Contacts of the strand formed by residues 380 - 397 (chain A) in PDB entry 1PO3
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 ARG 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A PHE* 6.3 0.2 - - - -
363A THR 3.6 1.0 - - - +
364A LEU* 3.5 6.3 - - - +
365A ARG* 2.9 56.5 + - - +
378A SER* 4.2 5.9 - - - +
379A PRO* 1.3 87.1 - - - +
381A ASN* 1.3 62.2 + - - +
382A TYR* 3.6 30.4 - - + -
416A HIS 3.4 5.4 - - - -
417A GLU* 3.3 24.7 + - + +
418A MET 5.0 1.6 + - - +
419A ARG* 6.2 0.2 - - - +
438A ARG* 3.7 18.2 - - - +
742A FLC 3.1 42.9 + - - +
743A FLC 2.6 48.2 + - - -
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Residues in contact with ASN 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A GLN* 5.9 2.4 + - + +
363A THR 3.2 5.2 - - - +
364A LEU* 3.2 33.8 - - - +
379A PRO* 4.9 6.3 - - - +
380A ARG* 1.3 74.2 - - - +
382A TYR* 1.3 71.9 + - - +
383A TRP* 3.7 29.3 - - + -
415A THR* 3.4 0.9 - - - -
416A HIS* 2.9 46.2 + - - +
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Residues in contact with TYR 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PHE* 3.0 74.6 - + + +
172A ALA* 4.3 2.2 - - + -
176A GLN* 3.7 23.6 - - + +
361A THR 3.6 1.7 - - - +
362A GLN* 3.3 5.0 - - - +
363A THR* 2.7 40.6 + - - +
365A ARG* 4.5 3.4 - - + -
380A ARG* 3.6 46.4 - - + -
381A ASN* 1.3 85.9 - - - +
383A TRP* 1.3 65.3 + - - +
384A VAL* 4.9 0.4 - - + -
413A GLU* 6.5 0.2 - - + -
414A SER 3.6 4.0 - - - +
415A THR* 3.2 38.1 - - + -
417A GLU* 3.6 12.8 + - + -
743A FLC 5.7 0.3 + - - -
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Residues in contact with TRP 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A TYR* 3.4 31.2 - + + -
361A THR 3.5 3.4 - - - -
362A GLN* 2.5 42.5 - - + +
381A ASN* 3.7 30.7 - - + -
382A TYR* 1.3 70.8 - - - +
384A VAL* 1.3 67.7 + - - +
412A ASN* 3.6 2.1 + - - +
413A GLU* 3.3 1.4 - - - -
414A SER* 2.9 69.7 + - - +
415A THR 4.3 13.9 - - - -
416A HIS* 4.3 10.8 - - + -
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A PRO* 5.7 0.4 - - + -
170A PRO 4.9 2.0 - - - +
171A PHE* 3.8 32.3 - - - +
172A ALA* 4.2 2.5 - - - +
173A PRO* 4.5 7.0 - - + -
359A PHE* 3.6 23.7 - - + +
360A TYR* 3.4 8.5 - - - -
361A THR* 2.9 45.1 + - - +
382A TYR* 4.9 0.9 - - + -
383A TRP* 1.3 81.7 - - - +
385A ARG* 1.3 65.0 + - - +
411A LEU* 3.8 20.4 - - + -
412A ASN 3.2 2.7 - - - -
413A GLU* 3.9 13.0 - - + -
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Residues in contact with ARG 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A PHE* 3.4 8.6 - - - +
360A TYR* 4.6 10.7 - - + +
383A TRP 4.2 0.4 - - - -
384A VAL* 1.3 75.9 - - - +
386A GLY* 1.3 59.9 + - - +
410A TYR* 5.6 4.9 - - + -
411A LEU* 3.4 11.6 - - - +
412A ASN* 2.8 43.2 + - + +
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Residues in contact with GLY 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A GLY* 3.1 2.4 - - - -
359A PHE* 2.6 58.6 + - - -
385A ARG* 1.3 79.4 - - - +
387A ILE* 1.3 61.4 + - - -
410A TYR* 3.3 14.8 - - - -
411A LEU* 4.4 0.2 - - - -
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Residues in contact with ILE 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A ILE* 4.2 24.7 - - + -
357A GLN 3.4 3.6 - - - +
358A GLY* 3.8 19.5 - - - +
386A GLY* 1.3 73.4 - - - -
388A GLU* 1.3 64.4 + - - +
389A PRO* 4.0 6.0 - - + +
408A TYR* 5.0 4.4 - - + -
409A ARG* 3.9 0.7 - - - +
410A TYR* 3.2 46.5 + - + +
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Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLY 4.9 6.9 - - - +
202A ARG* 4.3 16.8 + - - +
355A ASN 4.0 0.9 - - - +
356A ILE* 3.5 5.3 - - - -
357A GLN* 2.6 48.5 + - + +
359A PHE* 5.4 8.4 - - + -
386A GLY 5.5 0.4 - - - -
387A ILE* 1.3 79.0 - - - +
389A PRO* 1.3 61.5 - - - +
390A ARG* 4.7 9.5 + - - +
408A TYR 3.0 17.7 - - - +
409A ARG* 3.0 35.8 + - + +
450A TYR* 2.9 24.2 + - - +
467A ARG* 5.8 0.2 + - - -
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Residues in contact with PRO 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A PHE* 4.2 10.3 - - + -
355A ASN 3.5 5.6 - - - +
356A ILE* 3.5 25.4 - - + -
387A ILE* 4.0 6.1 - - + +
388A GLU* 1.3 85.1 - - - +
390A ARG* 1.3 62.8 + - - +
407A GLY* 3.7 0.5 - - - -
408A TYR* 3.0 62.0 + - + +
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Residues in contact with ARG 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ARG* 3.4 57.4 - - - +
353A LYS* 3.9 9.9 - - - +
354A PHE* 3.7 5.2 - - - -
355A ASN* 2.9 77.4 + - + +
388A GLU* 4.7 10.1 + - - +
389A PRO* 1.3 76.8 - - - +
391A TYR* 1.3 59.5 + - - +
392A SER* 5.3 6.0 + - - +
406A VAL* 3.4 18.2 - - - +
407A GLY* 3.9 6.5 - - - -
450A TYR* 4.0 10.1 - - + +
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Residues in contact with TYR 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A HIS* 3.0 25.8 - + + +
353A LYS 3.4 9.0 - - - -
354A PHE* 4.4 20.2 - + + +
390A ARG* 1.3 73.4 - - - +
392A SER* 1.3 81.6 + - - +
393A GLN* 2.9 46.0 + - + -
404A VAL* 4.2 2.8 - - + +
406A VAL* 3.1 47.7 + - + +
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Residues in contact with SER 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A HIS* 3.3 2.3 - - - -
353A LYS* 2.9 53.0 + - - -
390A ARG* 5.3 6.4 + - - +
391A TYR* 1.3 88.6 + - - +
393A GLN* 1.3 62.5 + - - +
394A ILE* 6.4 0.2 - - - -
403A GLU* 5.3 10.7 + - - -
404A VAL 3.5 9.0 - - - -
405A GLY* 4.3 7.7 - - - -
406A VAL 5.4 0.3 + - - -
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Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A GLN 3.4 10.8 - - - +
352A HIS* 2.9 28.3 + - + +
391A TYR* 2.9 25.2 + - + +
392A SER* 1.3 77.3 - - - +
394A ILE* 1.3 74.8 + - - +
395A PHE* 4.0 27.0 + - + -
402A HIS 3.5 1.7 - - - +
403A GLU* 3.4 2.8 - - - +
404A VAL* 3.0 38.8 + - + +
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Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A SER 4.0 15.5 - - - +
351A GLN* 2.9 24.5 + - - +
352A HIS* 6.1 0.2 - - - -
392A SER* 5.9 0.4 - - - -
393A GLN* 1.3 80.0 - - - +
395A PHE* 1.3 67.3 + - - +
401A ALA* 5.6 1.8 - - + -
402A HIS 3.3 14.8 - - - +
403A GLU* 3.3 33.2 - - + +
620B LYS* 5.0 6.3 - - + -
621B GLY* 3.9 30.9 - - - +
622B ASP* 4.2 5.5 - - - -
624B TYR* 4.5 16.6 - - + -
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Residues in contact with PHE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A GLN* 4.3 29.6 - - + -
394A ILE* 1.3 76.7 - - - +
396A MET* 1.3 65.6 - - - +
397A ILE* 5.0 3.1 - - + +
402A HIS* 3.0 47.9 + + + +
404A VAL* 3.6 32.3 - - + -
621B GLY* 4.6 2.0 - - - -
622B ASP* 3.5 17.9 - - + +
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Residues in contact with MET 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A PHE* 1.3 77.8 - - - +
397A ILE* 1.3 63.8 + - - +
400A SER 3.3 10.8 - - - -
401A ALA* 4.4 3.4 - - - +
528B GLN* 4.7 13.7 - - - +
620B LYS 5.0 0.9 - - - -
621B GLY* 4.0 10.7 - - - -
622B ASP* 3.1 25.6 + - - +
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Residues in contact with ILE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A PHE* 3.9 4.2 + - + +
396A MET* 1.3 75.5 - - - +
398A GLY* 1.3 70.2 + - - +
400A SER* 2.3 50.8 + - - +
402A HIS* 3.7 29.8 - - + +
528B GLN* 5.5 0.4 - - - -
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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
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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