Contacts of the strand formed by residues 292 - 299 (chain C) in PDB entry 2A19
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 292 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C GLU* 4.9 3.9 + - - +
283C LYS* 3.8 26.5 - - + -
284C ALA 3.5 6.7 - - - +
285C LYS* 4.0 21.4 - - - +
291C LYS* 1.3 90.3 - - - +
293C TYR* 1.3 64.9 + - - +
368C PHE* 3.3 45.7 + - + +
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Residues in contact with TYR 293 (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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313B ALA* 4.1 0.9 - - - +
323B TYR* 3.3 19.2 - - - -
324B ASN 5.3 0.2 - - - -
267C PHE* 4.0 9.2 - + + -
283C LYS* 3.4 4.9 - - - +
284C ALA 2.8 33.3 + - - +
286C HIS* 3.8 11.4 - - + -
289C ASP* 2.7 40.1 + - - -
291C LYS* 3.6 34.3 - - + +
292C THR* 1.3 76.8 - - - +
294C VAL* 1.3 61.5 + - - +
295C ILE* 3.9 2.1 - - + +
324C ASN* 3.1 35.8 + - - -
365C GLN* 3.2 32.5 - - + +
366C MET 3.5 11.0 - - - +
367C GLU* 4.3 4.5 - - + -
368C PHE* 3.9 7.2 - - - -
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Residues in contact with VAL 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ILE* 4.3 10.3 - - + -
281C VAL* 3.5 26.5 - - + -
282C PHE 3.3 3.1 - - - +
283C LYS* 5.1 0.2 - - + -
293C TYR* 1.3 73.6 - - - +
295C ILE* 1.3 68.0 + - - +
296C LYS* 4.7 5.2 - - + +
364C ILE 3.4 0.7 - - - +
365C GLN* 3.4 0.3 - - - +
366C MET* 2.7 52.1 + - + +
367C GLU 4.1 4.0 - - - +
368C PHE* 3.6 31.7 - - + +
2640C ANP 3.6 31.6 - - + +
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Residues in contact with ILE 295 (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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263C PHE* 3.7 39.9 - - + -
267C PHE* 3.6 32.3 - - + -
281C VAL* 3.7 0.5 - - - -
282C PHE* 2.7 44.0 + - + +
284C ALA* 3.9 8.1 - - + +
293C TYR 3.9 15.3 - - - +
294C VAL* 1.3 78.1 - - - +
296C LYS* 1.3 69.4 + - - +
327C TRP* 4.3 9.9 - - + -
363C PHE* 4.2 18.4 - - + -
364C ILE 3.2 5.2 - - - +
365C GLN* 4.3 16.2 - - + -
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Residues in contact with LYS 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C PHE 5.6 1.4 + - - -
279C GLY* 5.9 2.7 - - - -
280C GLN 3.4 7.4 - - - +
281C VAL* 4.3 26.7 - - + -
294C VAL* 4.2 2.8 - - + +
295C ILE* 1.3 74.7 - - - +
297C ARG* 1.3 58.7 + - - +
298C VAL* 3.7 27.1 - - - +
308C GLU* 3.4 33.5 + - - +
362C LEU 3.4 1.4 - - - +
363C PHE* 3.2 6.8 - - - +
364C ILE* 2.8 54.4 + - + +
366C MET* 4.9 9.2 - - + -
432C ASP* 5.1 4.2 + - - +
434C GLY* 4.1 16.1 + - - -
2640C ANP 5.4 4.3 + - - +
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Residues in contact with ARG 297 (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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257C HIS 2.4 31.9 + - - -
258C THR* 3.4 12.1 - - - +
279C GLY* 3.4 5.9 - - - -
280C GLN* 2.9 65.4 + - - +
282C PHE* 3.8 27.0 - - + -
295C ILE 3.9 0.4 + - - -
296C LYS* 1.3 72.7 - - - +
298C VAL* 1.3 62.0 + - - +
331C ASP* 2.8 30.9 + - - -
332C TYR* 4.0 18.0 + - - +
333C ASP 5.6 0.2 + - - -
334C PRO* 3.7 20.2 - - + +
361C CYS* 4.3 7.6 - - + -
362C LEU 3.4 3.4 - - - -
363C PHE* 3.6 27.5 - - + -
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Residues in contact with VAL 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C PHE 3.7 19.7 - - - +
279C GLY* 4.6 0.7 - - - -
296C LYS* 3.7 30.7 - - - +
297C ARG* 1.3 79.1 - - - +
299C LYS* 1.3 65.2 + - - +
305C ALA* 4.6 8.7 - - + +
308C GLU* 5.5 0.4 - - - +
334C PRO* 3.8 7.4 - - - -
361C CYS* 3.5 2.8 - - - +
362C LEU* 2.7 63.6 + - + +
364C ILE* 4.4 11.0 - - + -
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Residues in contact with LYS 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C PHE 5.1 2.0 + - - -
298C VAL* 1.3 74.2 - - - +
300C TYR* 1.3 61.7 + - - +
301C ASN* 3.3 39.8 + - + +
302C ASN* 4.9 1.7 + - - -
305C ALA* 3.6 16.5 - - - +
333C ASP* 2.8 40.6 + - - +
334C PRO* 3.7 16.8 - - + +
335C GLU* 3.8 30.8 + - + +
359C THR* 3.8 20.2 - - - +
360C LYS 4.0 9.4 - - - +
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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
------------------------------------------------------------
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