Contacts of the helix formed by residues 183 - 199 (chain A) in PDB entry 4DM8
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 THR 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A GLU* 3.8 14.6 + - + +
182A MET* 1.3 82.2 - - - +
184A ALA* 1.3 63.7 + - - +
185A GLU 3.5 1.8 - - - -
186A LEU* 3.6 23.7 + - + -
187A ASP* 2.5 45.6 + - - +
363A ILE* 3.9 27.3 - - + +
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A MET* 3.9 7.9 - - + +
183A THR* 1.3 73.3 - - - +
185A GLU* 1.3 68.3 + - + +
187A ASP* 3.1 16.4 + - - +
188A ASP* 3.1 13.5 + - - +
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Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A THR 3.5 0.4 - - - -
184A ALA* 1.3 79.2 - - + +
186A LEU* 1.3 64.7 + - + +
188A ASP* 3.1 16.6 + - - +
189A LEU* 3.2 13.3 + - - +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A THR* 3.6 21.3 + - + +
184A ALA 3.4 0.4 - - - -
185A GLU* 1.3 81.9 - - + +
187A ASP* 1.3 56.5 + - - +
189A LEU* 3.4 7.8 + - + +
190A THR* 2.7 38.2 + - - -
356A PRO* 3.8 36.6 - - + +
359A GLU* 3.4 41.7 - - + +
360A ALA* 4.3 9.2 - - + +
363A ILE* 3.8 21.1 - - + -
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Residues in contact with ASP 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A THR* 2.5 39.8 + - - +
184A ALA* 3.1 9.1 + - - +
186A LEU* 1.3 79.8 - - - +
188A ASP* 1.3 60.9 + - - +
190A THR* 3.9 7.1 - - - -
191A GLU* 3.3 21.7 + - - +
363A ILE* 4.7 6.1 - - - +
367A LYS* 5.7 5.9 - - - +
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Residues in contact with ASP 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ALA 3.1 11.2 + - - +
185A GLU* 3.1 11.0 + - - +
187A ASP* 1.3 75.7 - - - +
189A LEU* 1.3 59.4 + - - +
191A GLU* 3.2 7.8 + - - +
192A LYS* 2.9 51.9 + - - +
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A GLU 3.2 9.6 + - - +
186A LEU* 3.4 11.0 + - + +
188A ASP* 1.3 77.3 + - - +
190A THR* 1.3 66.5 + - - +
192A LYS* 3.1 7.4 + - - +
193A ILE* 2.9 52.5 + - + +
249A PRO* 3.5 33.7 - - + -
356A PRO* 3.7 36.1 - - + +
357A LEU* 4.0 18.4 - - + -
360A ALA* 4.6 6.1 - - + -
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Residues in contact with THR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LEU 2.7 22.5 + - - -
187A ASP* 3.9 7.7 - - - -
189A LEU* 1.3 78.3 - - - +
191A GLU* 1.3 57.3 + - - +
193A ILE* 3.4 1.4 + - - +
194A ARG* 2.9 27.9 + - - +
326A THR* 3.4 27.9 - - + +
330A LEU* 4.0 20.5 - - + +
360A ALA* 3.5 19.1 + - - +
364A TYR* 3.9 19.6 - - + +
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ASP 3.3 15.5 + - - +
188A ASP* 3.2 9.8 + - - +
189A LEU 3.2 0.6 - - - -
190A THR* 1.3 81.5 - - - +
192A LYS* 1.3 62.7 + - + +
194A ARG* 3.0 43.4 + - - +
195A LYS* 3.0 52.8 + - - +
326A THR* 5.8 0.2 - - - +
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Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ASP* 2.9 38.1 + - - +
189A LEU* 3.1 8.9 + - - +
191A GLU* 1.3 78.2 - - + +
193A ILE* 1.3 57.0 + - - +
195A LYS* 3.8 10.4 - - + +
196A ALA* 2.9 29.7 + - - +
247A ARG* 5.0 10.6 + - - +
249A PRO* 4.1 33.2 - - + +
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Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 2.9 31.9 + - + +
190A THR 3.9 3.4 - - - +
192A LYS* 1.3 73.9 - - - +
194A ARG* 1.3 65.3 + - - +
196A ALA* 3.6 6.4 - - - +
197A HIS* 3.0 23.6 + - - +
244A PHE* 4.1 9.0 - - + -
248A LEU* 4.3 11.9 - - + -
249A PRO* 4.5 5.6 - - + -
326A THR 5.0 0.2 - - - +
329A GLY* 3.5 33.0 - - - +
330A LEU* 3.6 21.3 - - + +
333A ALA* 4.3 4.7 - - + -
357A LEU* 3.2 35.7 - - + -
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Residues in contact with ARG 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A THR 2.9 18.8 + - - +
191A GLU* 3.0 39.3 + - - +
193A ILE* 1.3 77.2 - - - +
195A LYS* 1.3 82.8 + - - +
197A HIS* 3.2 5.6 + - - +
198A GLN* 2.3 76.1 + - + +
325A ASP 4.9 0.2 - - - -
326A THR* 3.5 44.6 - - + +
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Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLU* 3.0 45.7 + - - +
192A LYS* 3.8 8.6 - - + +
194A ARG* 1.3 90.7 - - - +
196A ALA* 1.3 65.8 + - - +
198A GLN* 4.1 8.1 - - - +
199A GLU* 2.9 50.9 + - - +
247A ARG* 5.7 1.1 - - - +
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS 2.9 18.4 + - - +
193A ILE* 3.6 8.7 - - - +
195A LYS* 1.3 76.4 - - - +
197A HIS* 1.3 53.6 + - - +
200A THR* 2.6 39.5 + - - +
244A PHE* 3.3 14.6 - - + +
247A ARG* 3.3 45.0 - - + +
248A LEU* 4.7 3.1 - - + -
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Residues in contact with HIS 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ILE 3.0 13.2 + - - +
194A ARG 3.5 7.4 - - - +
195A LYS 3.1 0.2 - - - -
196A ALA* 1.3 74.6 - - - +
198A GLN* 1.3 68.7 + - - +
200A THR* 2.8 6.1 + - - -
201A PHE* 2.8 59.7 + + + +
244A PHE* 3.3 15.0 - - + -
274A ARG* 4.2 18.5 + - + -
277A THR* 5.6 1.6 - - - +
325A ASP* 3.5 46.3 + - + +
328A THR* 3.6 28.7 + - + +
329A GLY* 3.9 13.6 - - - -
332A SER* 5.0 2.7 + - - -
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Residues in contact with GLN 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ARG* 2.3 58.3 + - - +
195A LYS* 4.1 6.0 - - - +
197A HIS* 1.3 77.9 - - - +
199A GLU* 1.3 64.0 + - + +
201A PHE 3.0 26.1 + - - +
202A PRO* 3.9 4.3 - - - +
206A GLN* 4.7 7.0 - - - +
325A ASP* 3.2 38.4 + - + +
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Residues in contact with GLU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LYS* 2.9 42.2 + - - +
196A ALA 4.3 2.2 - - - +
198A GLN* 1.3 79.6 - - + +
200A THR* 1.3 59.5 + - - +
201A PHE 3.5 0.2 - - - -
202A PRO* 5.9 0.2 - - - -
243A GLU* 4.4 5.5 - - - +
247A ARG* 2.5 43.7 + - - +
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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