Contacts of the strand formed by residues 384 - 396 (chain A) in PDB entry 1P9W
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 LEU 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A ILE* 3.8 24.9 - - + +
261A LEU* 4.6 14.1 - - + -
366A ALA* 6.0 0.2 - - + -
367A VAL* 3.8 28.9 - - + -
370A LEU* 4.9 8.5 - - + -
380A ILE* 3.0 24.3 + - + +
381A SER* 4.7 2.6 - - - +
382A SER 5.3 0.3 - - - -
383A SER* 1.3 78.9 + - - +
385A LEU* 1.3 57.7 + - - +
386A GLY 4.0 6.7 - - - +
387A VAL* 3.9 28.5 - - + -
448A LEU* 4.6 2.7 - - + -
450A VAL* 3.3 40.7 - - + +
458A ILE* 4.5 5.6 - - + -
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Residues in contact with LEU 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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252A LEU* 4.2 16.9 - - + +
255A ARG* 3.5 51.1 - - + +
257A HIS 3.3 26.2 - - - +
258A GLY* 3.8 14.6 - - - -
259A ILE 3.0 10.2 + - - +
260A ILE* 3.9 14.8 - - + -
353A LEU* 3.7 24.5 - - + -
383A SER 3.1 3.8 + - - +
384A LEU* 1.3 73.2 - - - +
386A GLY* 1.3 59.4 + - - +
449A LEU* 4.1 2.3 - - - -
450A VAL* 3.2 25.5 + - - +
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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
----------------------------------------------------------
252A LEU* 3.9 15.6 - - - +
259A ILE 3.5 2.2 + - - +
260A ILE* 3.4 6.5 - - - +
261A LEU 3.0 22.9 + - - +
384A LEU* 3.6 4.1 - - - +
385A LEU* 1.3 83.3 - - - +
387A VAL* 1.3 65.5 + - - +
388A LEU 4.2 0.2 - - - -
447A LEU* 5.3 0.4 - - - -
448A LEU* 3.2 19.3 - - - -
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 3.3 8.5 - - + -
263A THR* 3.8 26.9 - - + +
363A ALA* 3.5 34.7 - - + +
366A ALA* 3.8 15.7 - - + -
367A VAL* 5.5 0.9 - - + +
384A LEU* 3.9 29.2 - - + -
386A GLY* 1.3 78.0 - - - +
388A LEU* 1.3 60.1 + - - +
389A ALA 3.6 0.6 + - - +
446A GLU 3.5 3.5 - - - +
447A LEU* 3.9 2.8 - - - +
448A LEU* 3.0 42.3 + - + +
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Residues in contact with LEU 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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241A MSE 3.7 29.6 - - + -
249A PHE* 3.6 34.8 - - + -
260A ILE* 5.5 0.8 - - + +
261A LEU 2.7 13.3 + - - +
262A VAL* 3.4 9.3 - - + +
263A THR* 2.8 26.8 + - - +
273A THR* 4.1 15.9 - - - +
386A GLY 4.2 0.4 - - - -
387A VAL* 1.3 71.8 - - - +
389A ALA* 1.3 63.7 + - - +
390A GLN* 4.1 10.3 - - - +
445A HIS* 3.8 26.9 - - + -
446A GLU 3.6 8.3 - - - +
447A LEU* 4.0 22.2 - - + +
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Residues in contact with ALA 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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263A THR* 3.5 15.0 + - - +
264A GLY* 6.0 0.7 - - - -
361A ASN 5.5 1.1 - - - +
362A THR* 4.2 4.5 - - - -
363A ALA* 3.5 35.9 - - + +
387A VAL 3.6 2.6 + - - -
388A LEU* 1.3 71.0 - - - +
390A GLN* 1.3 61.9 + - - +
445A HIS* 3.3 5.9 - - - +
446A GLU* 2.9 40.8 + - + +
478A ILE* 4.6 10.5 - - + -
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Residues in contact with GLN 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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262A VAL* 4.0 6.4 - - + +
263A THR 3.0 13.8 + - - +
264A GLY* 3.7 9.1 - - - -
265A PRO* 3.9 0.5 - - - +
268A SER* 2.9 41.6 + - - +
269A GLY* 2.9 29.3 + - - -
270A LYS* 3.4 5.7 - - - +
273A THR* 2.8 28.3 + - - +
388A LEU* 4.1 7.3 - - - +
389A ALA* 1.3 77.3 - - - +
391A ARG* 1.3 73.8 + - - +
392A LEU* 5.6 0.9 - - + -
443A GLY* 5.4 1.1 - - - -
444A ILE 3.5 6.1 - - - +
445A HIS* 3.6 28.6 + - + +
478A ILE* 4.8 2.5 - - - +
701A ANP 5.1 1.4 + - - -
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Residues in contact with ARG 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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265A PRO* 4.8 13.9 - - + +
268A SER* 4.2 7.0 - - - -
361A ASN* 4.6 13.9 + - - +
362A THR* 5.9 1.4 - - - +
390A GLN* 1.3 80.7 - - - +
392A LEU* 1.3 67.2 + - - +
393A VAL* 5.4 1.6 - - + -
443A GLY* 3.4 5.2 - - - -
444A ILE* 3.0 57.6 + - + +
478A ILE* 3.2 43.5 - - + +
479A ARG* 4.8 5.1 - - - +
496A VAL* 4.6 3.4 + - - +
499A GLY* 3.7 26.9 + - - -
500A SER* 3.0 31.1 + - - +
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Residues in contact with LEU 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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267A GLY 3.3 22.6 + - - +
268A SER* 3.3 24.4 + - - +
390A GLN* 5.3 1.8 - - + +
391A ARG* 1.3 76.7 - - - +
393A VAL* 1.3 63.1 + - - +
394A ARG* 5.9 0.2 - - - +
441A ARG* 3.6 24.9 - - + +
442A THR* 3.5 15.7 - - - +
443A GLY* 4.0 3.8 - - - -
495A GLU* 4.5 3.8 - - - +
498A ARG* 5.1 4.0 + - - -
701A ANP 3.4 60.1 - - + +
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Residues in contact with VAL 393 (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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391A ARG* 4.0 2.8 + - + -
392A LEU* 1.3 78.1 - - - +
394A ARG* 1.3 62.6 - - - +
441A ARG* 3.2 3.9 - - - +
442A THR* 2.8 52.6 + - + +
444A ILE* 3.7 37.5 - - + -
485A LYS* 5.7 0.9 - - + -
491A THR* 4.1 22.2 - - + +
495A GLU* 3.7 29.6 - - + +
496A VAL* 4.2 9.0 - - + -
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Residues in contact with ARG 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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393A VAL* 1.3 73.6 - - - +
395A THR* 1.3 62.3 + - - +
396A LEU 3.6 0.7 + - - -
435A HIS 4.7 3.6 + - - -
436A LYS* 3.5 24.9 - - - +
438A TYR* 3.3 61.8 + - + +
440A GLY 3.6 11.4 - - - +
441A ARG* 3.9 12.3 - - + -
491A THR* 2.8 24.3 + - - -
495A GLU* 2.8 41.0 + - - +
498A ARG* 4.1 11.7 - - - +
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Residues in contact with THR 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 VAL 3.5 0.8 + - - -
394A ARG* 1.3 70.8 - - - +
396A LEU* 1.3 64.7 + - - +
438A TYR* 3.5 3.6 - - - -
439A ARG 2.7 47.4 + - - +
440A GLY* 2.9 17.1 + - - -
441A ARG 3.2 1.5 + - - -
442A THR* 3.7 37.7 - - + +
490A ILE* 3.7 22.4 - - + -
491A THR* 5.6 0.2 - - - -
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Residues in contact with LEU 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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394A ARG 3.6 3.4 + - - -
395A THR* 1.3 75.5 - - - +
397A CYS* 1.3 63.2 + - - +
398A PRO* 3.1 10.7 - - - +
401A LYS* 4.3 16.9 - - + +
425A TYR* 3.7 31.9 - - + -
426A ARG 3.8 5.4 - - - +
427A ALA* 3.5 33.4 - - - +
437A GLY 3.6 7.9 - - - +
438A TYR* 3.6 17.2 - - + -
439A ARG 4.5 0.7 - - - +
489A GLY 4.2 6.5 - - - +
490A ILE 3.1 13.0 + - - +
491A THR* 3.5 24.5 - - - +
492A SER* 3.6 15.5 - - - +
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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