -
186G GLU* 1.3 78.7 - - - +
188G VAL* 1.3 60.6 + - + +
189G LEU 3.2 0.2 - - - -
190G ALA* 3.4 6.5 + - - +
191G LYS* 2.9 27.2 + - - +
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Residues in contact with VAL 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184G GLU* 4.5 5.4 - - - +
185G GLN* 2.9 24.9 + - + +
187G ASP* 1.3 76.3 - - + +
189G LEU* 1.3 59.7 + - - +
191G LYS* 3.0 31.2 + - - +
192G GLU* 2.8 37.8 + - + +
205G ARG* 5.7 3.1 - - - -
209G LEU* 4.0 20.2 - - + -
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Residues in contact with LEU 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G GLN 3.0 11.4 + - - +
186G GLU* 3.8 17.9 - - + +
188G VAL* 1.3 76.5 - - - +
190G ALA* 1.3 59.8 + - + +
192G GLU* 3.0 5.2 + - - +
193G LEU* 2.9 42.7 + - + +
206G ILE* 3.9 18.4 - - + +
209G LEU* 3.6 49.9 - - + +
210G SER* 3.9 15.0 - - - +
217G VAL* 4.6 11.2 - - + -
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Residues in contact with ALA 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G GLU 3.3 15.6 + - - +
187G ASP* 3.7 7.0 - - - +
188G VAL 3.3 0.6 - - - -
189G LEU* 1.3 82.0 - - + +
191G LYS* 1.3 58.1 + - - +
193G LEU* 3.6 14.9 + - - +
194G GLU* 3.1 24.0 + - - +
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Residues in contact with LYS 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187G ASP 2.9 14.2 + - - +
188G VAL* 3.0 34.6 + - - +
190G ALA* 1.3 74.9 - - - +
192G GLU* 1.3 78.9 + - - +
194G GLU* 3.1 37.9 - - - +
195G ASP* 4.2 5.2 - - - +
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Residues in contact with GLU 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188G VAL* 2.8 20.9 + - + +
189G LEU 3.4 6.3 - - - +
191G LYS* 1.3 88.8 - - - +
193G LEU* 1.3 57.6 + - - +
194G GLU 2.8 11.3 + - - -
195G ASP* 3.0 23.2 + - - +
201G LEU* 3.5 12.7 - - + +
202G HIS* 4.5 8.4 - - - +
205G ARG* 3.0 43.4 + - - +
206G ILE* 3.7 24.0 - - + -
209G LEU* 3.8 18.8 - - + -
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Residues in contact with LEU 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G LEU* 2.9 32.3 + - + +
190G ALA* 3.9 11.9 - - - +
191G LYS 3.4 0.4 - - - -
192G GLU* 1.3 74.8 - - - +
194G GLU* 1.3 59.7 + - - +
195G ASP 3.1 1.2 + - - -
196G VAL* 3.3 27.8 + - + +
201G LEU* 4.8 1.8 - - + -
206G ILE* 3.9 24.7 - - + -
217G VAL* 3.4 34.8 - - + -
218G ILE* 4.2 9.2 - - + -
221G THR* 3.8 34.7 - - + +
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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