Contacts of the helix formed by residues 214 - 225 (chain B) in PDB entry 5DO7
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 SER 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B LEU* 1.3 102.1 - - - +
215B GLY* 1.3 60.0 + - - +
216B GLY* 3.7 9.7 + - - -
217B GLU* 3.5 30.5 + - - +
218B ARG 3.0 11.4 + - - -
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Residues in contact with GLY 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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207B ASN* 5.6 4.8 - - - +
213B LEU 3.9 1.0 + - - -
214B SER* 1.3 70.5 + - - +
216B GLY* 1.3 68.0 + - - +
217B GLU 3.0 1.3 - - - -
218B ARG* 2.8 20.4 + - - +
219B ARG* 2.8 16.6 + - - +
243B LEU* 4.8 6.1 - - - +
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Residues in contact with GLY 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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214B SER* 3.7 6.0 + - - -
215B GLY* 1.3 73.6 - - - +
217B GLU* 1.3 61.0 - - - +
219B ARG* 3.9 3.6 + - - +
220B ARG* 3.7 31.6 + - - +
243B LEU* 3.8 31.0 - - - +
247B THR* 4.4 11.9 - - - -
251B LEU* 5.6 0.3 - - - +
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Residues in contact with GLU 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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197B LEU* 4.1 11.8 - - + +
199B GLN* 4.3 14.4 + - - -
200B CYS* 2.9 36.6 - - - -
213B LEU* 3.2 22.3 - - + +
214B SER* 3.5 25.8 + - - +
215B GLY 3.0 0.6 - - - -
216B GLY* 1.3 74.1 - - - +
218B ARG* 1.3 67.8 + - - +
220B ARG* 2.8 26.0 + - - +
221B VAL* 3.0 15.7 + - + +
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Residues in contact with ARG 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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155B ASN* 3.0 39.5 + - - +
157B LEU* 3.6 30.2 - - + +
205B VAL* 4.1 9.9 - - + +
206B GLY* 4.8 2.7 - - - -
207B ASN* 4.2 22.4 - - + +
208B MET* 4.4 18.4 - - - +
213B LEU* 3.8 16.5 - - + +
214B SER 3.0 15.4 + - - +
215B GLY* 2.8 17.9 + - - +
217B GLU* 1.3 69.6 - - - +
219B ARG* 1.3 67.1 + - - +
221B VAL* 2.8 21.6 + - + +
222B SER* 3.1 9.5 + - - -
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Residues in contact with ARG 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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151B VAL* 4.9 8.5 - - - -
152B ARG 5.0 6.1 + - - -
153B GLN* 4.2 15.4 + - - +
155B ASN* 3.4 32.1 + - - +
215B GLY 2.8 17.8 + - - +
216B GLY 4.0 4.9 - - - +
218B ARG* 1.3 71.9 - - - +
220B ARG* 1.3 66.2 + - - +
222B SER* 2.8 31.4 + - - -
223B ILE* 2.8 22.6 + - + +
238B GLU 5.0 0.8 + - - -
239B PRO* 3.0 32.5 + - - +
241B SER* 3.2 25.7 + - - -
242B GLY* 5.3 0.2 - - - -
243B LEU* 4.0 14.4 - - + +
251B LEU* 4.1 22.2 - - + -
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Residues in contact with ARG 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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310A GLN* 4.0 15.8 + - - +
195B LEU* 3.4 43.9 + - + +
196B ARG 5.0 3.2 + - - -
197B LEU* 3.6 19.9 - - + +
216B GLY 3.7 19.7 + - - +
217B GLU* 2.8 22.6 + - - +
219B ARG* 1.3 75.8 - - - +
221B VAL* 1.3 54.2 + - - -
223B ILE* 3.3 12.0 - - + +
224B GLY 2.8 22.7 + - - -
243B LEU* 6.2 0.2 - - - -
247B THR* 4.0 20.9 - - - +
250B ASN* 3.0 35.0 + - - +
251B LEU* 3.7 27.0 - - + +
254B THR* 3.8 9.1 + - - -
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Residues in contact with VAL 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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157B LEU* 4.3 15.0 - - + -
163B VAL* 4.1 38.1 - - + +
166B THR* 5.3 5.6 - - - -
167B LEU* 4.3 8.3 - - + +
197B LEU* 3.8 22.2 - - + -
200B CYS* 5.6 0.7 - - + -
205B VAL* 5.0 7.6 - - + -
213B LEU* 6.2 2.0 - - + -
217B GLU* 3.0 16.3 + - + +
218B ARG* 2.8 21.6 + - + +
220B ARG* 1.3 71.9 - - - +
222B SER* 1.3 57.4 + - - +
224B GLY* 2.9 4.0 + - - +
225B VAL* 2.8 33.5 + - + +
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Residues in contact with SER 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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151B VAL* 4.6 10.5 - - - +
154B HIS 5.6 0.2 - - - -
155B ASN* 3.3 28.0 + - - -
156B GLN* 5.5 4.7 - - - -
157B LEU* 4.2 20.4 - - - +
218B ARG 3.1 5.8 + - - -
219B ARG* 2.8 30.2 + - - -
221B VAL* 1.3 73.2 - - - +
223B ILE* 1.3 61.8 + - - +
225B VAL* 3.6 20.7 - - - +
226B GLN* 4.0 10.6 - - - +
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Residues in contact with ILE 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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151B VAL* 3.9 29.8 - - + -
195B LEU* 4.4 10.3 - - + -
219B ARG* 2.8 27.7 + - + +
220B ARG* 3.3 12.3 - - + +
222B SER* 1.3 75.2 - - - +
224B GLY* 1.3 57.0 + - - +
226B GLN* 2.8 30.5 + - - +
227B LEU* 3.3 26.3 + - + +
234B LEU* 4.9 6.7 - - + -
236B LEU* 4.4 4.7 - - + -
239B PRO* 5.6 1.8 - - + -
251B LEU* 4.1 19.5 - - + -
255B LEU* 4.0 23.6 - - + -
258B LEU* 4.8 7.0 - - + -
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Residues in contact with GLY 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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167B LEU* 3.7 10.3 - - - +
191B VAL* 4.0 11.0 - - - +
195B LEU* 3.8 16.4 - - - -
197B LEU* 5.9 0.7 - - - -
220B ARG 2.8 17.9 + - - -
221B VAL* 2.9 6.2 + - - -
223B ILE* 1.3 72.7 - - - +
225B VAL* 1.3 54.9 + - - +
227B LEU* 2.8 26.2 + - - +
228B LEU* 3.6 13.0 - - - +
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Residues in contact with VAL 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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157B LEU* 4.3 16.2 - - + -
166B THR* 4.9 9.2 - - + +
167B LEU* 3.6 16.0 - - + +
170B ILE* 4.1 32.2 - - + +
174B ARG* 4.9 0.2 - - - -
221B VAL* 2.8 26.3 + - + +
222B SER* 3.6 17.9 - - - +
224B GLY* 1.3 71.5 - - - +
226B GLN* 1.3 70.7 + - - +
228B LEU* 4.0 12.9 - - - +
229B TRP* 4.0 8.7 - - - -
480B TYR* 6.1 3.6 - - + -
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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