Contacts of the helix formed by residues 324 - 338 (chain D) in PDB entry 1ORR
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 324 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D TYR* 4.5 0.7 - - - -
271D VAL* 6.5 0.2 - - - -
272D ASN* 3.3 8.7 - - - +
322D LYS 3.7 3.4 + - - -
323D VAL* 1.3 77.0 - - - +
325D ALA* 1.3 54.7 + - - +
326D LYS* 3.7 6.0 + - - +
327D ASP* 2.7 35.4 + - - +
328D GLY* 2.7 32.9 + - - -
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Residues in contact with ALA 325 (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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196D TYR* 3.9 10.1 - - - -
239D VAL* 3.7 25.6 - - + -
271D VAL 5.5 0.4 - - - +
272D ASN* 2.7 24.2 + - + +
273D SER 5.6 0.2 - - - +
274D LEU* 4.1 19.7 - - + -
282D LEU* 4.6 2.0 - - + -
323D VAL 3.8 0.2 + - - -
324D SER* 1.3 73.0 - - - +
326D LYS* 1.3 59.3 + - - +
329D VAL* 2.8 36.2 + - - +
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Residues in contact with LYS 326 (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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282D LEU* 4.2 26.0 - - + +
324D SER* 3.2 7.0 + - - +
325D ALA* 1.3 80.3 - - - +
327D ASP* 1.3 77.7 + - - +
330D GLN* 2.8 56.0 + - - +
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Residues in contact with ASP 327 (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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323D VAL* 4.8 4.7 - - + -
324D SER* 2.7 29.6 + - - +
326D LYS* 1.3 101.7 + - - +
328D GLY* 1.3 60.6 + - - +
330D GLN* 3.5 13.0 + - - +
331D LYS* 3.3 21.5 + - - +
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Residues in contact with GLY 328 (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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196D TYR* 3.4 24.4 - - - -
241D HIS* 3.9 14.7 - - - -
323D VAL* 3.9 6.6 - - - +
324D SER 2.7 15.6 + - - -
327D ASP* 1.3 71.1 - - - +
329D VAL* 1.3 59.5 + - - +
331D LYS* 3.3 6.7 + - - +
332D MET* 2.7 30.3 + - - +
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Residues in contact with VAL 329 (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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196D TYR* 4.2 11.2 - - + -
209D VAL* 4.0 20.6 - - + -
213D CYS* 4.3 5.0 - - - -
239D VAL* 4.9 1.8 - - + -
274D LEU* 4.4 8.7 - - + -
279D LEU* 3.7 28.7 - - + -
282D LEU* 3.9 17.0 - - + -
283D LEU* 3.8 19.3 - - + -
325D ALA* 2.8 28.3 + - + +
326D LYS 4.3 0.4 - - - +
328D GLY* 1.3 74.1 - - - +
330D GLN* 1.3 57.8 + - + +
332D MET* 3.1 4.7 + - - +
333D TYR* 2.8 28.2 + - - +
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Residues in contact with GLN 330 (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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282D LEU* 4.9 5.3 - - + +
286D TYR* 2.9 64.7 - - + +
326D LYS* 2.8 46.9 + - + +
327D ASP* 3.9 13.0 + - - +
329D VAL* 1.3 76.1 - - + +
331D LYS* 1.3 58.1 + - - +
333D TYR* 3.1 5.6 + - - +
334D ASP* 2.9 32.9 + - - +
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Residues in contact with LYS 331 (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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241D HIS* 4.4 16.6 + - + +
243D GLU* 3.1 34.6 + - - +
323D VAL* 5.5 5.3 - - - +
327D ASP 3.3 11.9 + - - +
328D GLY* 3.7 9.5 - - - +
330D GLN* 1.3 75.7 - - - +
332D MET* 1.3 56.1 + - - +
334D ASP* 3.2 14.1 + - + +
335D TRP* 2.7 36.1 + - - +
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Residues in contact with MET 332 (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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196D TYR* 4.1 15.3 - - + -
197D GLY* 3.3 42.2 - - - +
198D GLY 4.3 0.4 - - - -
200D GLN* 3.8 26.2 - - + +
209D VAL* 4.6 4.5 - - + -
210D GLY* 3.8 16.4 - - - -
213D CYS* 3.7 18.8 - - - -
241D HIS* 5.7 1.3 + - + -
328D GLY 2.7 21.3 + - - +
329D VAL* 3.1 6.5 + - - +
331D LYS* 1.3 70.2 - - - +
333D TYR* 1.3 63.9 - - - +
335D TRP* 3.2 23.6 + - + +
336D THR* 2.7 41.6 + - - +
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Residues in contact with TYR 333 (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 CYS* 3.9 17.0 - - + -
216D ALA* 3.7 16.8 + - + -
217D VAL* 3.4 33.9 - - + +
220D LYS* 3.9 31.5 + - - +
283D LEU* 3.9 26.2 - - + -
286D TYR* 3.8 23.8 - + + -
287D CYS* 4.1 15.7 - - - +
329D VAL 2.8 12.6 + - - +
330D GLN* 3.1 10.1 - - - +
332D MET* 1.3 78.8 - - - +
334D ASP* 1.3 64.1 + - - +
336D THR* 3.1 3.6 + - - -
337D SER* 2.9 39.8 + - - -
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Residues in contact with ASP 334 (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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286D TYR* 2.7 32.1 + - - -
330D GLN* 2.9 17.0 + - - +
331D LYS* 3.5 17.7 - - + +
333D TYR* 1.3 84.3 - - - +
335D TRP* 1.3 63.5 + - - +
337D SER* 3.3 6.0 + - - -
338D SER* 3.1 22.7 + - - -
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Residues in contact with TRP 335 (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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198D GLY* 3.7 16.7 - - - +
199D ARG* 3.0 56.1 - - - +
200D GLN 3.1 30.1 - - - -
201D PHE* 4.5 10.1 - + - -
331D LYS 2.7 19.7 + - - +
332D MET* 3.5 25.1 - - + +
334D ASP* 1.3 74.2 - - - +
336D THR* 1.3 69.1 + - - +
338D SER* 3.0 22.0 + - - -
339D ILE* 3.1 43.3 - - + +
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Residues in contact with THR 336 (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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210D GLY 4.7 1.3 + - - +
213D CYS* 3.7 13.2 - - - +
214D GLN* 2.9 42.3 - - + +
217D VAL* 3.4 20.3 - - + +
332D MET* 2.7 37.3 + - - +
333D TYR 3.3 5.4 - - - -
335D TRP* 1.3 75.5 - - - +
337D SER* 1.3 63.9 + - - +
339D ILE* 3.0 30.0 + - + +
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Residues in contact with SER 337 (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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217D VAL* 3.6 25.6 - - - +
220D LYS* 5.2 7.5 + - - -
333D TYR* 2.9 32.5 + - - -
334D ASP* 3.9 5.8 + - - -
335D TRP 3.3 0.2 - - - -
336D THR* 1.3 77.9 - - - +
338D SER* 1.3 57.4 + - - +
339D ILE 3.1 9.2 + - - +
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Residues in contact with SER 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D ASP 3.1 12.3 + - - -
335D TRP* 3.0 17.7 + - - -
337D SER* 1.3 76.6 + - - +
339D ILE* 1.3 62.5 + - - +
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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