Contacts of the helix formed by residues 214 - 225 (chain B) in PDB entry 4DHI
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 ASP 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B TYR* 2.6 41.8 + - - -
205B GLU* 5.3 3.8 + - - +
212B ASP 3.4 5.5 + - - +
213B ALA* 1.3 73.5 - - - +
215B HIS* 1.3 64.1 + - - +
216B LEU* 3.2 6.5 + - - +
217B ALA* 3.0 13.1 + - - +
218B ILE* 2.9 24.1 + - - +
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Residues in contact with HIS 215 (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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214B ASP* 1.3 75.8 - - - +
216B LEU* 1.3 61.6 + - - +
218B ILE* 3.4 12.7 + - + +
219B ASN* 3.1 30.7 + - - -
240B PRO* 3.7 31.8 - - + +
246B TYR* 2.8 38.6 + + - -
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Residues in contact with LEU 216 (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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181B LEU* 4.0 16.2 - - + -
188B TYR* 3.9 30.3 - - + +
191B PHE* 4.3 22.7 - - + +
192B ILE* 3.7 31.2 - - + -
201B TYR* 3.7 26.5 - - + +
214B ASP* 3.2 4.9 + - - +
215B HIS* 1.3 76.0 - - - +
217B ALA* 1.3 56.8 + - - +
219B ASN* 3.3 7.9 + - + +
220B SER* 2.7 38.5 + - - +
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Residues in contact with ALA 217 (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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90B TYR* 3.8 13.6 + - - +
177B THR* 3.7 3.1 - - - +
201B TYR* 3.5 1.0 + - - -
205B GLU 5.4 0.4 - - - +
206B ILE* 3.4 32.3 - - + -
213B ALA* 3.8 7.6 - - + -
214B ASP* 3.0 28.2 + - - +
216B LEU* 1.3 76.6 - - - +
218B ILE* 1.3 58.4 + - - +
220B SER* 3.3 5.2 + - - -
221B LEU* 2.9 32.8 + - - +
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Residues in contact with ILE 218 (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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89B PHE* 3.5 48.0 - - + -
213B ALA* 4.0 15.0 - - + +
214B ASP 2.9 20.1 + - - +
215B HIS* 3.6 15.5 - - + +
217B ALA* 1.3 77.6 - - - +
219B ASN* 1.3 65.5 + - - +
221B LEU* 3.5 1.4 + - - +
222B ILE* 3.2 25.4 + - + +
231B ILE* 4.7 3.8 - - + -
233B TYR* 6.2 0.2 - - - +
240B PRO* 6.4 2.0 - - + -
248B ILE* 3.6 27.6 - - + -
268B TYR* 3.6 23.8 - - + +
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Residues in contact with ASN 219 (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 TYR* 6.1 2.9 - - + -
215B HIS* 3.1 28.3 + - - +
216B LEU* 3.7 12.3 - - + +
218B ILE* 1.3 78.3 - - - +
220B SER* 1.3 62.0 + - - +
222B ILE* 3.4 2.1 + - - +
223B LYS* 3.1 51.8 + - - +
246B TYR* 3.5 25.2 + - - -
248B ILE* 3.7 25.2 - - - +
249B PRO* 4.7 3.1 - - - +
250B SER* 5.1 3.8 + - - -
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Residues in contact with SER 220 (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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177B THR* 3.8 17.9 - - - -
180B PHE* 4.0 20.1 - - - -
181B LEU* 3.3 34.7 - - - +
188B TYR* 5.6 2.3 - - - -
216B LEU* 2.7 24.9 + - - +
217B ALA 3.7 3.8 - - - -
219B ASN* 1.3 73.6 - - - +
221B LEU* 1.3 58.8 + - - +
223B LYS* 3.4 1.6 + - - +
224B ALA* 2.8 32.8 + - - +
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Residues in contact with LEU 221 (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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89B PHE* 3.7 28.9 - - + -
90B TYR* 3.7 24.5 - - + -
93B ILE* 3.8 25.8 - - + -
173B PHE* 3.8 36.1 - - + +
176B ILE* 5.0 3.4 - - + -
177B THR* 3.4 25.9 - - + +
217B ALA 2.9 20.6 + - - +
218B ILE 3.8 3.4 - - - +
220B SER* 1.3 71.5 - - - +
222B ILE* 1.3 58.0 + - - +
224B ALA* 3.3 2.4 + - - +
225B ALA* 2.8 35.8 + - + +
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Residues in contact with ILE 222 (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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89B PHE* 3.9 21.1 - - + -
93B ILE* 4.4 9.6 - - + -
218B ILE* 3.2 21.9 + - + +
219B ASN 4.0 3.4 - - - +
221B LEU* 1.3 77.0 - - + +
223B LYS* 1.3 63.1 + - + +
226B GLY 3.1 16.3 + - - -
227B THR* 3.1 46.0 + - + +
229B VAL* 3.7 30.3 - - + -
248B ILE* 3.7 43.3 - - + +
249B PRO* 4.3 2.9 - - + -
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Residues in contact with LYS 223 (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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180B PHE* 3.6 27.8 - - + -
187B GLU* 5.2 1.8 + - - -
188B TYR* 3.0 34.5 + - - +
219B ASN* 3.1 34.3 + - - +
220B SER 3.9 1.6 - - - +
222B ILE* 1.3 74.4 - - + +
224B ALA* 1.3 65.8 + - - +
226B GLY* 3.1 13.7 + - - -
227B THR 5.5 0.2 - - - -
249B PRO* 4.0 31.9 - - + -
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Residues in contact with ALA 224 (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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118B TRP* 3.2 35.6 + - + -
176B ILE* 3.6 39.6 - - + +
177B THR 4.3 0.7 - - - +
180B PHE* 3.8 12.3 - - + -
220B SER 2.8 22.6 + - - +
221B LEU 3.7 4.5 - - - +
223B LYS* 1.3 73.7 - - - +
225B ALA* 1.3 59.9 + - - +
226B GLY 3.4 0.7 + - - -
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Residues in contact with ALA 225 (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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93B ILE* 5.0 0.9 - - + -
97B LEU* 3.8 27.3 - - + +
107B ARG* 4.9 2.1 + - - -
111B PHE* 3.6 24.8 - - + -
173B PHE* 4.5 5.6 - - + -
176B ILE* 4.2 13.2 - - + -
221B LEU* 2.8 22.4 + - + +
222B ILE 4.1 2.5 - - - +
224B ALA* 1.3 76.3 - - - +
226B GLY* 1.3 63.2 + - - +
227B THR* 3.5 10.6 + - + -
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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