Contacts of the strand formed by residues 358 - 366 (chain B) 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 LYS 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259B VAL* 3.9 31.4 + - - +
330B PHE* 4.9 36.4 + - + +
331B ASP* 3.7 9.0 - - - +
332B TYR* 5.3 9.4 - - + +
356B ARG 4.0 6.2 + - - +
357B SER* 1.3 76.0 + - - +
359B THR* 1.3 68.3 + - - +
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Residues in contact with THR 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B LYS* 4.5 4.9 - - + +
330B PHE* 3.4 13.5 - - - -
331B ASP 3.2 30.3 + - - +
333B ASP* 2.8 37.9 + - - +
357B SER* 4.5 8.5 - - - +
358B LYS* 1.3 80.9 - - - +
360B LYS* 1.3 73.2 + - - +
361B CYS* 3.4 3.1 + - - +
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Residues in contact with LYS 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B LYS* 4.1 6.1 - - - +
300B TYR* 3.2 69.2 + - + +
301B ASN* 5.5 0.9 - - + -
328B ASP* 3.7 27.1 - - + +
329B GLY* 3.9 3.1 - - - +
330B PHE* 3.4 22.2 - - + -
359B THR* 1.3 81.8 + - - +
361B CYS* 1.3 69.4 + - - +
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Residues in contact with CYS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B ARG* 3.3 35.2 - - - -
298B VAL 3.0 23.1 - - - -
299B LYS* 4.3 2.9 - - - -
300B TYR* 3.4 5.8 - - - -
327B TRP 3.9 0.3 - - - +
328B ASP* 3.1 11.1 - - - +
329B GLY 2.9 38.6 + - - +
331B ASP* 4.4 7.6 - - - +
332B TYR 4.7 6.5 - - - -
333B ASP* 5.9 1.8 - - - -
359B THR* 3.9 6.3 - - - +
360B LYS* 1.3 80.8 - - - +
362B LEU* 1.3 58.6 + - - +
363B PHE* 4.0 10.8 - - + -
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B LYS 3.3 4.9 - - - +
298B VAL* 2.8 42.7 + - + +
300B TYR* 3.4 43.3 - - + +
305B ALA* 3.7 28.7 - - + +
306B GLU* 4.5 1.6 - - - +
309B VAL* 4.5 12.1 - - + -
326B CYS* 4.5 7.4 - - + -
327B TRP 3.6 14.1 - - - +
361B CYS* 1.3 71.6 - - - +
363B PHE* 1.3 61.4 + - - +
364B ILE* 3.9 18.1 + - + +
288C ILE* 4.0 26.7 - - + -
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Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B THR* 4.3 0.4 - - + -
260B ASP* 3.9 19.3 - - + -
263B PHE* 3.6 24.5 - + - -
295B ILE* 3.5 19.3 - - + -
296B LYS 3.4 1.3 - - - -
297B ARG* 3.7 37.9 - - + -
326B CYS* 2.9 29.1 - - - +
327B TRP* 2.9 57.0 + + + -
329B GLY 4.6 3.8 - - - -
331B ASP* 3.9 18.4 - - + -
361B CYS* 4.0 22.9 - - + -
362B LEU* 1.3 76.0 - - - +
364B ILE* 1.3 60.9 + - - +
365B GLN 3.8 0.8 + - - -
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Residues in contact with ILE 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B VAL 3.5 0.9 - - - +
295B ILE* 3.3 4.4 - - - -
296B LYS* 2.8 54.6 + - + +
298B VAL* 5.1 8.1 - - + -
305B ALA 5.3 0.9 - - - +
308B GLU* 3.8 30.5 - - + +
309B VAL* 3.6 33.9 - - + -
312B LEU* 4.2 18.6 - - + -
323B TYR* 4.2 9.6 - - + -
325B GLY 3.6 1.8 - - - -
362B LEU* 4.3 18.6 - - + +
363B PHE* 1.3 75.5 - - - +
365B GLN* 1.3 62.2 + - - +
366B MET* 3.4 15.2 + - - +
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Residues in contact with GLN 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B PHE* 4.1 20.1 - - + -
286B HIS* 4.7 7.2 + - - -
293B TYR* 3.8 41.3 - - + -
294B VAL 3.6 4.0 - - - -
295B ILE* 4.4 4.9 - - + -
323B TYR* 3.9 3.1 - - - -
324B ASN* 2.8 44.5 + - + +
325B GLY* 2.6 29.0 + - - +
327B TRP* 4.4 17.2 - - + -
363B PHE 3.8 1.4 + - - -
364B ILE* 1.3 71.7 - - - +
366B MET* 1.3 60.9 + - - +
324C ASN 4.1 6.5 + - - +
325C GLY* 5.0 5.9 - - - -
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Residues in contact with MET 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B TYR* 3.7 8.0 - - - +
294B VAL* 2.9 37.9 + - + +
296B LYS* 4.4 17.7 - - + -
308B GLU* 5.3 2.5 - - - +
312B LEU* 4.9 9.9 - - + -
321B VAL* 3.5 21.1 - - + -
322B HIS 3.6 12.8 - - - +
323B TYR* 4.4 6.5 - - + -
324B ASN* 3.6 11.8 - - - +
364B ILE* 4.3 21.8 - - + +
365B GLN* 1.3 75.0 - - - +
367B GLU* 1.3 68.1 + - - +
368B PHE 3.6 0.3 + - - -
421B PHE* 4.9 0.2 - - + -
431B GLY 3.5 25.4 - - - +
1640B ANP 3.2 34.3 - - - +
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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