Contacts of the helix formed by residues 368 - 383 (chain B) in PDB entry 5FW2
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 368 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362B TYR* 4.2 1.6 - - - -
366B GLY 3.7 2.0 + - - -
367B ALA* 1.3 75.7 - - - +
369B GLN* 1.3 66.4 + - - +
370B GLU* 3.7 8.4 + - - +
371B GLU* 3.0 36.9 + - - +
372B PHE* 2.8 22.5 + - - +
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Residues in contact with GLN 369 (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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362B TYR* 3.6 31.4 + - + +
368B SER* 1.3 73.7 - - - +
370B GLU* 1.3 57.2 + - - +
372B PHE* 3.7 0.4 - - - +
373B TYR* 2.9 71.1 + - + +
396B GLU* 4.1 15.4 + - - +
400B ARG* 2.7 47.0 + - - +
404B THR* 4.7 4.0 - - - +
405B PHE* 4.2 28.9 - - + -
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Residues in contact with GLU 370 (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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368B SER* 3.1 9.3 + - - +
369B GLN* 1.3 82.1 - - - +
371B GLU* 1.3 59.7 + - + +
373B TYR* 3.5 7.0 + - - +
374B LYS* 2.9 33.9 + - + +
405B PHE* 5.8 1.9 - - + -
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Residues in contact with GLU 371 (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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357B ASN* 3.6 28.7 + - - +
366B GLY 3.9 5.5 - - - +
367B ALA* 3.7 7.0 - - + -
368B SER* 3.0 35.3 + - - +
370B GLU* 1.3 76.6 - - + +
372B PHE* 1.3 60.7 + - - +
374B LYS* 3.8 11.3 - - + +
375B PHE* 2.9 31.4 + - - +
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Residues in contact with PHE 372 (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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357B ASN* 3.7 11.5 + - - +
358B GLY* 3.4 18.8 - - - -
359B TYR* 3.5 30.7 - + + -
362B TYR* 3.7 31.0 - + + -
367B ALA* 5.0 1.7 - - + +
368B SER 2.8 16.3 + - - +
369B GLN 3.7 2.7 - - - +
371B GLU* 1.3 73.4 - - - +
373B TYR* 1.3 94.5 + + - +
375B PHE* 2.9 4.3 + - - +
376B ILE* 2.8 53.0 + - + +
398B LEU* 4.9 0.7 - - + -
399B LEU* 3.6 38.4 - - + -
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Residues in contact with TYR 373 (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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369B GLN* 2.9 51.9 + - + +
370B GLU* 3.8 6.1 - - - +
372B PHE* 1.3 96.5 - + - +
374B LYS* 1.3 55.2 + - - +
376B ILE* 3.6 5.0 - - - +
377B LYS* 2.7 41.5 + - - +
393B LEU* 4.1 27.5 - - + +
396B GLU* 3.9 20.6 - - + -
398B LEU* 3.1 48.8 + - + -
399B LEU 3.4 12.3 + - - -
400B ARG* 3.8 16.5 - - - +
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Residues in contact with LYS 374 (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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370B GLU* 2.9 21.9 + - + +
371B GLU* 3.8 11.2 - - + +
373B TYR* 1.3 77.8 - - - +
375B PHE* 1.3 62.9 + - - +
377B LYS* 3.6 23.8 + - - +
378B PRO* 3.5 15.8 - - - +
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Residues in contact with PHE 375 (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 GLU* 4.1 28.5 - - + -
350B ILE* 4.5 17.7 - - + -
356B LYS* 3.0 26.9 - - + -
357B ASN* 3.3 22.4 - - + +
358B GLY* 3.5 19.7 - - - -
371B GLU 2.9 18.8 + - - +
372B PHE 3.5 2.2 - - - +
374B LYS* 1.3 78.3 - - - +
376B ILE* 1.3 70.6 + - + +
378B PRO* 3.7 7.6 - - - +
379B ILE* 3.2 28.6 - - + +
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Residues in contact with ILE 376 (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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335B LEU* 3.6 35.9 - - + -
350B ILE* 4.8 14.6 - - + -
372B PHE* 2.8 43.5 + - + +
373B TYR* 3.9 9.6 - - - +
375B PHE* 1.3 84.5 - - + +
377B LYS* 1.3 68.7 + - - +
378B PRO* 3.4 1.3 - - - -
379B ILE* 3.3 22.5 + - + -
380B LEU* 3.2 25.2 + - + +
393B LEU* 4.4 11.4 - - + -
398B LEU* 4.5 9.0 - - + -
399B LEU* 5.4 0.4 - - + -
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Residues in contact with LYS 377 (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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373B TYR* 2.7 20.7 + - - +
374B LYS* 3.6 30.0 + - - +
376B ILE* 1.3 74.9 - - - +
378B PRO* 1.3 71.5 - - + +
380B LEU* 3.2 9.3 + - - +
381B GLU* 3.2 25.5 + - - +
390B LEU* 4.5 10.6 - - + +
393B LEU* 4.1 35.9 - - + -
394B ASN* 5.7 3.6 - - - +
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Residues in contact with PRO 378 (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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374B LYS 3.5 12.6 - - - +
375B PHE 3.7 10.8 - - - +
376B ILE 3.6 1.3 - - - -
377B LYS* 1.3 95.0 - - + +
379B ILE* 1.3 62.5 + - + +
381B GLU* 3.6 15.2 - - + +
382B LYS* 2.8 46.0 + - - +
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Residues in contact with ILE 379 (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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335B LEU* 5.4 0.4 - - + -
339B VAL* 5.0 4.0 - - + -
343B LEU* 4.3 7.0 - - + -
346B LYS* 4.3 22.4 - - + +
350B ILE* 4.6 20.2 - - + -
375B PHE* 3.2 40.6 - - + +
376B ILE* 3.7 24.2 - - + +
377B LYS 3.3 1.0 - - - -
378B PRO* 1.3 81.4 - - + +
380B LEU* 1.3 66.0 + - + +
382B LYS* 3.5 9.1 + - - +
383B MET* 3.1 44.5 + - - +
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Residues in contact with LEU 380 (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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335B LEU* 3.8 24.7 - - + -
376B ILE* 3.2 18.5 + - + +
377B LYS 3.8 6.1 - - - +
379B ILE* 1.3 80.8 - - + +
381B GLU* 1.3 59.0 + - - +
382B LYS 3.0 0.2 - - - -
383B MET* 3.0 21.3 + - - +
386B THR* 2.8 34.9 + - + +
389B LEU* 3.6 50.7 - - + +
390B LEU* 4.2 8.3 - - + +
393B LEU* 4.3 11.7 - - + -
398B LEU* 4.0 22.2 - - + -
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Residues in contact with GLU 381 (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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377B LYS* 3.2 22.8 + - - +
378B PRO* 3.6 20.9 - - + +
380B LEU* 1.3 77.9 - - - +
382B LYS* 1.3 61.3 + - - +
383B MET 3.5 4.8 - - - +
384B ASP* 5.4 0.3 - - - +
387B GLU* 6.1 0.4 - - - -
390B LEU* 3.8 28.5 - - + +
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Residues in contact with LYS 382 (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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343B LEU* 4.3 26.7 - - + -
346B LYS* 4.4 16.7 - - - +
378B PRO* 2.8 35.3 + - - +
379B ILE* 3.7 5.1 - - - +
381B GLU* 1.3 80.4 - - - +
383B MET* 1.3 61.1 + - - +
384B ASP* 4.6 3.3 - - - +
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Residues in contact with MET 383 (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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335B LEU* 5.1 3.6 - - + -
338B LEU* 3.2 50.9 - - + +
339B VAL* 3.3 17.7 - - + +
342B GLN* 3.3 22.2 - - + +
343B LEU* 3.5 28.9 - - + -
379B ILE* 3.1 30.4 + - - +
380B LEU* 3.0 12.9 + - - +
381B GLU 3.9 4.5 - - - +
382B LYS* 1.3 80.7 - - + +
384B ASP* 1.3 71.2 + - - +
386B THR* 3.6 17.1 + - + +
387B GLU* 4.3 4.3 - - - +
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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