Contacts of the helix formed by residues 202 - 210 (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 HIS 202 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192D GLU* 4.5 8.5 - - - +
195D ASP* 5.8 0.4 - - - +
200D GLY 3.3 4.7 + - - +
201D LEU* 1.3 75.2 - - - +
203D VAL* 1.3 60.7 + - - +
204D PHE* 3.2 37.3 + + + -
205D ARG* 3.1 54.3 + - + +
206D ILE* 3.3 25.2 + - - +
424D GLN* 3.1 28.8 + - - -
425D LEU* 4.1 11.6 - - + +
428D GLN* 3.8 5.8 + - - -
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Residues in contact with VAL 203 (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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201D LEU* 3.0 17.2 + - + +
202D HIS* 1.3 70.2 - - - +
204D PHE* 1.3 73.0 + - + +
206D ILE* 3.3 10.8 + - - +
207D ALA* 2.8 26.9 + - - +
214D PRO* 4.5 2.7 - - + -
218D ILE* 4.0 22.9 - - + -
260D ILE* 3.8 27.4 - - + +
263D ALA* 4.2 5.6 - - + -
264D ASP* 4.4 15.5 - - + +
425D LEU* 4.7 4.3 - - + -
429D TRP* 4.0 25.8 - - + +
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Residues in contact with PHE 204 (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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202D HIS* 3.2 11.7 + - + -
203D VAL* 1.3 75.5 - - + +
205D ARG* 1.3 64.9 + - - +
207D ALA* 3.2 18.3 - - - +
208D GLU* 3.3 15.3 + - - +
260D ILE* 4.0 13.0 - - + -
425D LEU* 3.8 21.8 - - + -
428D GLN* 3.4 45.8 - - + +
429D TRP* 3.5 51.8 - + - -
432D ARG* 3.1 42.2 - - - -
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Residues in contact with ARG 205 (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* 5.7 3.6 - - - -
192D GLU* 3.0 29.3 + - - +
202D HIS* 3.1 49.5 + - + +
204D PHE* 1.3 72.9 - - - +
206D ILE* 1.3 68.0 + - - +
208D GLU* 2.9 18.7 + - - +
209D LEU* 2.9 42.8 + - + +
424D GLN* 4.5 7.9 + - - +
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Residues in contact with ILE 206 (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* 3.9 16.9 - - + +
192D GLU* 3.7 24.9 - - + -
193D LEU* 3.9 31.2 - - + -
201D LEU* 3.6 39.9 - - + -
202D HIS 3.3 13.0 - - - +
203D VAL* 3.3 9.3 + - - +
205D ARG* 1.3 77.1 - - - +
207D ALA* 1.3 52.3 + - - +
209D LEU* 4.5 2.4 - - - +
210D SER* 2.7 34.1 + - - -
214D PRO* 4.5 6.3 - - + -
217D VAL* 4.5 5.8 - - + -
218D ILE* 4.3 15.0 - - + -
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Residues in contact with ALA 207 (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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203D VAL 2.8 14.3 + - - +
204D PHE* 3.2 15.7 - - + +
205D ARG 3.0 0.4 - - - -
206D ILE* 1.3 78.0 - - - +
208D GLU* 1.3 56.0 + - + +
210D SER* 3.0 9.0 + - - -
212D ASN* 2.8 36.3 + - - +
214D PRO* 3.9 23.6 - - + -
260D ILE* 4.2 19.7 - - + -
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Residues in contact with GLU 208 (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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204D PHE 3.7 14.1 - - - +
205D ARG* 2.9 18.2 + - - +
207D ALA* 1.3 73.8 - - + +
209D LEU* 1.3 56.9 - - + +
210D SER 2.8 5.1 + - - -
211D GLY* 2.8 26.0 + - - +
212D ASN 4.8 0.9 - - - +
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Residues in contact with LEU 209 (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* 4.2 38.8 - - + +
186D GLU* 5.7 2.3 - - - +
188D VAL* 4.0 13.2 - - + -
189D LEU* 3.5 41.5 - - + +
192D GLU* 3.8 29.8 - - + -
205D ARG* 2.9 37.3 + - + +
206D ILE 4.6 0.7 - - - +
208D GLU* 1.3 75.1 - - + +
210D SER* 1.3 56.6 + - - +
211D GLY 3.5 0.4 - - - -
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Residues in contact with SER 210 (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* 3.9 8.3 - - - -
206D ILE 2.7 22.1 + - - -
207D ALA 3.0 3.3 + - - -
208D GLU 2.8 1.6 + - - -
209D LEU* 1.3 77.6 - - - +
211D GLY* 1.3 64.0 + - - +
213D ARG* 2.9 38.1 + - - +
214D PRO 3.4 0.3 - - - -
217D VAL* 3.6 29.8 - - - +
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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