Contacts of the helix formed by residues 217 - 223 (chain D) in PDB entry 1OVM
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 217 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216D ALA* 1.3 73.2 - - - +
218D PHE* 1.3 65.9 + - + +
219D LEU 2.8 16.5 + - - -
220D VAL* 2.8 21.6 - - - +
221D LEU 4.2 0.9 + - - -
243D MET* 3.0 41.5 + - + +
245D MET* 2.9 25.6 - - - +
246D GLY* 2.8 25.1 + - - -
249D ILE* 5.2 2.0 - - - -
283D VAL 2.9 8.5 + - - -
284D GLY 3.3 14.7 - - - +
285D THR* 4.1 8.9 - - - +
286D ARG 5.0 1.0 + - - -
291D LEU* 3.9 7.1 - - - +
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Residues in contact with PHE 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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91D ALA 4.9 3.4 - - - -
92D GLU* 3.6 27.8 - - - -
93D HIS* 3.8 14.8 - + + -
217D ASP* 1.3 90.4 - - - +
219D LEU* 1.3 91.6 + - + +
220D VAL 3.1 0.4 - - - -
221D LEU* 2.8 27.3 + - - +
222D ARG* 3.0 30.4 + - + +
245D MET* 3.7 45.8 - - + +
246D GLY* 3.4 9.7 - - - -
284D GLY 4.0 3.6 - - - -
286D ARG* 3.7 33.2 - - + -
406D LEU* 5.6 2.5 - - + -
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Residues in contact with LEU 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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93D HIS* 3.8 28.9 - - + +
217D ASP 2.8 5.9 + - - -
218D PHE* 1.3 106.2 - - + +
220D VAL* 1.3 60.6 + - - +
222D ARG* 3.4 3.3 + - + -
223D HIS* 3.0 34.4 + - + +
284D GLY* 3.4 24.9 - - - +
286D ARG* 3.3 36.1 - - - +
308D GLN* 3.4 11.4 - - - +
309D PRO* 3.9 17.7 - - + -
324D MET* 4.1 7.6 - - + +
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Residues in contact with VAL 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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216D ALA* 4.1 0.9 - - + -
217D ASP 2.8 22.2 - - - +
219D LEU* 1.3 72.9 - - - +
221D LEU* 1.3 64.9 + - - +
223D HIS 3.4 0.9 + - - -
224D GLY 3.3 3.6 + - - -
225D LEU* 2.9 58.3 + - + +
226D LYS* 3.9 8.0 + - - +
229D LEU* 4.0 30.7 - - + -
249D ILE* 4.5 12.8 - - + -
283D VAL* 3.8 26.5 - - + +
284D GLY* 4.5 0.6 - - - -
324D MET* 4.5 6.5 - - - -
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Residues in contact with LEU 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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218D PHE* 2.8 13.7 + - - +
220D VAL* 1.3 82.5 - - - +
222D ARG* 1.3 80.4 + - - +
224D GLY* 3.2 12.8 + - - -
225D LEU 5.1 0.4 - - - +
226D LYS* 4.4 26.7 - - + +
245D MET 4.2 19.1 - - - +
246D GLY* 4.4 3.6 - - - +
247D LYS 4.7 5.6 - - - +
248D GLY* 5.0 1.8 - - - -
249D ILE* 3.8 32.5 - - + +
400D ASN* 5.8 7.0 - - - +
401D PHE 5.2 5.8 - - - +
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Residues in contact with ARG 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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64D ARG* 3.2 48.1 - - - +
92D GLU* 2.7 29.8 + - - +
93D HIS* 2.8 33.8 + - + +
94D VAL* 3.7 9.8 - - - +
95D PRO* 5.2 3.6 - - - -
160D ARG* 3.3 30.9 + - + -
218D PHE* 3.0 30.4 + - + +
219D LEU* 3.7 8.1 - - - +
220D VAL 3.3 0.2 - - - -
221D LEU* 1.3 104.8 - - - +
223D HIS* 1.3 65.7 + - + +
224D GLY 3.4 2.3 + - - -
245D MET* 4.9 2.4 + - - +
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Residues in contact with HIS 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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93D HIS* 5.2 1.1 - + - -
158D ARG 3.9 11.1 + - - -
159D GLU 4.6 4.7 + - - -
160D ARG* 3.7 34.0 - - + +
187D GLN* 4.5 19.1 - - - -
219D LEU* 3.0 30.3 + - + +
220D VAL 3.4 0.2 + - - -
221D LEU 3.2 0.2 - - - -
222D ARG* 1.3 79.0 - - + +
224D GLY* 1.3 64.4 + - - +
225D LEU* 3.3 26.3 + - + +
309D PRO* 3.9 35.4 - - + +
310D HIS* 5.3 2.7 + + - -
324D MET* 4.4 13.2 - - + -
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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