Contacts of the helix formed by residues 365 - 377 (chain B) in PDB entry 2FQQ
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 ASP 365 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364B ALA* 1.3 74.4 - - - +
366B VAL* 1.3 53.1 + - - +
367B GLU* 3.2 13.0 + - - +
368B GLU* 2.8 41.8 + - - +
369B ILE* 2.8 34.3 + - - +
397B ALA* 4.1 14.3 - - + +
398B PHE 3.4 29.6 + - - +
399B TYR* 3.4 27.1 + - + +
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Residues in contact with VAL 366 (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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231A PHE* 4.7 5.2 - - + -
279A VAL* 4.8 8.1 - - + -
328B ILE* 4.8 1.1 - - + -
357B MET* 4.5 13.5 - - + -
365B ASP* 1.3 71.7 - - - +
367B GLU* 1.3 59.4 + - + +
369B ILE* 3.2 15.3 + - + +
370B PHE* 3.0 50.1 + - + -
394B LEU* 4.7 12.8 - - + -
398B PHE* 3.1 48.8 + - + +
400B LEU* 3.7 23.5 - - + +
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Residues in contact with GLU 367 (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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328B ILE* 3.8 23.3 - - + -
365B ASP* 3.2 9.9 + - - +
366B VAL* 1.3 81.2 - - + +
368B GLU* 1.3 60.4 + - - +
370B PHE* 3.7 5.3 + - - +
371B ARG* 3.5 17.8 + - - +
374B ARG* 4.7 5.2 + - - +
389B THR* 5.2 5.6 - - + -
392B VAL* 3.8 29.2 - - + +
394B LEU* 4.1 17.1 - - + +
396B ARG 5.1 2.8 - - - +
397B ALA* 6.0 1.3 - - - -
398B PHE 6.3 0.4 - - - +
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Residues in contact with GLU 368 (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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364B ALA* 3.4 11.7 - - + +
365B ASP* 2.8 33.4 + - - +
367B GLU* 1.3 74.1 - - - +
369B ILE* 1.3 63.8 + - - +
371B ARG* 2.8 49.3 + - - +
372B LYS* 3.2 37.7 + - - +
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Residues in contact with ILE 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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353B LEU* 5.4 0.2 - - + -
356B HIS* 4.2 28.9 - - + +
357B MET* 4.4 29.6 - - + +
360B TYR* 3.5 28.7 - - + +
361B ALA* 4.4 6.5 - - + -
364B ALA* 3.4 26.7 - - + +
365B ASP 2.8 17.3 + - - +
366B VAL* 3.2 16.1 + - + +
368B GLU* 1.3 74.8 - - - +
370B PHE* 1.3 65.2 + - + +
372B LYS* 3.0 19.3 + - + +
373B VAL* 3.0 15.7 + - + +
400B LEU* 6.0 2.7 - - + -
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Residues in contact with PHE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 3.9 24.5 - - + -
281A ILE* 4.7 3.1 - - + -
328B ILE* 3.8 34.3 - - + -
330B PHE* 3.5 64.0 - + + -
353B LEU* 3.8 10.3 - - + -
357B MET* 3.7 27.1 - - + -
366B VAL* 3.0 27.9 + - + +
367B GLU* 3.9 5.8 - - - +
369B ILE* 1.3 76.5 - - - +
371B ARG* 1.3 56.1 + - - +
373B VAL* 3.4 6.5 + - - +
374B ARG* 3.0 30.8 + - - +
389B THR* 3.9 11.9 - - + +
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Residues in contact with ARG 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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367B GLU 3.5 10.6 + - - +
368B GLU* 2.8 42.0 + - - +
369B ILE 3.1 0.2 - - - -
370B PHE* 1.3 79.6 - - - +
372B LYS* 1.3 69.0 + - - +
374B ARG* 3.2 27.7 + - + +
375B PHE* 2.7 55.6 + - - +
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Residues in contact with LYS 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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356B HIS* 3.2 24.3 + - + -
360B TYR* 3.7 50.1 + - + -
364B ALA* 4.4 5.8 - - - -
368B GLU* 3.2 37.6 + - - +
369B ILE* 3.0 12.4 + - - +
371B ARG* 1.3 85.6 - - - +
373B VAL* 1.3 59.8 + - - +
375B PHE* 3.8 9.3 - - + +
376B SER* 3.1 21.1 + - - -
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Residues in contact with VAL 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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330B PHE* 3.8 21.3 - - + -
349B PHE* 5.3 2.5 - - + +
352B ARG* 4.6 6.1 - - + -
353B LEU* 4.2 25.8 - - + +
356B HIS* 3.8 25.6 - - + +
369B ILE* 3.0 15.8 + - + +
370B PHE* 3.5 12.1 - - - +
372B LYS* 1.3 76.4 - - - +
374B ARG* 1.3 60.7 + - - +
376B SER* 2.7 20.9 + - - -
377B PHE* 3.2 32.4 + - + -
387B PRO* 4.3 3.8 - - + -
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Residues in contact with ARG 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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330B PHE* 5.1 0.8 - - - -
367B GLU* 4.7 4.6 + - - +
370B PHE* 3.0 13.8 + - - +
371B ARG* 3.2 53.0 + - - +
373B VAL* 1.3 77.9 - - - +
375B PHE* 1.3 59.7 + - - +
377B PHE* 3.4 11.2 + - - -
378B GLU* 3.5 10.4 + - - +
386B MET* 3.8 29.2 - - - +
387B PRO* 3.3 35.8 + - + +
388B THR* 4.8 1.1 - - - +
389B THR* 2.7 37.0 + - - +
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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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371B ARG* 2.7 38.6 + - + +
372B LYS* 3.8 10.3 - - + +
373B VAL 3.3 0.4 - - - -
374B ARG* 1.3 72.5 - - - +
376B SER* 1.3 62.7 + - - +
378B GLU* 3.4 44.5 - - - +
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Residues in contact with SER 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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352B ARG* 3.2 29.5 + - - +
356B HIS* 3.4 23.3 - - - -
372B LYS 3.1 14.5 + - - -
373B VAL* 2.7 22.9 + - - -
375B PHE* 1.3 79.6 - - - +
377B PHE* 1.3 56.0 + - - +
378B GLU 3.3 2.5 + - - -
379B GLN 4.8 5.5 + - - +
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Residues in contact with PHE 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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348B VAL* 3.6 32.3 - - + -
349B PHE* 4.8 7.0 - + - -
352B ARG* 3.4 48.7 - - + -
373B VAL* 3.2 32.4 + - + +
374B ARG* 3.4 8.2 + - - +
375B PHE 3.3 0.8 - - - -
376B SER* 1.3 78.3 + - - +
378B GLU* 1.3 63.8 + - - +
379B GLN 3.3 10.1 + - - -
380B PRO* 4.6 4.3 - - - +
383B ARG 4.5 7.6 - - - -
385B GLN* 3.2 50.0 - - + +
386B MET* 3.5 12.4 - - + +
387B PRO* 4.3 11.2 - - + -
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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