Contacts of the helix formed by residues 509 - 526 (chain C) in PDB entry 3SV1
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 509 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415B LYS* 5.4 9.4 - - + +
373C PHE* 4.6 15.5 - - + +
374C ALA 4.3 6.3 - - - +
507C SER* 2.5 29.3 + - - -
508C GLU* 1.3 82.0 - - - +
510C ALA* 1.3 62.1 + - - +
511C GLN 3.2 2.2 - - - -
512C LEU* 3.3 28.4 + - + -
513C ILE* 2.8 33.4 + - + +
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Residues in contact with ALA 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C ASP* 3.9 4.7 - - - +
465C GLY 3.1 25.4 - - - +
466C ASN* 3.7 5.8 - - - -
467C ILE 3.9 2.9 - - - +
468C VAL* 3.4 31.4 - - + +
507C SER 3.0 16.2 + - - +
508C GLU 3.5 1.4 + - - -
509C ASP* 1.3 75.9 - - - +
511C GLN* 1.3 65.1 + - - +
513C ILE* 3.2 4.7 + - - +
514C ALA* 3.2 23.6 + - - +
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Residues in contact with GLN 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C ASP* 2.5 55.9 + - - +
465C GLY 4.7 1.6 + - - -
509C ASP 3.2 0.4 - - - -
510C ALA* 1.3 81.0 - - - +
512C LEU* 1.3 73.3 + - + +
514C ALA* 3.4 2.1 + - - +
515C GLN* 3.0 54.7 + - - +
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Residues in contact with LEU 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ILE* 6.0 4.0 - - + -
415B LYS* 5.8 9.9 - - + -
418B ALA* 5.6 10.1 - - + -
373C PHE* 4.3 18.5 - - + -
509C ASP* 3.3 36.1 - - + +
511C GLN* 1.3 87.4 - - + +
513C ILE* 1.3 57.7 + - - +
515C GLN* 3.4 14.2 + - - +
516C SER* 2.5 36.6 + - - -
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Residues in contact with ILE 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C PHE* 3.9 27.3 - - + -
375C ALA* 4.3 8.1 - - + -
432C LEU* 4.5 15.3 - - + -
434C ILE* 4.3 19.7 - - + +
468C VAL* 4.2 14.6 - - + -
507C SER* 3.0 40.4 - - - +
509C ASP* 2.8 25.5 + - - +
510C ALA* 3.7 6.7 - - - +
512C LEU* 1.3 74.9 - - - +
514C ALA* 1.3 59.6 + - - +
516C SER* 3.2 10.3 + - - -
517C ILE* 2.7 32.6 - - + +
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Residues in contact with ALA 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C ILE* 4.5 20.9 - - + +
462C ALA 4.4 4.7 - - - +
463C ASP* 3.6 41.1 - - + +
468C VAL* 4.6 5.6 - - + +
510C ALA 3.2 5.2 + - - +
511C GLN 3.9 0.2 - - - +
513C ILE* 1.3 77.8 - - - +
515C GLN* 1.3 57.9 + - - +
517C ILE* 2.7 35.0 + - - +
518C GLY* 3.0 10.2 + - - -
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Residues in contact with GLN 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C ASP* 4.6 3.1 - - - +
511C GLN* 3.0 46.9 + - - +
512C LEU* 3.4 14.5 + - - +
514C ALA* 1.3 75.3 - - - +
516C SER* 1.3 57.4 + - - +
518C GLY* 3.3 3.4 + - - +
519C GLN* 3.0 36.0 + - - +
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Residues in contact with SER 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ILE* 6.4 1.8 - - - -
367C LEU* 3.4 20.9 - - - +
371C ILE* 4.4 13.9 - - - -
373C PHE* 3.4 22.6 - - - -
434C ILE* 3.8 4.6 - - - +
512C LEU 2.5 23.4 + - - -
513C ILE 3.2 8.8 + - - -
515C GLN* 1.3 75.0 - - - +
517C ILE* 1.3 62.5 + - - +
519C GLN* 3.5 9.7 - - - +
520C ALA* 3.2 15.4 + - - +
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Residues in contact with ILE 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C LEU* 6.1 3.1 - - + -
434C ILE* 3.8 24.7 - - + -
439C ILE* 3.6 28.9 - - + -
455C LEU* 4.7 0.3 - - - +
458C ILE* 5.4 0.2 - - + -
461C ILE* 3.5 34.3 - - + -
468C VAL* 5.0 7.0 - - + -
470C LEU* 5.5 6.7 - - + -
513C ILE* 2.7 35.0 - - + +
514C ALA* 2.7 13.2 + - - +
516C SER* 1.3 75.7 - - - +
518C GLY* 1.3 64.2 + - - +
519C GLN 3.0 1.3 - - - -
520C ALA* 3.0 15.1 + - - +
521C PHE* 3.2 23.2 + - + -
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Residues in contact with GLY 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C ILE* 4.9 5.5 - - - +
514C ALA 3.0 11.6 + - - -
515C GLN* 3.3 4.2 + - - -
517C ILE* 1.3 77.3 - - - +
519C GLN* 1.3 57.4 + - - +
521C PHE* 2.9 40.8 + - - +
522C SER* 3.2 9.5 + - - -
756F GLY 4.7 3.1 - - - -
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Residues in contact with GLN 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C SER* 4.2 23.5 + - - +
367C LEU* 4.7 9.4 - - + -
515C GLN* 3.0 21.4 + - - +
516C SER* 3.5 14.7 - - - +
518C GLY* 1.3 71.8 - - - +
520C ALA* 1.3 63.0 + - - +
521C PHE 2.9 5.2 + - - -
522C SER* 3.1 15.6 + - - -
523C VAL* 3.0 30.1 + - + +
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Residues in contact with ALA 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C LEU* 4.1 12.1 - - + +
434C ILE* 4.2 5.4 - - + -
435C SER 3.1 33.2 - - - +
436C THR* 4.1 3.5 - - - +
455C LEU* 3.0 11.6 - - + +
516C SER 3.2 10.3 + - - +
517C ILE 3.0 10.8 + - - +
519C GLN* 1.3 78.7 - - - +
521C PHE* 1.3 57.5 + - - +
523C VAL* 3.7 9.3 - - - +
524C ALA* 2.9 26.6 + - - +
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Residues in contact with PHE 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C LEU* 3.4 38.8 - - + -
458C ILE* 3.8 18.8 - - + -
460C TYR 5.1 0.2 - - - -
461C ILE* 4.3 6.3 - - + -
517C ILE* 3.2 24.8 + - + -
518C GLY* 2.9 30.7 + - - +
519C GLN 2.9 0.4 - - - -
520C ALA* 1.3 76.2 - - - +
522C SER* 1.3 51.9 + - - +
524C ALA* 2.6 8.2 + - + +
525C TYR* 2.6 37.8 + - - +
756F GLY 3.2 25.8 - - - -
757F TYR* 3.2 40.6 - - + +
758F GLU* 5.7 1.8 - - + +
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Residues in contact with SER 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518C GLY 3.2 9.4 + - - -
519C GLN* 3.1 19.0 + - - -
521C PHE* 1.3 77.3 - - - +
523C VAL* 1.3 56.9 + - - +
524C ALA 2.6 11.1 + - - -
525C TYR* 4.4 4.3 - - - +
526C GLN* 2.8 50.6 + - - +
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Residues in contact with VAL 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C SER* 4.4 29.4 - - - +
367C LEU* 4.9 4.5 - - + -
368C ILE* 3.8 19.3 - - + -
436C THR* 3.7 20.9 - - - +
519C GLN* 3.0 22.6 + - + +
520C ALA* 3.7 8.7 - - - +
522C SER* 1.3 75.1 - - - +
524C ALA* 1.3 56.1 + - - +
526C GLN* 4.6 8.9 - - - +
527C GLU* 3.1 28.0 + - + +
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Residues in contact with ALA 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436C THR* 3.9 12.1 - - - +
455C LEU* 3.6 16.8 - - + -
520C ALA 2.9 15.9 + - - +
521C PHE* 2.6 22.7 + - + +
523C VAL* 1.3 72.9 - - - +
525C TYR* 1.3 63.6 + - - +
527C GLU* 3.3 18.2 + - - +
528C PHE* 4.6 1.0 - - - -
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Residues in contact with TYR 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521C PHE 2.6 17.2 + - - +
522C SER* 3.9 4.0 - - - +
524C ALA* 1.3 69.0 - - - +
526C GLN* 1.3 57.5 + - + +
528C PHE* 2.7 41.0 + - - +
758F GLU 4.8 13.5 - - - +
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Residues in contact with GLN 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C SER* 2.8 42.8 + - - +
523C VAL* 4.8 6.3 - - - +
525C TYR* 1.3 72.9 - - + +
527C GLU* 1.3 54.2 + - - +
528C PHE* 2.7 13.5 + - - +
529C LEU 4.5 5.0 + - - +
531C ALA* 6.1 0.5 - - - +
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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
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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