Contacts of the helix formed by residues 391 - 402 (chain F) in PDB entry 3FZ7
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 THR 391 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F LEU* 4.6 8.5 - - + -
390F TYR* 1.3 87.0 - - - +
392F LEU* 1.3 64.7 + - - +
393F TYR* 3.1 28.7 + - + +
394F ASP* 2.9 31.5 + - - +
395F LEU 3.2 8.8 + - - -
419F VAL* 6.2 1.3 - - - -
455F GLN* 4.7 7.0 - - + +
456F GLY* 4.2 16.2 - - - +
458F ALA 4.5 1.3 + - - +
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Residues in contact with LEU 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363F TYR* 4.4 3.1 - - + -
380F PHE* 3.7 39.0 - - + +
381F LYS* 3.9 12.8 - - - -
382F LEU* 4.3 24.2 - - + +
390F TYR* 4.5 2.5 - - + -
391F THR* 1.3 74.9 - - - +
393F TYR* 1.3 56.8 + - - +
395F LEU* 3.3 22.7 + - + +
396F SER* 2.9 30.0 + - - -
408F ALA* 3.9 13.9 - - + -
419F VAL* 3.6 33.0 - - + +
421F MET* 3.7 21.2 - - + +
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Residues in contact with TYR 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391F THR* 3.1 14.2 + - + +
392F LEU* 1.3 76.5 - - - +
394F ASP* 1.3 64.3 - - - +
396F SER* 3.4 3.6 + - - -
397F GLU* 3.1 17.5 + - - +
400F ARG* 4.9 1.6 + - - -
408F ALA* 3.7 24.9 - - + -
409F PHE* 4.6 0.2 - - - -
410F THR* 3.4 20.0 + - + +
419F VAL* 3.7 29.0 - - + +
458F ALA* 3.3 38.2 - - + +
459F GLN* 4.7 9.3 + - - -
460F GLN 3.5 29.2 - - - -
461F ASN* 2.7 28.9 + - - -
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Residues in contact with ASP 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390F TYR* 3.6 1.7 - - + -
391F THR* 2.9 33.2 + - - +
393F TYR* 1.3 73.2 - - - +
395F LEU* 1.3 64.9 + - - +
397F GLU* 3.2 6.5 + - - +
398F ARG* 3.0 29.3 + - - +
448F LEU* 4.1 19.1 - - + -
454F LEU* 3.7 9.3 - - + +
455F GLN* 3.4 6.4 - - - -
456F GLY 2.9 26.5 + - - -
457F ILE 3.6 1.4 + - - -
458F ALA* 3.3 27.9 + - - +
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Residues in contact with LEU 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363F TYR* 4.3 4.0 - - - +
390F TYR* 4.4 11.0 - - + -
391F THR 3.2 8.8 + - - +
392F LEU* 3.5 20.0 - - + +
394F ASP* 1.3 78.6 - - - +
396F SER* 1.3 57.2 + - - +
398F ARG* 3.4 1.8 + - - +
399F LEU* 3.0 38.4 + - + +
421F MET* 3.9 15.3 - - + -
441F TYR* 3.3 43.5 - - + +
444F SER* 3.7 26.5 - - - -
445F LEU* 4.2 15.5 - - + -
448F LEU* 4.2 9.3 - - + +
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Residues in contact with SER 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392F LEU 2.9 17.5 + - - -
393F TYR* 3.6 5.8 - - - -
394F ASP 3.2 0.2 - - - -
395F LEU* 1.3 76.4 - - - +
397F GLU* 1.3 55.7 + - - +
399F LEU* 3.5 5.3 + - - +
400F ARG* 3.0 47.6 + - - +
404F TRP 4.6 0.9 - - - +
406F VAL 2.6 28.1 + - - +
408F ALA* 4.1 14.0 + - - -
421F MET* 3.8 10.3 - - - +
462F SER* 4.1 2.6 + - - -
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Residues in contact with GLU 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398E ARG* 2.8 35.4 + - - -
401E LEU* 3.8 21.5 - - + +
447E TYR* 4.5 5.9 + - - -
454E LEU* 5.1 2.1 - - - +
393F TYR 3.1 12.2 + - - +
394F ASP* 3.2 8.9 + - - +
396F SER* 1.3 73.0 - - - +
398F ARG* 1.3 93.8 + - - +
400F ARG* 3.0 32.2 + - - +
401F LEU* 3.2 8.9 + - + +
454F LEU* 5.1 2.8 - - - +
457F ILE* 6.1 2.1 - - - +
458F ALA* 4.3 17.0 - - + +
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Residues in contact with ARG 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397E GLU* 2.7 40.6 + - - -
457E ILE* 6.1 0.2 - - - +
394F ASP 3.0 20.6 + - - +
395F LEU 3.8 3.1 - - - +
397F GLU* 1.3 100.5 + - - +
399F LEU* 1.3 58.3 + - - +
401F LEU* 2.9 43.3 + - - +
402F ARG* 3.4 8.8 + - - +
444F SER* 3.5 27.6 - - - +
447F TYR* 3.7 31.7 - - + +
448F LEU* 3.9 32.3 - - + -
454F LEU* 3.8 20.3 - - - +
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Residues in contact with LEU 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395F LEU* 3.0 37.1 + - + +
396F SER* 3.7 4.9 - - - +
398F ARG* 1.3 75.0 - - - +
400F ARG* 1.3 57.1 - - - +
402F ARG* 2.8 22.0 + - - +
403F GLY 3.3 0.5 + - - -
404F TRP* 3.2 29.8 + - + +
406F VAL* 3.9 27.8 - - + -
421F MET* 4.1 7.9 - - + -
437F LEU* 4.2 17.0 - - + -
440F ASP* 4.0 9.0 - - + +
441F TYR* 3.9 37.2 - - + +
444F SER* 3.8 15.5 - - - +
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Residues in contact with ARG 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LEU* 3.6 38.3 - - - +
400E ARG 5.6 1.7 - - - +
401E LEU* 3.9 25.9 - - + +
393F TYR 4.9 2.6 + - - -
396F SER* 3.0 37.7 + - - +
397F GLU* 3.0 37.0 + - - +
399F LEU* 1.3 76.3 - - - +
401F LEU* 1.3 62.3 + - - +
402F ARG 3.0 0.4 - - - -
403F GLY* 3.1 13.0 + - - -
404F TRP 3.1 20.8 + - - +
405F GLN* 3.3 24.8 + - + +
406F VAL 5.3 0.2 - - - +
458F ALA* 5.6 2.6 - - - +
462F SER* 4.2 1.4 + - - -
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Residues in contact with LEU 401 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397E GLU* 3.5 21.1 - - + +
400E ARG* 3.8 42.2 - - + +
401E LEU* 3.9 24.5 - - + +
397F GLU 3.2 10.5 + - - +
398F ARG* 2.9 52.4 + - - +
400F ARG* 1.3 75.8 - - - +
402F ARG* 1.3 62.8 + - + +
403F GLY 3.4 0.4 + - - -
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Residues in contact with ARG 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D GLY* 5.3 11.1 - - - -
58F GLN* 3.5 13.7 + - - -
398F ARG 4.0 10.3 - - - +
399F LEU* 2.8 10.9 + - - +
401F LEU* 1.3 86.4 - - + +
403F GLY* 1.3 54.6 + - - +
404F TRP* 3.5 5.5 + - + -
439F GLU 5.2 0.8 + - - -
440F ASP* 3.0 50.9 + - + +
443F ALA* 3.8 27.8 - - - +
444F SER* 4.9 2.9 - - - +
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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
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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