Contacts of the helix formed by residues 392 - 409 (chain A) in PDB entry 5F0P
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 SER 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A ILE* 4.2 12.0 - - - +
389A ALA* 3.4 22.9 + - - +
390A THR 3.3 2.7 - - - +
391A SER* 1.3 84.0 + - - +
393A ALA* 1.3 65.8 + - - +
394A VAL* 3.6 18.9 + - - +
395A SER* 3.3 13.2 + - - -
396A LYS* 3.3 9.7 + - - +
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Residues in contact with ALA 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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345A GLU* 3.9 31.4 - - + +
391A SER 3.7 2.5 + - - -
392A SER* 1.3 72.2 + - - +
394A VAL* 1.3 65.8 + - + +
396A LYS* 3.3 13.8 + - + +
397A GLU* 3.2 26.8 + - + +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A SER* 4.3 13.5 - - - +
345A GLU* 4.1 29.2 - - - +
348A VAL* 4.5 10.3 - - + +
380A PHE* 3.5 36.1 - - + -
385A LEU* 5.8 5.8 - - + -
388A ILE* 4.1 17.9 - - + -
392A SER* 3.2 10.1 - - - +
393A ALA* 1.3 76.9 - - - +
395A SER* 1.3 57.0 + - - +
397A GLU* 3.2 5.4 + - - +
398A LEU* 2.9 27.4 + - - +
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Residues in contact with SER 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ILE* 4.0 10.6 + - - +
389A ALA 3.2 27.6 + - - -
390A THR* 3.9 8.1 + - - +
392A SER 3.3 5.2 + - - -
393A ALA 3.3 0.2 - - - -
394A VAL* 1.3 77.3 - - - +
396A LYS* 1.3 62.0 + - - +
398A LEU* 4.4 3.8 - - - -
399A THR* 2.8 35.1 + - - -
428A PHE* 3.4 28.8 - - - -
429A ASP 5.3 0.3 + - - -
432A SER* 3.6 12.0 + - - -
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Residues in contact with LYS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A THR* 3.4 24.8 + - - +
391A SER* 3.5 20.0 + - - +
392A SER 3.3 11.0 + - - +
393A ALA* 3.3 15.8 + - + +
395A SER* 1.3 77.8 - - - +
397A GLU* 1.3 62.5 + - + +
399A THR* 3.6 5.6 - - - -
400A ARG* 3.1 27.6 + - - +
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Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLU* 3.9 11.7 - - + +
348A VAL* 3.6 22.2 - - + -
349A SER* 3.0 33.9 + - - +
352A VAL* 4.1 4.2 - - + +
393A ALA* 3.2 13.3 + - + +
394A VAL* 3.7 4.5 - - - +
395A SER 3.2 0.2 - - - -
396A LYS* 1.3 80.0 - - + +
398A LEU* 1.3 54.8 + - - +
399A THR 3.2 0.4 - - - -
400A ARG* 3.0 40.2 + - - +
401A LEU* 2.6 37.1 + - - +
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A VAL* 3.9 3.5 - - + +
380A PHE* 3.8 39.9 - - + -
388A ILE* 5.7 1.3 - - + -
394A VAL* 2.9 18.0 + - + +
395A SER* 4.0 3.8 - - - +
397A GLU* 1.3 75.6 - - - +
399A THR* 1.3 56.5 + - - +
401A LEU* 3.5 16.1 - - + +
402A LEU* 3.1 45.5 + - + +
424A LEU* 4.0 41.1 - - + +
427A TYR* 4.8 6.3 - - + -
428A PHE* 3.9 25.6 - - + +
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Residues in contact with THR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A THR* 6.2 0.2 - - - +
395A SER* 2.8 26.1 + - - -
396A LYS* 3.6 6.9 - - - +
398A LEU* 1.3 75.5 - - - +
400A ARG* 1.3 57.2 + - - +
402A LEU* 3.3 3.1 + - - +
403A LYS* 3.0 62.6 + - + +
428A PHE* 3.3 21.8 - - - -
432A SER* 5.1 2.9 + - - -
436A MET* 4.4 11.8 - - + +
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A SER* 5.0 4.6 + - - +
352A VAL* 3.8 28.8 - - - +
396A LYS 3.1 14.4 + - - +
397A GLU* 3.0 40.7 + - - +
399A THR* 1.3 79.9 - - - +
401A LEU* 1.3 60.0 + - - +
403A LYS* 3.8 9.4 + - + +
404A ILE* 3.4 32.4 + - + +
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A VAL* 4.1 13.9 - - + -
351A GLN* 3.9 28.0 - - + -
352A VAL* 3.6 17.7 - - + +
355A ILE* 3.4 29.9 - - + +
373A LEU* 3.4 23.8 - - + -
376A THR* 4.0 20.0 - - + +
397A GLU 2.6 21.0 + - - +
398A LEU* 3.5 9.0 - - + +
400A ARG* 1.3 72.9 - - - +
402A LEU* 1.3 71.6 + - + +
404A ILE* 3.4 8.9 + - - +
405A PRO* 3.3 18.2 - - + +
424A LEU* 4.6 2.5 - - + -
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 4.0 7.0 - - + -
398A LEU* 3.1 28.8 + - + +
399A THR 3.9 0.9 - - - +
401A LEU* 1.3 82.1 - - + +
403A LYS* 1.3 61.3 + - - +
404A ILE 3.4 0.9 + - - -
405A PRO* 3.4 10.7 - - - +
406A VAL* 3.7 7.1 - - - +
421A PHE* 3.5 49.6 - - + +
424A LEU* 3.6 31.0 - - + -
425A PHE* 4.6 11.0 - - + -
428A PHE* 3.6 28.9 - - + -
436A MET* 3.6 19.3 - - + -
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Residues in contact with LYS 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A THR* 3.0 40.1 + - + +
400A ARG* 4.1 8.7 - - + +
401A LEU 3.3 0.2 - - - -
402A LEU* 1.3 75.6 - - - +
404A ILE* 1.3 53.8 + - + +
405A PRO 3.6 0.2 - - - -
406A VAL* 3.3 5.4 + - - +
407A ASP* 2.7 50.6 + - - +
435A SER* 6.0 0.2 + - - -
436A MET* 3.9 14.6 - - + -
439A TYR* 3.9 48.3 - - + +
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Residues in contact with ILE 404 (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 VAL* 3.5 33.7 - - + +
355A ILE* 4.1 16.4 - - + -
356A ASN* 5.3 13.5 - - + +
359A MET* 4.5 10.3 - - + -
400A ARG* 3.4 26.7 - - + +
401A LEU 3.4 5.3 + - - +
402A LEU 3.2 0.4 - - - -
403A LYS* 1.3 73.7 - - + +
405A PRO* 1.4 71.9 - - + +
407A ASP* 4.7 3.6 - - - +
408A THR* 2.8 47.5 + - - +
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Residues in contact with PRO 405 (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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355A ILE* 4.5 11.9 - - + -
359A MET* 4.2 6.7 - - + -
369A VAL* 4.3 19.1 - - + -
373A LEU* 5.2 3.4 - - + -
401A LEU 3.3 16.4 - - - +
402A LEU* 3.4 9.9 - - - +
404A ILE* 1.4 94.1 - - + +
406A VAL* 1.3 61.5 + - - +
409A TYR* 3.2 47.4 + - + +
415A VAL* 3.6 13.9 - - + +
418A LEU* 4.7 6.7 - - + -
421A PHE* 4.6 14.6 - - + -
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Residues in contact with VAL 406 (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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402A LEU 3.7 14.4 - - - +
403A LYS* 3.3 10.0 + - - +
404A ILE 3.3 0.6 - - - -
405A PRO* 1.3 76.9 - - - +
407A ASP* 1.3 61.0 + - - +
409A TYR* 4.4 5.0 - - - +
412A ILE* 4.3 24.3 - - + +
415A VAL* 4.0 17.9 - - + -
421A PHE* 3.8 20.4 - - + -
436A MET* 4.8 1.1 - - + -
439A TYR* 4.0 17.9 - - + -
440A VAL* 4.2 19.7 - - + -
443A ASN* 3.7 31.1 + - + +
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Residues in contact with ASP 407 (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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403A LYS* 2.7 38.5 + - - +
404A ILE* 4.1 3.7 - - - +
406A VAL* 1.3 76.8 - - - +
408A THR* 1.3 63.1 + - - +
409A TYR 4.2 3.7 - - - +
439A TYR* 2.7 34.7 + - - -
443A ASN* 4.4 5.4 + - - +
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Residues in contact with THR 408 (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 MET* 3.6 24.2 - - + -
360A LYS* 6.4 3.6 - - + -
404A ILE* 2.8 35.7 + - - +
407A ASP* 1.3 74.2 - - - +
409A TYR* 1.3 65.4 + - - +
410A ASN* 3.7 4.9 + - - +
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Residues in contact with TYR 409 (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 MET* 4.1 23.6 - - + -
363A PRO* 4.5 18.0 + - + -
365A ARG 5.2 0.2 + - - -
366A VAL* 3.6 28.9 - - + +
369A VAL* 4.0 20.5 - - + +
405A PRO* 3.2 36.3 + - + +
406A VAL 4.4 6.3 - - - +
407A ASP 3.7 5.2 - - - +
408A THR* 1.3 81.1 - - - +
410A ASN* 1.3 66.8 + - - +
411A ASN 4.1 5.3 - - - +
412A ILE* 5.0 4.4 - - - +
414A THR* 3.5 36.3 - - + -
415A VAL* 3.8 12.1 - - + -
418A LEU* 5.1 9.0 - - + -
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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