Contacts of the helix formed by residues 185 - 193 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183D THR 5.4 0.2 - - - +
184D GLU* 1.3 94.7 - - + +
186D GLU* 1.3 81.1 + - - +
187D ASP 2.9 6.3 - - - -
188D VAL* 2.9 32.3 + - + +
189D LEU* 2.9 13.5 + - - +
209D LEU* 4.2 34.0 - - + +
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Residues in contact with GLU 186 (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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183D THR* 3.1 49.6 + - - +
184D GLU 3.1 0.6 - - - -
185D GLN* 1.3 95.7 + - - +
187D ASP* 1.3 60.6 + - - +
189D LEU* 3.8 16.3 - - + +
190D ALA* 3.3 21.3 + - - +
209D LEU 5.7 2.0 - - - +
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Residues in contact with ASP 187 (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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183D THR* 2.7 28.7 + - - +
184D GLU* 2.9 11.3 - - - +
185D GLN 2.9 0.2 - - - -
186D GLU* 1.3 79.8 - - - +
188D VAL* 1.3 61.8 + - + +
189D LEU 3.3 0.2 - - - -
190D ALA* 3.4 6.7 + - - +
191D LYS* 2.9 27.5 + - - +
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Residues in contact with VAL 188 (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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184D GLU* 4.5 4.9 - - - +
185D GLN* 2.9 25.3 + - + +
187D ASP* 1.3 74.6 - - + +
189D LEU* 1.3 60.0 + - - +
191D LYS* 3.0 31.6 + - - +
192D GLU* 2.8 38.1 + - + +
205D ARG* 5.7 3.6 - - - -
209D LEU* 4.0 20.4 - - + -
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Residues in contact with LEU 189 (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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185D GLN 2.9 11.6 + - - +
186D GLU* 3.8 19.1 - - + +
188D VAL* 1.3 76.3 - - - +
190D ALA* 1.3 59.8 + - + +
192D GLU* 3.0 5.2 + - - +
193D LEU* 2.9 44.1 + - + +
206D ILE* 3.9 19.3 - - + +
209D LEU* 3.5 48.6 - - + +
210D SER* 3.8 16.4 - - - +
217D VAL* 4.6 9.4 - - + -
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Residues in contact with ALA 190 (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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186D GLU 3.3 15.6 + - - +
187D ASP* 3.7 6.5 - - - +
188D VAL 3.3 0.4 - - - -
189D LEU* 1.3 82.5 - - + +
191D LYS* 1.3 58.4 + - - +
193D LEU* 3.7 14.1 + - - +
194D GLU* 3.1 23.5 + - - +
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Residues in contact with LYS 191 (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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187D ASP 2.9 14.6 + - - +
188D VAL* 3.0 33.6 + - - +
190D ALA* 1.3 75.3 - - - +
192D GLU* 1.3 79.3 + - - +
194D GLU* 3.1 37.8 - - - +
195D ASP* 4.2 5.4 - - - +
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Residues in contact with GLU 192 (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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188D VAL* 2.8 21.0 + - + +
189D LEU* 3.4 6.7 - - - +
191D LYS* 1.3 89.9 - - - +
193D LEU* 1.3 58.0 + - - +
194D GLU 2.8 11.4 + - - -
195D ASP* 3.0 22.2 + - - +
201D LEU* 3.5 12.6 - - + +
202D HIS* 4.5 8.3 - - - +
205D ARG* 3.0 42.8 + - - +
206D ILE* 3.7 23.8 - - + -
209D LEU* 3.8 18.8 - - + -
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Residues in contact with LEU 193 (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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189D LEU* 2.9 31.9 + - + +
190D ALA* 3.9 11.4 - - - +
191D LYS 3.4 0.2 - - - -
192D GLU* 1.3 75.0 - - - +
194D GLU* 1.3 61.2 + - - +
195D ASP 3.1 1.4 + - - -
196D VAL* 3.3 26.1 + - + +
201D LEU* 4.8 2.5 - - + -
206D ILE* 3.9 24.2 - - + -
217D VAL* 3.4 36.6 - - + -
218D ILE* 4.2 8.7 - - + -
221D THR* 3.7 34.4 - - + +
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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