Contacts of the helix formed by residues 395 - 416 (chain B) in PDB entry 5FLZ
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 PRO 395 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B PRO 3.7 0.2 - - - -
392B ALA* 3.5 15.0 - - + +
393B PHE 3.9 4.3 - - - +
394B ILE* 1.3 89.0 - - - +
396B LYS* 1.3 65.7 + - - +
397B GLU* 4.0 22.9 - - + -
398B LEU* 3.1 22.5 + - + +
399B ALA* 3.1 19.1 + - - +
442B SER* 4.7 5.2 - - - +
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Residues in contact with LYS 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B GLN* 2.9 57.0 + - - +
388B GLU* 4.7 2.8 + - - +
390B VAL* 3.0 28.5 + - + +
391B PRO 3.6 11.2 + - - +
392B ALA* 3.8 18.9 - - + +
395B PRO* 1.3 72.2 - - - +
397B GLU* 1.4 56.0 + - - +
399B ALA* 3.3 3.8 + - - +
400B TYR* 2.9 29.0 + - - +
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PRO* 4.0 14.4 - - + -
396B LYS* 1.4 74.1 - - - +
398B LEU* 1.3 91.3 + - - +
400B TYR* 3.3 8.4 + - - +
401B LYS* 2.9 52.6 + - - +
446B PHE* 5.7 1.4 - - - -
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ILE* 3.8 25.8 - - + -
395B PRO* 3.1 27.5 + - + +
397B GLU* 1.3 91.7 + - - +
399B ALA* 1.3 61.3 + - - +
401B LYS* 3.4 10.8 + - - +
402B ILE* 3.2 47.9 + - + +
442B SER* 3.8 24.9 - - - +
443B THR* 5.1 2.5 - - + +
445B PHE* 5.7 1.6 - - + -
446B PHE* 3.6 31.9 - - + +
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B PHE* 3.8 22.5 - - + -
390B VAL* 3.3 31.4 - - + -
391B PRO* 4.7 5.2 - - + +
394B ILE* 5.0 6.5 - - + +
395B PRO 3.1 6.6 + - - +
396B LYS 3.3 1.8 + - - +
398B LEU* 1.3 79.7 - - - +
400B TYR* 1.4 56.5 + - - +
402B ILE* 3.2 15.4 + - + +
403B PHE* 2.9 28.4 + - - +
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Residues in contact with TYR 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B PHE* 3.3 44.7 - + + -
387B GLN* 5.7 3.4 - - - +
390B VAL* 5.0 0.2 - - - +
396B LYS 2.9 13.0 + - - +
397B GLU* 3.5 13.5 - - - +
399B ALA* 1.4 75.5 - - - +
401B LYS* 1.3 62.1 + - + +
403B PHE* 3.3 29.9 + + - +
404B MET* 3.2 50.9 + - + +
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Residues in contact with LYS 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B GLU* 2.9 55.2 + - - +
398B LEU* 3.6 6.3 - - - +
400B TYR* 1.3 77.0 - - + +
402B ILE* 1.4 61.4 + - - +
404B MET* 3.2 17.1 + - - +
405B ILE* 3.1 31.2 + - + +
446B PHE* 3.6 37.7 - - + -
453B TYR* 6.4 0.9 - - + -
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Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 4.0 27.1 - - + -
349B TRP* 3.6 23.5 + - + -
350B LEU* 4.1 11.4 - - + +
363B PHE* 5.3 4.7 - - + -
394B ILE* 4.4 10.8 - - + -
398B LEU* 3.2 38.3 + - + +
399B ALA* 3.3 15.7 - - + +
401B LYS* 1.4 71.3 - - - +
403B PHE* 1.4 66.1 + - - +
405B ILE* 3.4 10.3 + - - +
406B GLY 3.0 19.2 + - - -
445B PHE* 4.8 2.9 - - + -
446B PHE* 4.5 5.4 - - + -
449B ILE* 4.5 19.3 - - + -
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Residues in contact with PHE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B TRP* 3.5 24.9 - + - +
363B PHE* 4.2 14.1 - + + -
364B ILE* 5.2 2.0 - - + -
383B ILE 4.5 1.6 - - - -
384B GLU* 3.8 16.2 - - + -
385B PHE* 3.5 43.1 - + + -
399B ALA 2.9 13.2 + - - +
400B TYR* 3.3 42.4 + + - +
402B ILE* 1.4 76.4 - - - +
404B MET* 1.4 67.2 + - + +
407B LYS* 3.1 68.8 + - + +
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Residues in contact with MET 404 (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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400B TYR* 3.2 44.1 + - + +
401B LYS* 3.2 18.4 + - - +
403B PHE* 1.4 92.5 - - + +
405B ILE* 1.3 53.9 + - + +
407B LYS* 3.4 14.5 + - - +
408B SER* 2.6 38.3 + - - -
453B TYR* 5.3 9.6 - - + +
720B ASN* 4.4 31.2 - - - +
722B ASP* 5.7 3.8 - - - +
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Residues in contact with ILE 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 3.6 20.6 - - + +
401B LYS* 3.1 20.2 + - + +
402B ILE* 3.6 7.9 - - - +
404B MET* 1.3 74.6 - - - +
406B GLY* 1.4 61.1 + - - +
408B SER* 3.4 8.6 + - - -
409B TYR* 3.0 20.8 + - - +
446B PHE* 4.8 6.5 - - + -
449B ILE* 3.4 26.5 - - + -
452B GLN* 3.4 31.2 - - - +
453B TYR* 3.4 45.1 - - + -
456B ILE* 5.6 1.3 - - + +
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Residues in contact with GLY 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B TRP* 3.6 43.3 - - - -
350B LEU* 4.6 2.9 - - - +
353B GLY* 3.5 5.4 - - - -
402B ILE 3.0 13.5 + - - -
405B ILE* 1.4 73.3 - - - +
407B LYS* 1.4 61.2 - - - +
409B TYR* 3.1 3.8 + - - +
410B ILE* 3.1 26.2 + - - +
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Residues in contact with LYS 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B TRP* 3.6 14.8 - - + -
383B ILE* 4.4 20.4 - - + +
403B PHE* 3.1 59.5 + - + +
404B MET* 3.4 15.4 - - - +
406B GLY* 1.4 74.0 - - - +
408B SER* 1.3 63.1 + - - +
410B ILE* 3.5 9.1 + - - +
411B PHE* 3.2 25.4 + - + +
720B ASN* 6.4 0.2 - - - +
721B ILE* 6.2 4.4 - - - +
722B ASP* 5.0 9.8 + - - -
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B MET 2.6 23.9 + - - -
405B ILE* 3.4 9.3 - - - -
407B LYS* 1.3 75.6 - - - +
409B TYR* 1.4 65.6 + - - +
411B PHE* 3.3 11.5 + - - +
412B LEU* 3.0 25.4 + - - +
453B TYR* 4.9 8.5 - - - -
456B ILE* 6.1 7.4 - - - -
457B VAL* 6.4 0.7 - - - -
719B LEU 5.5 1.2 + - - -
720B ASN* 4.7 11.6 + - - -
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Residues in contact with TYR 409 (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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350B LEU 4.4 12.3 - - - +
351B THR 3.3 28.5 - - - -
352B LYS* 4.1 11.9 - - - -
353B GLY 4.3 7.0 - - - +
405B ILE 3.0 13.8 + - - +
406B GLY 3.1 9.1 + - - +
408B SER* 1.4 76.2 - - - +
410B ILE* 1.3 62.4 + - - +
412B LEU* 3.3 10.4 + - + +
413B GLU* 3.1 53.4 + - + +
419B VAL* 3.5 6.6 - - + +
420B GLN* 3.1 15.6 + - + -
423B ASN* 5.5 3.1 - - - -
424B GLU* 2.8 38.2 + - + +
452B GLN* 5.4 1.8 - - - -
456B ILE* 3.3 35.2 - - + +
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Residues in contact with ILE 410 (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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349B TRP* 3.7 15.7 - - + -
352B LYS 4.1 5.4 - - - +
353B GLY* 3.2 32.3 - - - +
383B ILE* 3.8 31.6 - - + -
406B GLY 3.1 17.2 + - - +
407B LYS 3.5 9.2 - - - +
409B TYR* 1.3 75.7 - - - +
411B PHE* 1.4 60.6 + - - +
413B GLU* 3.1 12.4 + - + +
414B LYS* 3.1 21.1 + - - +
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Residues in contact with PHE 411 (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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407B LYS* 3.2 17.7 + - + +
408B SER* 3.6 11.7 - - - +
409B TYR 3.2 0.2 - - - -
410B ILE* 1.4 77.9 - - - +
412B LEU* 1.3 64.1 + - + +
414B LYS* 3.3 34.4 + - + -
415B TYR* 3.0 37.8 + + + +
464B LEU* 6.2 5.8 - - + -
566B PRO 3.8 11.2 - - - -
567B PRO* 3.9 32.3 - - + -
570B LEU* 4.5 14.4 - - + -
571B VAL* 5.9 0.7 - - + -
721B ILE* 5.8 8.7 - - + -
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B SER 3.0 17.2 + - - +
409B TYR* 3.5 20.0 - - + +
411B PHE* 1.3 78.6 - - + +
413B GLU* 1.3 67.2 + - - +
415B TYR* 3.1 19.4 + - + +
416B CYS* 2.9 18.7 + - - +
419B VAL* 3.8 26.5 - - + +
420B GLN* 5.2 4.9 - - + +
456B ILE* 4.5 11.2 - - + -
460B THR* 4.1 33.7 - - + +
463B ILE* 4.9 24.0 - - + -
464B LEU* 5.2 4.7 - - + -
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Residues in contact with GLU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B LYS* 4.4 14.8 + - - +
409B TYR* 3.1 49.7 - - + +
410B ILE* 3.1 14.9 + - + +
412B LEU* 1.3 77.3 - - - +
414B LYS* 1.4 57.7 + - - +
416B CYS 2.6 24.6 - - - +
417B LYS* 3.1 14.4 + - - +
419B VAL* 3.0 44.4 - - - +
421B TRP* 4.4 3.1 - - - -
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Residues in contact with LYS 414 (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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410B ILE 3.1 9.8 + - - +
411B PHE* 3.4 43.6 + - + +
412B LEU 3.3 0.2 - - - -
413B GLU* 1.4 74.9 - - - +
415B TYR* 1.4 77.4 + - - +
416B CYS* 3.4 0.5 + - - -
566B PRO* 3.8 27.8 + - - +
569B SER* 4.5 10.5 - - - -
570B LEU* 4.2 21.1 - - + -
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Residues in contact with TYR 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B PHE* 3.0 32.0 + + + +
412B LEU* 3.1 19.2 + - + +
414B LYS* 1.4 84.6 - - - +
416B CYS* 1.4 62.1 + - + +
464B LEU* 5.2 6.7 - - + -
468B PHE* 3.1 54.8 - + - +
470B TYR* 3.2 31.1 + - - -
565B TYR* 5.1 2.4 - - - -
566B PRO* 3.7 41.4 - - + +
567B PRO* 4.1 4.7 - - + -
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Residues in contact with CYS 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LEU 2.9 11.6 - - - +
413B GLU* 2.6 20.5 + - - +
414B LYS 4.5 0.7 - - - -
415B TYR* 1.4 85.6 - - + +
417B LYS* 1.4 65.1 + - - +
418B GLU* 3.4 32.5 - - - +
419B VAL* 3.6 3.9 - - + +
468B PHE* 5.2 10.3 - - + -
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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
------------------------------------------------------------
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