Contacts of the helix formed by residues 384 - 405 (chain F) in PDB entry 6VVT
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 VAL 384 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037C THR* 6.5 0.4 - - + -
380F SER 5.9 1.3 - - - +
382F ALA 4.0 8.3 - - - +
383F VAL* 1.3 78.2 - - - +
385F ALA* 1.3 67.5 + - - +
386F VAL* 3.6 21.3 - - + -
387F ASP* 3.0 29.7 + - + +
388F ALA* 3.0 22.7 + - - +
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Residues in contact with ALA 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037C THR* 5.0 14.2 - - + +
1090C ARG 4.6 1.1 - - - +
1091C VAL* 4.0 30.0 - - + +
1094C TYR* 3.6 37.0 - - + -
383F VAL* 3.9 3.6 + - - +
384F VAL* 1.3 73.0 - - - +
386F VAL* 1.3 64.7 + - - +
388F ALA* 3.3 2.4 + - - +
389F VAL* 3.2 27.2 + - - +
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Residues in contact with VAL 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094C TYR* 3.8 29.2 - - + +
457D MET* 5.0 0.9 - - + -
469D ILE* 4.1 20.2 - - + +
470D LYS* 6.2 1.8 - - - -
473D LYS* 3.9 38.8 - - + +
384F VAL* 3.6 21.3 - - + -
385F ALA* 1.3 76.7 - - - +
387F ASP* 1.3 67.8 + - - +
389F VAL* 3.4 4.2 + - - +
390F SER* 3.0 26.9 + - - +
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Residues in contact with ASP 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D LYS* 5.1 3.1 + - - -
384F VAL* 3.0 37.9 + - + +
386F VAL* 1.3 84.9 - - - +
388F ALA* 1.3 57.9 + - - +
389F VAL 3.0 1.6 - - - -
390F SER* 2.8 9.6 + - - +
391F PHE* 2.5 39.8 + - + +
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Residues in contact with ALA 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091C VAL* 4.5 12.3 - - + -
1095C GLU* 6.1 0.9 - - - +
383F VAL* 4.2 19.3 - - + +
384F VAL 3.0 14.5 + - - +
385F ALA 3.8 4.5 - - - +
387F ASP* 1.3 75.6 - - - +
389F VAL* 1.3 54.7 + - + +
391F PHE* 4.1 6.6 - - - +
392F THR* 2.6 34.8 + - - -
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Residues in contact with VAL 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091C VAL* 5.3 1.1 - - + +
1094C TYR* 4.6 6.3 - - + -
1095C GLU* 3.8 43.1 - - + +
1098C VAL* 4.6 14.4 - - + -
1099C LYS* 5.8 7.4 - - + -
469D ILE* 4.1 18.8 - - + -
385F ALA* 3.2 16.0 + - - +
386F VAL* 3.7 6.5 - - - +
387F ASP 3.0 0.6 - - - -
388F ALA* 1.3 78.3 - - + +
390F SER* 1.3 60.6 + - - +
392F THR* 3.1 6.4 + - - -
393F LEU* 2.8 45.8 + - + +
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Residues in contact with SER 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D ILE* 4.4 17.9 - - - +
470D LYS* 5.6 7.6 - - - -
386F VAL* 3.0 13.2 + - - -
387F ASP* 2.8 31.4 + - - +
389F VAL* 1.3 75.3 - - - +
391F PHE* 1.3 51.1 + - - +
393F LEU* 3.1 8.3 + - - -
394F LEU 2.7 31.4 + - - -
464F TYR* 3.3 21.4 - - - -
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Residues in contact with PHE 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806C THR* 3.7 33.2 - - + -
808C GLU* 3.5 32.1 - - + -
809C GLU* 5.3 1.1 - - + -
387F ASP* 2.5 24.2 + - + +
388F ALA* 4.1 6.5 - - - +
390F SER* 1.3 73.4 + - - +
392F THR* 1.3 60.4 + - - +
394F LEU* 3.2 14.1 + - + +
395F GLN* 3.0 56.6 + - + +
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Residues in contact with THR 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095C GLU* 6.2 0.8 - - - -
1099C LYS* 5.7 8.5 - - - +
388F ALA 2.6 23.0 + - - -
389F VAL* 3.1 9.6 + - - -
391F PHE* 1.3 80.1 - - - +
393F LEU* 1.3 64.2 + - + +
395F GLN* 3.4 13.0 + - - +
396F ASP* 2.7 43.4 + - - +
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Residues in contact with LEU 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098C VAL* 6.0 2.0 - - + -
1099C LYS* 5.9 7.2 - - + -
468D ASN* 6.0 1.1 - - + -
469D ILE* 3.4 36.1 - - + +
389F VAL* 2.8 33.0 + - + +
390F SER* 3.5 4.3 - - - +
392F THR* 1.3 76.7 - - + +
394F LEU* 1.3 58.5 + - - +
396F ASP* 3.4 12.9 + - + +
397F GLN* 2.9 30.3 + - - +
464F TYR* 3.3 16.6 + - - +
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Residues in contact with LEU 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808C GLU* 4.0 21.8 - - + +
809C GLU* 5.1 3.6 - - + +
812C LEU* 3.6 40.2 - - + -
390F SER 2.7 14.9 + - - +
391F PHE* 3.2 15.5 + - + +
393F LEU* 1.3 70.6 - - - +
395F GLN* 1.3 59.9 + - - +
397F GLN* 3.1 1.6 + - - +
398F LEU* 2.8 40.4 + - + +
461F LEU* 4.5 7.4 - - + -
464F TYR* 3.4 41.0 - - + +
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Residues in contact with GLN 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808C GLU* 3.1 43.1 + - + +
391F PHE* 3.0 41.4 + - + +
392F THR* 3.7 14.8 + - - +
393F LEU 3.4 0.2 - - - -
394F LEU* 1.3 76.2 - - - +
396F ASP* 1.3 66.8 + - - +
398F LEU* 3.4 6.3 + - - +
399F GLN* 3.0 22.2 + - - +
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Residues in contact with ASP 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392F THR* 2.7 33.9 + - - +
393F LEU* 3.6 15.4 - - + +
394F LEU 3.2 0.2 - - - -
395F GLN* 1.3 78.7 - - - +
397F GLN* 1.3 65.0 + - - +
399F GLN* 3.3 20.5 + - - +
400F SER* 3.4 7.3 + - - -
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Residues in contact with GLN 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393F LEU 2.9 17.8 + - - +
394F LEU* 3.1 7.2 + - + +
396F ASP* 1.3 76.6 + - - +
398F LEU* 1.3 63.3 + - - +
400F SER* 2.5 31.1 + - - +
401F VAL* 3.1 13.1 - - + +
460F VAL* 3.1 22.7 - - + +
461F LEU* 3.4 29.4 - - + -
464F TYR* 4.8 9.5 + - + +
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Residues in contact with LEU 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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808C GLU* 3.7 29.2 - - + +
811C LEU* 4.0 26.9 - - + -
812C LEU* 3.5 27.1 - - + -
815C ILE* 4.8 2.2 - - + -
394F LEU* 2.8 24.2 + - + +
395F GLN* 3.8 4.9 - - - +
397F GLN* 1.3 73.1 - - - +
399F GLN* 1.3 55.7 + - - +
401F VAL* 3.1 8.1 + - + +
402F LEU* 2.7 42.0 + - + +
419F LEU* 5.2 4.3 - - + -
461F LEU* 3.3 33.2 - - + -
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Residues in contact with GLN 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395F GLN 3.0 14.4 + - - +
396F ASP* 3.3 14.1 - - - +
397F GLN 3.2 0.4 - - - -
398F LEU* 1.3 75.4 - - - +
400F SER* 1.3 59.2 + - - +
402F LEU* 3.2 10.2 + - - +
403F GLU* 2.9 49.0 + - + +
414F ARG* 3.6 23.1 + - - +
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Residues in contact with SER 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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396F ASP 3.4 5.8 + - - -
397F GLN* 2.5 37.4 + - - -
399F GLN* 1.3 79.4 - - - +
401F VAL* 1.3 60.2 + - - +
403F GLU* 2.8 33.0 + - - +
404F THR* 3.4 5.0 + - - -
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Residues in contact with VAL 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815C ILE* 5.6 2.2 - - + -
397F GLN* 3.1 20.6 - - + +
398F LEU* 3.1 12.9 + - + +
400F SER* 1.3 78.3 + - - +
402F LEU* 1.3 61.9 + - + +
404F THR* 2.8 32.1 - - + +
405F LEU* 3.8 4.2 + - - +
452F LEU* 4.5 21.1 - - + -
457F ARG* 4.3 32.3 - - + +
460F VAL* 5.3 4.3 - - + -
461F LEU* 4.1 24.0 - - + -
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Residues in contact with LEU 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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811C LEU* 4.5 21.3 - - + -
398F LEU* 2.7 20.3 + - + +
399F GLN* 3.4 16.2 - - - +
401F VAL* 1.3 77.3 - - + +
403F GLU* 1.3 64.2 + - - +
405F LEU* 3.3 26.9 + - + +
410F ALA* 3.5 30.4 - - + +
413F VAL* 4.8 9.4 - - + -
414F ARG* 3.1 55.9 - - + +
419F LEU* 4.8 7.6 - - + -
452F LEU* 6.2 0.9 - - + -
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Residues in contact with GLU 403 (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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399F GLN* 2.9 47.2 + - + +
400F SER* 2.8 19.5 + - - +
402F LEU* 1.3 80.0 - - - +
404F THR* 1.3 61.0 + - - +
405F LEU 3.3 7.8 - - - +
414F ARG* 4.9 4.1 + - - -
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Residues in contact with THR 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400F SER 3.4 3.6 + - - -
401F VAL* 2.8 30.2 + - + +
403F GLU* 1.3 79.5 - - - +
405F LEU* 1.3 63.6 + - + +
451F LYS* 5.8 0.7 - - - -
452F LEU* 5.5 0.2 - - + -
457F ARG* 2.9 67.3 + - + +
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Residues in contact with LEU 405 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401F VAL 3.8 12.8 - - - +
402F LEU* 3.3 25.8 + - + +
403F GLU 3.2 10.5 - - - +
404F THR* 1.3 83.1 - - + +
406F SER* 1.3 72.1 + - - +
407F GLU 3.7 0.5 + - - -
409F GLU* 4.4 11.2 - - + +
410F ALA* 4.1 7.4 - - - +
413F VAL* 4.1 25.6 - - + -
448F THR* 4.7 2.0 - - - +
451F LYS* 4.2 17.0 - - + +
452F LEU* 3.5 32.3 - - + -
457F ARG* 3.1 30.5 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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