Contacts of the helix formed by residues 214 - 225 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212D GLY 4.4 0.4 + - - -
213D LEU* 1.3 72.1 - - - +
215D GLY* 1.3 59.7 + - - +
216D GLY* 4.6 3.4 - - - -
217D GLU* 2.8 57.1 + - - +
218D ARG 3.0 8.7 + - - -
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Residues in contact with GLY 215 (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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207D ASN* 6.0 3.8 - - - -
213D LEU 3.6 2.7 + - - -
214D SER* 1.3 72.6 - - - +
216D GLY* 1.3 57.0 + - - +
218D ARG* 2.8 30.9 + - - +
219D ARG* 2.8 16.8 + - - +
243D LEU* 4.8 5.3 - - - +
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Residues in contact with GLY 216 (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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214D SER* 3.3 3.1 - - - -
215D GLY* 1.3 74.6 - - - +
217D GLU* 1.3 61.4 + - - +
219D ARG* 3.9 3.5 + - - +
220D ARG* 3.7 30.6 + - - +
243D LEU* 3.8 31.6 - - - +
247D THR* 4.4 11.4 - - - -
251D LEU* 5.6 0.5 - - - +
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Residues in contact with GLU 217 (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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310C GLN* 6.3 0.4 - - - +
197D LEU* 5.0 2.9 - - + +
200D CYS* 2.9 37.2 - - + -
213D LEU* 3.5 22.1 - - + +
214D SER* 2.8 31.2 + - - +
216D GLY* 1.3 75.1 - - - +
218D ARG* 1.3 67.8 + - - +
220D ARG* 2.8 31.2 + - - +
221D VAL* 3.0 15.6 + - + +
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Residues in contact with ARG 218 (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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155D ASN* 3.0 38.6 + - - +
157D LEU* 3.9 23.8 - - + -
205D VAL* 4.8 9.6 - - + +
206D GLY 4.0 12.5 + - - -
207D ASN* 3.7 26.0 - - - +
208D MET* 4.5 9.7 - - - +
213D LEU* 3.2 25.7 - - + +
214D SER 3.0 5.3 + - - -
215D GLY* 2.8 21.0 + - - +
217D GLU* 1.3 70.3 - - - +
219D ARG* 1.3 67.2 + - - +
221D VAL* 2.8 18.7 + - + +
222D SER* 3.1 9.4 + - - -
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Residues in contact with ARG 219 (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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151D VAL* 4.9 8.7 - - - -
152D ARG 5.1 5.1 + - - -
153D GLN* 4.2 16.2 + - - +
155D ASN* 3.4 32.9 + - - +
215D GLY 2.8 17.1 + - - +
216D GLY 4.0 5.8 - - - +
218D ARG* 1.3 72.1 - - - +
220D ARG* 1.3 65.4 + - - +
222D SER* 2.8 30.7 + - - -
223D ILE* 2.8 23.8 + - + +
238D GLU 5.1 0.6 + - - -
239D PRO* 3.0 31.2 + - - +
241D SER 3.2 24.9 + - - -
242D GLY* 5.3 0.4 - - - -
243D LEU* 4.0 16.8 - - + +
251D LEU* 4.1 21.5 - - + -
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Residues in contact with ARG 220 (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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310C GLN* 4.0 16.6 + - - +
195D LEU* 3.4 42.3 + - + +
196D ARG 4.9 3.6 + - - -
197D LEU* 3.7 17.9 - - + +
216D GLY 3.7 20.8 + - - +
217D GLU* 2.8 26.4 + - - +
219D ARG* 1.3 74.6 - - - +
221D VAL* 1.3 54.6 + - - +
223D ILE* 3.3 11.5 - - + +
224D GLY 2.8 23.0 + - - -
247D THR* 4.0 20.8 - - - +
250D ASN* 3.0 36.2 + - - +
251D LEU* 3.7 26.0 - - + +
254D THR* 3.8 9.5 + - - -
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Residues in contact with VAL 221 (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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157D LEU* 4.3 15.0 - - + -
163D VAL* 4.1 37.5 - - + +
166D THR* 5.3 6.3 - - - -
167D LEU* 4.3 7.6 - - + +
197D LEU* 3.8 22.7 - - + -
200D CYS* 5.7 0.7 - - + -
205D VAL* 5.1 5.6 - - + -
213D LEU* 4.6 7.0 - - + -
217D GLU* 3.0 15.7 + - + +
218D ARG* 2.8 20.3 + - - +
220D ARG* 1.3 71.7 - - - +
222D SER* 1.3 57.7 + - - +
224D GLY* 2.9 3.4 + - - +
225D VAL* 2.8 34.8 + - + +
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Residues in contact with SER 222 (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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151D VAL* 4.6 9.6 - - - +
154D HIS 5.7 0.4 - - - -
155D ASN* 3.2 29.9 + - - -
156D GLN* 5.6 3.6 - - - -
157D LEU* 4.2 20.4 - - - +
218D ARG 3.1 6.0 + - - -
219D ARG* 2.8 29.4 + - - -
221D VAL* 1.3 73.3 - - - +
223D ILE* 1.3 60.8 + - - +
225D VAL* 3.6 21.6 - - - +
226D GLN* 4.0 10.7 - - - +
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Residues in contact with ILE 223 (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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151D VAL* 4.0 31.6 - - + -
195D LEU* 4.4 7.0 - - + -
219D ARG* 2.8 26.2 + - + +
220D ARG* 3.3 12.8 - - + +
222D SER* 1.3 75.4 - - - +
224D GLY* 1.3 56.6 + - - +
226D GLN* 2.8 30.3 + - - +
227D LEU* 3.3 26.0 + - + +
234D LEU* 5.0 5.4 - - + -
236D LEU* 4.5 4.9 - - + -
239D PRO* 5.6 1.6 - - + -
251D LEU* 4.1 19.7 - - + -
255D LEU* 4.0 23.8 - - + -
258D LEU* 4.4 12.8 - - + -
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Residues in contact with GLY 224 (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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167D LEU* 3.7 10.3 - - - +
191D VAL* 4.0 10.8 - - - +
195D LEU* 3.7 16.6 - - - -
197D LEU* 5.9 0.7 - - - -
220D ARG 2.8 17.9 + - - -
221D VAL* 2.9 5.8 + - - -
223D ILE* 1.3 72.8 - - - +
225D VAL* 1.3 55.9 + - - +
227D LEU* 2.8 23.8 + - - +
228D LEU* 3.6 12.8 - - - +
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Residues in contact with VAL 225 (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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157D LEU* 4.3 15.9 - - + -
166D THR* 4.9 4.7 - - + +
167D LEU* 3.6 15.2 - - + +
170D ILE* 3.3 49.8 - - + +
174D ARG* 4.9 0.2 - - - -
221D VAL* 2.8 25.6 + - + +
222D SER* 3.6 18.8 - - - +
224D GLY* 1.3 72.5 - - - +
226D GLN* 1.3 69.8 + - - +
228D LEU* 4.0 8.4 - - - +
229D TRP* 4.0 8.8 - - - -
480D TYR* 6.2 0.7 - - + -
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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