Contacts of the helix formed by residues 377 - 390 (chain B) in PDB entry 1F89
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 377 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B GLU 4.5 1.2 + - - -
370B VAL* 2.7 39.1 - - - +
371B ILE* 3.2 27.4 - - - -
376B PRO* 1.3 73.6 - - - +
378B THR* 1.3 61.9 + - - +
380B VAL* 3.4 9.0 - - - +
381B GLN* 2.6 32.8 + - - +
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Residues in contact with THR 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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325B LYS* 5.0 8.7 - - + -
326B MET* 3.7 29.8 - - + -
329B LEU* 4.3 6.9 - - + +
370B VAL* 4.9 4.9 - - - -
377B SER* 1.3 78.1 + - - +
379B SER* 1.3 58.5 + - - +
381B GLN* 4.0 3.8 - - - +
382B PHE* 3.3 23.6 + - + +
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Residues in contact with SER 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LYS* 3.2 17.7 - - - -
329B LEU* 3.9 16.6 - - - +
356B ASN* 3.2 18.9 + - - -
370B VAL* 3.4 14.1 - - - +
377B SER* 3.2 2.8 + - - -
378B THR* 1.3 74.8 - - - +
380B VAL* 1.3 65.1 + - - +
381B GLN 3.2 1.8 - - - -
382B PHE* 3.7 5.5 - - - +
383B LEU* 3.1 33.8 + - - +
399B ILE* 4.0 17.5 - - - -
414B ILE* 4.9 1.3 - - - -
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Residues in contact with VAL 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B VAL* 3.4 9.4 - - + -
371B ILE 3.9 2.2 - - - +
372B ASN* 3.2 30.1 - - + +
373B PRO* 5.5 3.1 - - + +
376B PRO* 4.4 11.4 - - + +
377B SER* 3.1 32.5 + - - +
379B SER* 1.3 77.4 - - - +
381B GLN* 1.3 59.3 + - - +
384B SER* 3.0 27.3 + - - -
414B ILE* 4.5 2.9 - - + -
416B PHE* 3.5 23.8 - - + -
422B LEU* 4.1 19.3 - - + -
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Residues in contact with GLN 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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376B PRO* 3.3 30.1 - - + +
377B SER 2.6 23.0 + - - +
378B THR* 4.0 4.3 - - - +
380B VAL* 1.3 73.8 - - - +
382B PHE* 1.3 63.8 + - - +
384B SER* 3.1 9.8 + - - -
385B ASN* 2.6 67.1 + - - +
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Residues in contact with PHE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B MET* 5.6 6.3 - - + -
329B LEU* 3.1 65.1 - - + -
330B GLN* 3.6 22.0 - - - -
332B ALA* 5.2 0.9 - - + -
333B ALA* 3.7 18.4 - - + -
378B THR* 3.3 16.1 + - + +
379B SER* 3.4 7.4 + - - +
381B GLN* 1.3 80.7 - - - +
383B LEU* 1.3 65.8 + - + +
385B ASN* 3.3 10.8 + - - +
386B LEU* 3.2 33.8 + - + +
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Residues in contact with LEU 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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329B LEU* 5.2 1.3 - - + -
332B ALA* 5.5 1.6 - - + -
336B ILE* 5.4 0.2 - - + -
351B LEU* 4.1 9.6 - - + -
355B PHE* 3.8 28.3 - - + -
379B SER* 3.1 14.1 + - - +
382B PHE* 1.3 83.3 - - + +
384B SER* 1.3 60.2 + - - +
386B LEU* 3.2 12.5 + - + -
387B ALA* 2.8 29.1 + - - +
394B LEU* 3.7 25.6 - - + +
396B GLY* 3.6 26.0 - - - +
399B ILE* 5.2 2.9 - - + -
414B ILE* 3.5 28.5 - - + -
416B PHE* 3.7 15.4 - - + -
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Residues in contact with SER 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B PRO* 5.9 2.7 - - - +
380B VAL* 3.0 23.4 + - - -
381B GLN* 3.1 14.7 + - - -
383B LEU* 1.3 77.3 - - - +
385B ASN* 1.3 59.8 + - - +
387B ALA* 3.0 18.1 + - - +
388B ASN* 3.0 16.0 + - - +
416B PHE* 3.7 15.8 - - - -
420B GLY* 2.6 27.2 + - - -
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Residues in contact with ASN 385 (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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381B GLN* 2.6 52.6 + - - +
382B PHE* 3.7 9.8 - - - +
383B LEU 3.2 0.2 - - - -
384B SER* 1.3 76.4 + - - +
386B LEU* 1.3 58.8 + - + +
388B ASN* 3.5 8.1 - - - +
389B LYS* 3.2 29.6 + - - +
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Residues in contact with LEU 386 (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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332B ALA 4.9 0.7 - - - -
333B ALA* 4.0 30.3 - - + +
336B ILE* 4.1 20.2 - - + -
337B GLU* 4.7 4.3 - - - +
382B PHE* 3.2 43.3 + - + +
383B LEU* 3.7 16.4 - - + +
385B ASN* 1.3 75.8 - - + +
387B ALA* 1.3 69.0 + - - +
389B LYS* 4.4 6.7 - - + +
390B PHE* 3.2 45.9 + - + -
392B ILE* 3.6 6.4 - - + +
394B LEU* 4.2 8.3 - - + -
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Residues in contact with ALA 387 (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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383B LEU 2.8 13.7 + - - +
384B SER 3.0 11.9 - - - +
386B LEU* 1.3 80.0 - - - +
388B ASN* 1.3 52.4 + - - +
390B PHE 2.4 28.1 - - - +
391B LYS 3.8 0.3 - - - +
392B ILE* 3.3 23.1 - - - +
394B LEU* 4.5 5.8 - - + +
416B PHE* 3.7 16.2 - - + -
417B ASN 3.4 20.2 - - - +
420B GLY* 3.6 7.6 - - - -
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Residues in contact with ASN 388 (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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384B SER 3.0 15.9 - - - +
385B ASN* 3.5 11.5 - - - +
387B ALA* 1.3 73.3 - - - +
389B LYS* 1.3 68.9 + - - +
390B PHE 3.0 7.5 + - - +
391B LYS* 5.3 0.2 - - - -
418B GLU 3.1 13.9 - - - +
419B ASP* 3.1 34.4 + - - +
420B GLY* 4.1 0.5 - - - -
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Residues in contact with LYS 389 (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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337B GLU* 4.7 14.6 + - - +
385B ASN 3.2 22.1 + - - +
386B LEU* 4.4 4.9 - - + +
387B ALA 3.4 0.6 - - - -
388B ASN* 1.3 80.9 - - - +
390B PHE* 1.3 95.4 + - + +
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Residues in contact with PHE 390 (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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336B ILE* 4.2 8.3 - - + -
337B GLU* 3.8 31.4 - - + -
340B MET* 3.4 40.4 - - + -
386B LEU* 3.2 45.7 + - + -
387B ALA 2.4 25.3 - - - +
388B ASN* 3.2 8.8 - - - +
389B LYS* 1.3 106.9 - - + +
391B LYS* 1.3 61.7 + - - +
392B ILE* 3.7 21.1 - - + -
418B GLU 3.9 1.0 - - - +
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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
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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