Contacts of the helix formed by residues 281 - 290 (chain D) in PDB entry 3OP5
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 ASN 281 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ASP* 5.5 2.6 - - - +
277D ARG* 3.1 12.9 + - + +
278D TYR 3.1 10.4 - - - +
280D GLU* 1.3 78.7 - - + +
282D ILE* 1.3 62.6 + - - +
283D ALA* 3.7 12.8 + - - +
284D SER* 2.7 53.9 + - - +
285D LEU 3.4 2.9 + - - -
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Residues in contact with ILE 282 (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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278D TYR 3.4 14.4 - - - +
279D ARG* 3.6 19.3 + - + +
280D GLU 4.0 0.6 - - - -
281D ASN* 1.3 69.2 - - - +
283D ALA* 1.4 59.6 + - - +
285D LEU* 3.0 9.2 + - + +
286D MET* 2.9 41.8 + - + +
300D ALA* 4.1 16.2 - - + +
303D MET* 3.7 48.7 - - + +
304D GLU* 3.7 35.1 + - + +
307D LYS* 3.8 10.0 - - + +
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Residues in contact with ALA 283 (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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76B ASP* 4.5 23.1 - - + +
281D ASN* 3.3 11.0 - - - +
282D ILE* 1.4 77.3 - - - +
284D SER* 1.4 55.7 + - - +
286D MET* 3.4 9.1 + - - +
287D ASP* 3.0 38.6 + - - +
304D GLU* 5.2 1.6 + - - -
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Residues in contact with SER 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D ARG* 4.7 3.1 + - - +
278D TYR* 3.6 17.5 - - - -
281D ASN* 2.7 46.2 + - - +
283D ALA* 1.4 74.3 - - - +
285D LEU* 1.4 59.7 + - - +
287D ASP* 3.7 10.3 - - - +
288D LYS* 3.0 30.0 + - - +
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Residues in contact with LEU 285 (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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249D TYR* 5.2 4.7 - - + -
252D ILE* 3.8 22.9 - - + -
260D PRO* 3.8 14.1 - - + -
261D TRP* 4.3 7.9 - - + -
278D TYR* 3.5 50.3 - - + +
281D ASN 3.4 0.6 + - - -
282D ILE* 3.0 12.9 + - + +
284D SER* 1.4 79.7 + - - +
286D MET* 1.4 72.0 + - + +
288D LYS* 3.3 1.7 + - - +
289D CYS* 3.0 53.7 + - - -
303D MET* 3.9 18.4 - - + -
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Residues in contact with MET 286 (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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252D ILE* 4.2 6.5 - - + -
282D ILE* 2.9 28.4 + - + +
283D ALA* 3.6 10.1 - - - +
285D LEU* 1.4 99.8 - - + +
287D ASP* 1.4 59.0 + - - +
290D PHE* 2.9 57.2 + - + +
295D ALA* 4.1 19.1 - - + -
296D PRO 5.0 0.4 - - - +
299D ILE* 4.0 26.7 - - + -
300D ALA* 4.0 25.4 - - + -
303D MET* 4.4 4.7 - - + -
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Residues in contact with ASP 287 (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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283D ALA* 3.0 29.7 + - - +
284D SER* 3.7 9.5 - - - +
285D LEU 3.3 0.2 - - - -
286D MET* 1.4 77.7 - - - +
288D LYS* 1.3 61.7 + - - +
290D PHE 4.2 4.3 - - - -
291D PRO* 3.5 23.4 - - - +
293D ALA* 5.6 6.8 - - - +
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Residues in contact with LYS 288 (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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260D PRO* 3.8 39.2 + - + -
278D TYR* 3.5 24.4 + - + +
284D SER 3.0 18.6 + - - +
285D LEU 3.7 4.5 - - - +
286D MET 3.3 0.2 - - - -
287D ASP* 1.3 77.1 - - - +
289D CYS* 1.3 59.5 + - - +
291D PRO* 3.8 13.2 - - - +
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Residues in contact with CYS 289 (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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252D ILE* 3.6 33.0 - - + -
256D THR* 3.3 24.3 - - + +
258D HIS 5.2 1.6 - - - -
259D LEU* 5.3 0.2 - - - -
260D PRO* 3.7 31.0 - - - -
285D LEU* 3.0 28.4 + - - +
288D LYS* 1.3 74.5 - - - +
290D PHE* 1.3 72.9 + - + +
291D PRO* 3.4 9.0 - - - +
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Residues in contact with PHE 290 (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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252D ILE* 4.7 12.3 - - + -
255D LEU* 4.4 19.3 - - + -
256D THR* 3.5 27.4 - - + -
286D MET* 2.9 46.7 + - + +
287D ASP* 3.6 5.6 - - - +
289D CYS* 1.3 87.6 - - + +
291D PRO* 1.4 64.9 - - - +
292D ALA 3.3 3.1 - - - -
293D ALA* 3.3 13.9 + - - -
294D ASN* 4.1 12.6 - - - +
295D ALA* 3.7 28.9 - - + +
296D PRO* 3.5 32.3 - - + -
299D ILE* 4.8 2.7 - - + -
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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