Contacts of the strand formed by residues 281 - 291 (chain C) in PDB entry 5PAO
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 GLN 281 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266C ALA 3.7 0.7 - - - +
267C VAL* 3.4 2.5 - - - -
268C LEU* 2.8 47.6 + - + +
279C ASP 4.1 6.0 + - - +
280C GLU* 1.3 80.6 - - - +
282C SER* 1.3 62.9 + - - +
283C ARG* 3.4 23.8 + - - +
312C VAL* 3.6 8.6 - - + +
313C VAL* 2.8 52.9 + - - +
315C THR* 3.8 12.3 - - - +
318C VAL* 3.6 18.6 - - + +
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Residues in contact with SER 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C ILE* 4.1 16.4 - - - +
266C ALA 3.4 4.5 - - - -
267C VAL* 3.8 18.5 - - - +
280C GLU* 4.3 2.1 - - - +
281C GLN* 1.3 74.5 - - - +
283C ARG* 1.3 81.3 + - - +
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Residues in contact with ARG 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C ILE* 3.4 8.8 - - - -
266C ALA* 2.8 35.5 + - - +
281C GLN* 3.4 27.1 + - - +
282C SER* 1.3 107.7 + - - +
284C ARG* 1.3 67.9 + - - +
308C LEU* 4.1 18.2 - - + -
309C HIS 4.9 0.2 - - - +
310C GLN* 3.2 35.5 + - - +
311C PRO 3.0 28.3 + - - -
312C VAL* 3.7 20.5 - - + +
313C VAL* 4.2 9.9 - - - +
507C CL 3.8 16.4 - - + -
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Residues in contact with ARG 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ARG 5.0 11.4 - - - +
264C LEU 3.8 6.1 - - - +
265C ILE* 3.8 17.0 - - + -
283C ARG* 1.3 73.7 - - - +
285C VAL* 1.3 64.5 + - - +
286C ALA 3.8 0.2 - - - -
308C LEU* 3.5 4.5 - - - -
309C HIS* 2.8 72.5 + - + -
507C CL 3.4 15.4 - - + +
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Residues in contact with VAL 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C LEU* 4.8 1.1 - - + -
261C TRP 4.5 5.7 - - - +
262C ARG* 5.7 1.6 - - - -
264C LEU* 3.1 56.7 + - + +
265C ILE 4.3 0.4 - - - -
266C ALA* 4.1 21.5 - - + +
284C ARG* 1.3 74.6 - - - +
286C ALA* 1.3 59.0 + - - +
287C GLN 3.5 23.6 - - - +
288C VAL* 3.7 9.2 - - + -
306C LEU* 4.0 20.0 - - + -
307C ARG 3.8 5.6 - - - +
308C LEU* 4.5 4.7 - - + +
459C VAL* 4.3 12.7 - - + +
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ARG* 3.6 2.6 + - - -
285C VAL* 1.3 73.2 - - - +
287C GLN* 1.3 61.1 + - + +
307C ARG* 2.8 23.3 + - + +
308C LEU 4.2 2.5 - - - +
309C HIS* 4.0 30.5 - - + +
455C PRO* 6.5 0.9 - - + -
456C ARG 5.3 0.9 - - - +
458C GLY 4.6 0.9 - - - +
459C VAL* 3.7 22.0 + - - +
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Residues in contact with GLN 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C TRP* 5.9 0.2 - - + -
285C VAL* 3.5 5.2 - - - +
286C ALA* 1.3 79.8 + - + +
288C VAL* 1.3 63.4 + - - +
289C ILE* 3.6 25.5 - - + +
305C LEU 4.4 0.2 - - - -
306C LEU* 3.2 5.7 - - - -
307C ARG* 2.9 45.0 + - + +
455C PRO* 3.5 12.0 - - + +
456C ARG* 3.0 37.1 + - - +
458C GLY 2.7 30.3 + - - -
459C VAL* 3.2 14.2 + - - +
461C LEU* 4.2 20.0 - - + +
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C PHE* 3.9 32.8 - - + -
261C TRP* 4.1 17.7 - - + -
264C LEU* 3.7 17.7 - - + -
285C VAL* 3.7 20.0 - - + -
287C GLN* 1.3 74.2 - - - +
289C ILE* 1.3 62.5 + - - +
290C ILE* 4.1 16.4 - - + -
304C ALA* 4.4 0.9 - - + -
305C LEU 3.8 2.5 - - - -
306C LEU* 4.2 9.9 - - + -
459C VAL* 2.9 18.4 + - + +
460C LEU* 3.4 4.4 - - + +
461C LEU 2.9 25.1 + - - +
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Residues in contact with ILE 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C TRP* 4.2 23.8 - - + -
287C GLN* 3.6 28.0 - - + +
288C VAL* 1.3 72.7 - - - +
290C ILE* 1.3 62.6 + - - +
304C ALA* 3.3 6.4 - - - -
305C LEU* 2.8 58.8 + - + +
446C TRP* 3.8 5.2 - - + -
450C LEU* 3.6 38.1 - - + +
453C SER* 5.5 2.2 - - - +
461C LEU* 3.2 22.0 - - + +
463C ALA* 3.7 16.8 - - + -
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Residues in contact with ILE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C ALA* 4.0 26.0 - - + +
255C PHE* 4.4 4.9 - - + -
288C VAL* 4.1 17.0 - - + -
289C ILE* 1.3 79.8 - - - +
291C PRO* 1.4 85.7 - - + +
294C TYR* 3.8 23.1 - - + +
304C ALA* 4.1 8.3 - - + -
446C TRP* 3.8 3.8 - - - -
460C LEU* 4.0 18.4 - - + -
461C LEU 2.9 9.1 + - - +
462C ARG* 3.3 12.9 - - + +
463C ALA 3.0 20.3 + - - -
505C GOL 3.7 22.0 - - - +
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Residues in contact with PRO 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C ILE* 1.4 94.0 - - + +
292C SER* 1.3 64.9 + - - +
293C THR* 3.7 7.6 - - - +
294C TYR* 3.1 19.5 + - + +
301C HIS* 3.6 26.5 - - + +
303C ILE* 3.1 31.6 - - + +
443C TYR* 4.7 2.0 - - + -
446C TRP* 3.5 18.6 - - + -
462C ARG* 4.9 2.5 + - - -
463C ALA 3.5 6.7 - - - +
465C PHE* 3.7 23.6 - - + -
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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