Contacts of the helix formed by residues 182 - 199 (chain B) in PDB entry 1DKF
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 PRO 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B GLU* 1.3 63.3 + - + +
184B VAL* 3.1 32.1 + - + +
185B GLY* 3.6 9.6 + - - -
186B GLU* 3.3 20.1 + - - +
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B PRO* 1.3 79.7 - - + +
184B VAL* 1.3 61.3 + - - +
185B GLY 3.4 0.4 - - - -
186B GLU* 3.7 23.7 + - - +
187B LEU* 3.3 18.2 + - - +
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B PRO* 3.2 30.0 - - + +
183B GLU* 1.3 80.2 - - - +
185B GLY* 1.3 68.4 + - - +
186B GLU 3.2 0.2 - - - -
187B LEU* 2.9 9.1 + - + +
188B ILE* 2.8 34.6 + - + +
354B PRO 5.2 1.3 - - - +
357B GLU* 4.8 4.0 - - + -
358B ALA* 3.5 36.3 - - + +
361B VAL* 4.3 13.0 - - + -
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Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B PRO 3.6 10.5 + - - -
183B GLU 3.4 0.4 - - - -
184B VAL* 1.3 88.4 - - - +
186B GLU* 1.3 55.9 + - - +
188B ILE* 3.4 12.1 + - - +
189B GLU* 2.8 36.1 + - - +
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Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PRO 3.3 19.4 - - - +
183B GLU* 3.8 22.5 - - - +
184B VAL 3.2 0.2 - - - -
185B GLY* 1.3 73.6 - - - +
187B LEU* 1.3 60.9 + - - +
189B GLU* 3.7 6.3 - - - +
190B LYS* 2.8 47.3 + - - +
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B GLU 3.3 12.8 + - - +
184B VAL* 2.9 13.1 + - + +
186B GLU* 1.3 80.4 - - - +
188B ILE* 1.3 62.2 + - - +
190B LYS* 3.2 5.8 + - + +
191B VAL* 2.9 39.2 + - + +
247B PRO* 3.3 35.0 - - + -
328B LEU* 5.2 0.4 - - + -
354B PRO* 3.6 44.9 - - + +
355B LEU* 4.0 13.5 - - + +
358B ALA* 4.2 10.3 - - + -
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B VAL* 2.8 30.0 + - + +
185B GLY* 3.6 10.5 - - - +
187B LEU* 1.3 77.2 - - - +
189B GLU* 1.3 65.3 + - - +
191B VAL* 3.1 6.8 + - - +
192B ARG* 2.9 29.5 + - - +
324B ALA* 4.1 18.9 - - + +
328B LEU* 4.5 9.6 - - + -
358B ALA* 3.7 23.6 - - + +
361B VAL* 4.5 5.4 - - + -
362B TYR* 3.8 46.9 - - + -
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B GLY* 2.8 20.2 + - - +
186B GLU* 3.7 7.6 - - - +
188B ILE* 1.3 78.8 - - - +
190B LYS* 1.3 63.5 + - - +
192B ARG* 2.9 33.0 + - - +
193B LYS* 3.1 24.1 + - - +
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLU* 2.8 36.1 + - - +
187B LEU* 3.5 7.2 - - - +
189B GLU* 1.3 76.0 - - - +
191B VAL* 1.3 58.2 + - - +
193B LYS* 3.2 16.8 + - - +
194B ALA* 3.0 26.7 + - - +
245B GLN 5.6 3.8 - - - +
247B PRO* 4.5 31.0 - - + +
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 2.9 32.5 + - + +
188B ILE 3.8 2.9 - - - +
190B LYS* 1.3 72.3 - - - +
192B ARG* 1.3 66.2 + - - +
194B ALA* 3.5 7.0 - - - +
195B HIS* 3.0 21.8 + - - +
242B PHE* 4.1 1.1 - - + -
246B LEU* 4.2 24.5 - - + -
247B PRO* 4.6 5.4 - - + -
324B ALA 4.8 0.4 - - - +
327B GLY* 3.5 34.7 - - - +
328B LEU* 3.7 24.0 - - + +
331B ALA* 4.7 0.9 - - + -
355B LEU* 4.4 6.3 - - + -
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Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B ILE* 2.9 18.0 + - - +
189B GLU* 2.9 42.5 + - - +
191B VAL* 1.3 76.7 - - - +
193B LYS* 1.3 53.6 + - - +
195B HIS* 3.3 4.4 + - - +
196B GLN* 2.7 64.3 + - - +
322B ASP* 5.0 1.8 + - - -
323B ASP* 3.9 12.3 - - + +
324B ALA* 3.9 26.2 - - - +
362B TYR* 2.9 40.6 + - - -
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Residues in contact with LYS 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B GLU 3.1 13.0 + - - +
190B LYS* 3.5 20.0 + - - +
192B ARG* 1.3 76.5 - - - +
194B ALA* 1.3 59.2 + - - +
196B GLN* 3.8 14.1 - - + +
197B GLU* 2.8 72.1 + - + +
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B LYS 3.0 13.8 + - - +
191B VAL* 3.5 11.7 - - - +
192B ARG 3.3 0.2 - - - -
193B LYS* 1.3 75.7 - - - +
195B HIS* 1.3 54.4 + - - +
197B GLU* 3.6 4.8 + - - +
198B THR* 2.6 36.2 + - - +
242B PHE* 3.6 17.7 - - + +
245B GLN* 3.6 36.1 - - + -
246B LEU* 4.7 4.5 - - + -
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Residues in contact with HIS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B VAL 3.0 16.0 + - - +
192B ARG 3.5 3.1 - - - +
194B ALA* 1.3 74.0 - - - +
196B GLN* 1.3 67.3 + - - +
198B THR* 2.8 6.5 + - - -
199B PHE* 2.8 63.1 + + + +
242B PHE* 3.6 12.1 - - + -
272B ARG* 4.3 16.3 + - + -
275B THR* 5.5 0.6 + - - -
323B ASP* 3.6 40.6 + - - +
326B THR* 3.7 29.3 - - + +
327B GLY* 3.9 13.7 - - - -
330B SER* 4.9 3.6 + - - -
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Residues in contact with GLN 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ARG* 2.7 47.4 + - - +
193B LYS* 3.8 17.6 - - + +
195B HIS* 1.3 74.8 - - - +
197B GLU* 1.3 62.1 + - + +
198B THR 3.5 0.2 + - - -
199B PHE 3.5 19.6 + - - +
200B PRO* 4.1 5.4 - - - +
323B ASP* 3.0 31.8 + - - +
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LYS* 2.8 57.9 + - - +
194B ALA* 3.9 6.5 - - - +
196B GLN* 1.3 79.1 - - + +
198B THR* 1.3 62.8 + - + +
199B PHE 3.5 0.2 - - - -
200B PRO* 5.9 0.6 - - - +
238B LYS* 4.7 9.2 + - - -
245B GLN* 5.2 8.6 - - + +
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Residues in contact with THR 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ALA 2.6 22.8 + - - +
195B HIS 2.8 5.8 + - - -
197B GLU* 1.3 78.6 - - + +
199B PHE* 1.3 58.8 + - - +
200B PRO* 4.3 4.2 - - - +
238B LYS* 3.4 44.4 - - - +
241B GLU* 4.1 18.6 - - + +
242B PHE* 3.4 19.6 - - - +
245B GLN* 5.4 3.4 - - + -
272B ARG* 2.9 37.1 + - - -
287B SER* 5.2 1.0 + - - -
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Residues in contact with PHE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B HIS* 2.8 41.8 + + + +
196B GLN* 3.5 14.2 - - - +
197B GLU 3.5 1.8 - - - -
198B THR* 1.3 79.4 - - - +
200B PRO* 1.3 83.0 - - - +
201B ALA* 3.6 1.9 + - - -
235B CYS* 4.4 2.5 - - - -
272B ARG* 3.2 62.6 - - + +
273B ILE 4.2 0.2 - - - -
275B THR* 3.4 20.9 - - - -
276B ARG* 3.2 34.3 - - + -
287B SER* 3.8 5.4 - - - -
323B ASP* 5.1 2.1 - - - +
600B BMS 3.4 21.8 - + - -
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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