Contacts of the helix formed by residues 378 - 395 (chain B) in PDB entry 5UFL
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 ASN 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B GLN* 4.8 11.9 + - - -
373B VAL* 3.5 14.9 - - + +
376B ALA* 3.3 17.2 + - - +
377B ALA* 1.3 83.9 - - - +
379B CYS* 1.3 62.1 + - - +
380B SER* 3.3 3.8 - - - +
381B SER* 3.4 25.9 + - - +
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Residues in contact with CYS 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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373B VAL* 3.8 9.0 - - + -
374B ILE* 4.1 24.7 - - - -
377B ALA* 3.0 18.0 + - - -
378B ASN* 1.3 77.6 - - - +
380B SER* 1.3 59.1 + - - +
381B SER 3.4 0.2 + - - -
382B ALA* 3.4 4.3 + - - +
383B ASP* 3.0 28.5 + - - +
429B ASP* 3.3 38.6 - - + +
431B THR* 5.9 0.4 - - - -
432B LEU* 4.6 8.1 - - + +
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Residues in contact with SER 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ASN* 3.3 1.1 - - - -
379B CYS* 1.3 76.9 - - - +
381B SER* 1.3 63.6 + - - +
383B ASP* 3.7 18.9 + - - +
384B ARG* 4.3 4.0 + - - +
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Residues in contact with SER 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE* 3.8 30.1 + - - +
322B GLU* 5.6 0.3 - - - -
373B VAL* 6.3 0.7 - - - -
378B ASN* 3.4 22.8 + - - +
379B CYS 3.2 0.6 - - - -
380B SER* 1.3 80.9 - - - +
382B ALA* 1.3 60.8 + - - +
384B ARG* 4.2 9.9 + - - +
385B PHE* 4.9 1.0 + - - +
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Residues in contact with ALA 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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321B PHE* 4.0 36.7 - - + +
370B PHE* 4.1 16.8 - - + -
373B VAL* 4.2 15.9 - - + -
378B ASN 4.0 0.6 + - - -
379B CYS 3.4 8.2 + - - +
381B SER* 1.3 75.0 + - - +
383B ASP* 1.3 56.3 + - - +
384B ARG 3.2 3.1 - - - -
385B PHE* 2.8 27.0 + - - +
386B VAL* 3.0 13.8 + - + +
432B LEU* 5.6 2.2 - - + -
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Residues in contact with ASP 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B CYS 3.0 17.5 + - - +
380B SER* 3.7 16.0 - - - +
381B SER 3.4 0.6 - - - -
382B ALA* 1.3 76.0 - - - +
384B ARG* 1.3 62.6 + - - +
386B VAL* 3.4 10.3 + - - +
387B THR* 3.6 12.5 + - - -
429B ASP* 5.4 0.2 - - - +
431B THR* 3.4 27.1 - - - +
432B LEU* 3.6 22.3 - - - +
435B HIS* 3.3 24.9 + - - -
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Residues in contact with ARG 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B SER 4.3 3.4 + - - +
381B SER 4.2 9.7 + - - +
382B ALA 3.0 0.6 + - - -
383B ASP* 1.3 77.8 - - - +
385B PHE* 1.3 61.5 + - - +
387B THR* 3.5 19.0 + - - -
388B LEU* 3.9 4.2 + - - +
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Residues in contact with PHE 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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321B PHE* 3.4 31.2 - + + -
338B LEU* 6.2 5.2 - - + -
341B THR* 3.4 34.1 - - + -
345B LEU* 4.3 14.4 - - + -
366B PHE* 3.5 30.1 - + - -
370B PHE* 3.7 16.6 - + - -
381B SER 4.9 0.6 + - - +
382B ALA* 2.8 15.4 + - - +
384B ARG* 1.3 71.4 - - - +
386B VAL* 1.3 57.8 + - - +
387B THR 3.2 2.5 - - - -
388B LEU* 2.9 20.5 + - + +
389B LEU* 2.9 57.6 + - + +
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Residues in contact with VAL 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B PHE* 3.5 33.9 - - + -
382B ALA* 3.0 16.1 + - + +
383B ASP 3.7 8.7 - - - +
384B ARG 3.4 0.6 - - - -
385B PHE* 1.3 75.6 - - - +
387B THR* 1.3 60.2 + - - +
389B LEU* 4.4 7.0 - - + -
390B LEU* 3.1 49.3 + - + +
426B LEU* 4.2 13.5 - - + -
432B LEU* 3.7 33.2 - - + +
435B HIS* 4.4 8.7 - - + -
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Residues in contact with THR 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ASP* 3.6 11.6 + - - -
384B ARG* 3.5 12.1 + - - -
385B PHE 3.2 0.4 - - - -
386B VAL* 1.3 76.9 - - - +
388B LEU* 1.3 60.7 + - - +
390B LEU* 5.3 1.6 - - - -
391B PRO* 3.3 21.7 - - - +
435B HIS* 3.8 18.5 + - + -
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Residues in contact with LEU 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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338B LEU* 5.3 12.6 - - + -
341B THR* 5.5 1.3 - - - +
342B VAL* 4.8 13.9 - - + -
345B LEU* 4.4 18.9 - - + +
384B ARG 3.9 2.4 + - - +
385B PHE* 2.9 29.3 + - + +
387B THR* 1.3 80.9 - - - +
389B LEU* 1.3 59.9 + - - +
391B PRO* 4.0 6.6 - - - +
392B THR* 4.2 9.9 + - - +
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 3.4 28.7 - - + -
348B LEU* 4.5 1.6 - - + -
366B PHE* 4.0 20.0 - - + -
370B PHE* 3.3 40.2 - - + -
385B PHE* 2.9 26.7 + - + +
386B VAL* 4.2 4.9 - - + +
387B THR 3.3 0.2 - - - -
388B LEU* 1.3 77.8 - - - +
390B LEU* 1.3 66.7 + - + +
391B PRO 3.3 1.1 - - - -
392B THR* 2.5 24.6 + - - +
393B ILE* 3.2 38.1 + - + -
426B LEU* 5.6 3.4 - - + -
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Residues in contact with LEU 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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386B VAL* 3.1 39.3 + - + +
387B THR* 4.7 1.1 - - - +
389B LEU* 1.3 77.4 - - + +
391B PRO* 1.4 64.0 - - + +
393B ILE* 3.1 8.7 + - + +
394B LEU* 2.8 37.4 + - + +
423B LEU* 3.4 33.4 - - + -
426B LEU* 3.8 11.9 - - + -
435B HIS* 3.7 36.1 - - + +
436B ILE* 3.8 14.4 - - + +
439B ILE* 4.7 12.6 - - + -
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Residues in contact with PRO 391 (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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387B THR 3.3 20.4 - - - +
388B LEU 4.0 4.7 - - - +
389B LEU 3.5 3.6 - - - -
390B LEU* 1.4 93.0 - - + +
392B THR* 1.3 57.2 + - + +
394B LEU* 3.5 9.4 + - + +
395B ASP* 3.1 26.3 + - - +
439B ILE* 5.9 8.7 - - + -
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Residues in contact with THR 392 (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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345B LEU* 3.2 34.0 - - + +
348B LEU* 4.8 8.9 - - - +
349B SER* 5.2 9.9 - - - +
388B LEU 4.8 6.5 - - - +
389B LEU* 2.5 23.4 + - - +
391B PRO* 1.3 75.0 - - + +
393B ILE* 1.3 62.2 + - - +
395B ASP* 3.4 19.2 + - - +
396B GLN* 3.5 18.1 + - - +
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Residues in contact with ILE 393 (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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348B LEU* 4.3 9.4 - - + -
363B LEU* 4.6 5.2 - - + -
366B PHE* 5.0 2.9 - - + -
389B LEU* 3.2 42.2 + - + +
390B LEU* 3.1 13.3 + - + +
392B THR* 1.3 74.4 - - - +
394B LEU* 1.3 63.7 + - - +
396B GLN* 3.1 23.2 + - - +
397B LEU* 3.8 6.8 - - - +
419B ALA* 3.7 31.4 - - + +
422B VAL* 3.4 32.8 - - + -
423B LEU* 4.0 21.1 - - + -
426B LEU* 5.6 0.2 - - + -
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Residues in contact with LEU 394 (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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390B LEU* 2.8 28.1 + - + +
391B PRO* 3.8 8.1 - - + +
393B ILE* 1.3 72.7 - - - +
395B ASP* 1.3 56.5 + - - +
397B LEU* 3.1 31.9 + - + +
423B LEU* 3.7 35.9 - - + -
436B ILE* 5.5 0.9 - - + -
439B ILE* 3.8 41.3 - - + +
440B LEU* 4.1 22.9 - - + -
444B LYS* 3.6 28.8 + - + -
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Residues in contact with ASP 395 (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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391B PRO 3.1 14.3 + - - +
392B THR* 3.5 14.8 - - - +
393B ILE 3.2 0.8 - - - -
394B LEU* 1.3 75.4 - - - +
396B GLN* 1.3 65.8 + - - +
397B LEU 3.3 0.4 - - - -
398B GLN* 2.9 45.7 + - - +
412B LYS* 5.1 1.9 + - - -
444B LYS* 5.3 0.9 - - - +
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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