Contacts of the strand formed by residues 212 - 216 (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 THR 212 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206D LEU* 4.7 8.6 + - + +
209D SER* 3.1 12.8 + - - -
211D ARG* 1.3 81.1 - - - +
213D ALA* 1.3 71.6 + - - +
238D MET* 3.6 30.5 - - - +
239D ALA* 4.1 3.8 + - - +
277D ALA* 4.1 2.0 - - - -
279D THR* 3.0 26.8 + - - +
281D LEU* 4.1 23.3 - - + -
335D CYS* 5.0 7.4 - - - -
340D HIS* 5.4 4.3 + - - -
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Residues in contact with ALA 213 (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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212D THR* 1.3 79.3 - - - +
214D LEU* 1.3 55.2 + - - +
238D MET* 4.4 1.1 - - - -
239D ALA* 3.3 13.0 - - + +
273D ALA 3.5 24.0 - - - +
274D ILE* 4.1 16.6 - - + +
277D ALA* 3.7 12.3 - - + +
279D THR 3.1 5.3 + - - -
280D VAL* 3.3 6.8 - - + -
281D LEU* 2.7 36.4 + - - +
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Residues in contact with LEU 214 (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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213D ALA* 1.3 73.8 - - - +
215D LEU* 1.3 84.3 + - - +
216D ALA* 4.0 13.0 - - + +
229D LEU* 4.7 4.9 - - + +
232D TRP* 3.9 42.0 - - + -
233D VAL* 5.0 7.0 - - + -
238D MET* 4.1 12.3 - - + -
239D ALA 2.9 10.2 + - - +
240D HIS* 3.1 15.0 - - + +
241D ALA 2.9 26.5 + - - +
250D PHE* 4.1 22.0 - - + -
274D ILE* 4.1 4.0 - - - +
281D LEU* 3.7 10.5 - - + +
283D VAL* 4.1 13.7 - - + -
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Residues in contact with LEU 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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213D ALA 4.2 0.6 + - - -
214D LEU* 1.3 75.5 - - - +
216D ALA* 1.3 54.2 + - - +
241D ALA* 3.4 24.9 - - + +
242D THR* 4.0 7.9 - - - +
243D MET* 4.4 10.1 - - + -
261D TYR* 3.8 46.0 - - + -
274D ILE* 4.3 11.7 - - + -
280D VAL* 4.2 9.9 - - + -
281D LEU 2.6 14.1 + - - +
282D CYS* 3.2 5.3 - - - -
283D VAL 2.7 32.1 + - - +
285D THR* 4.8 3.4 - - - +
287D PHE* 4.1 15.3 - - + -
299D LEU* 4.1 19.5 - - + -
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Residues in contact with ALA 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 LEU* 4.0 8.7 - - + +
215D LEU* 1.3 76.7 - - - +
217D ASP* 1.3 61.6 + - - +
220D VAL* 4.1 1.6 - - + -
229D LEU* 3.2 34.8 - - + -
241D ALA 3.0 6.9 + - - -
242D THR* 2.9 31.9 - - - -
243D MET* 3.8 0.8 + - - -
249D ILE* 3.5 13.7 - - + -
250D PHE* 4.4 2.9 - - + -
283D VAL* 3.2 9.4 - - + +
285D THR* 5.6 0.4 - - - -
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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