Contacts of the helix formed by residues 509 - 530 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A LYS* 5.6 6.1 - - - +
373B PHE* 3.4 27.7 - - + +
374B ALA 4.7 5.0 + - - +
507B SER* 3.2 7.0 + - - -
508B GLU* 1.3 86.0 - - - +
510B ALA* 1.3 54.5 + - - +
511B GLN 3.2 2.9 - - - -
512B LEU* 2.9 20.6 + - + +
513B ILE* 2.6 56.0 + - + +
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Residues in contact with ALA 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B ASP* 4.1 3.9 - - - -
464B ILE 5.3 0.4 - - - +
465B GLY 3.2 27.4 - - - +
466B ASN* 3.7 9.2 - - - +
467B ILE 3.8 7.9 - - - +
468B VAL* 3.6 21.7 - - + +
507B SER 3.3 18.6 + - - +
508B GLU 3.0 4.8 - - - +
509B ASP* 1.3 78.9 - - - +
511B GLN* 1.3 67.2 + - - +
513B ILE* 3.5 0.8 + - - -
514B ALA* 3.4 16.5 + - - +
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Residues in contact with GLN 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B ASP* 3.1 44.0 + - - +
508B GLU 4.8 1.4 + - - +
510B ALA* 1.3 81.9 - - - +
512B LEU* 1.3 75.5 + - + +
514B ALA* 3.1 11.1 + - - +
515B GLN* 3.2 41.1 + - - +
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ILE* 5.8 10.5 - - + +
415A LYS* 5.7 9.2 - - + -
418A ALA* 5.1 15.3 - - + -
373B PHE* 4.3 12.8 - - + -
508B GLU 4.4 4.7 - - - +
509B ASP* 2.9 31.8 + - + +
511B GLN* 1.3 85.9 - - + +
513B ILE* 1.3 52.9 + - - +
515B GLN* 3.4 22.1 + - - +
516B SER* 2.5 40.1 + - - +
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Residues in contact with ILE 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B PHE* 3.9 24.0 - - + -
374B ALA 4.5 1.3 - - - +
375B ALA* 4.7 4.9 - - + -
432B LEU* 3.7 25.1 - - + -
434B ILE* 3.5 20.2 - - + +
468B VAL* 4.2 18.1 - - + +
507B SER* 3.0 39.7 - - - +
509B ASP* 2.6 41.5 + - + +
510B ALA* 3.7 6.5 - - - +
512B LEU* 1.3 72.0 - - - +
514B ALA* 1.3 61.5 + - - +
516B SER* 4.2 3.6 - - - -
517B ILE* 3.5 20.8 + - + +
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Residues in contact with ALA 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ILE* 2.9 29.5 - - + +
462B ALA 4.4 2.2 - - - +
463B ASP* 3.2 46.4 - - + +
468B VAL* 5.3 4.9 - - + +
510B ALA 3.4 3.8 + - - +
511B GLN 3.1 2.4 + - - +
512B LEU 3.1 0.4 - - - -
513B ILE* 1.3 76.0 - - - +
515B GLN* 1.3 67.9 + - - +
517B ILE* 2.7 13.6 + - - -
518B GLY 2.7 9.9 + - - -
757E TYR* 4.3 0.7 - - + -
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Residues in contact with GLN 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B ASP* 5.8 0.2 - - + -
511B GLN* 3.2 43.3 + - - +
512B LEU* 3.7 21.3 - - - +
514B ALA* 1.3 76.4 - - + +
516B SER* 1.3 57.1 + - - +
518B GLY* 2.5 26.0 + - - -
519B GLN* 2.9 29.0 + - - +
757E TYR* 3.5 28.0 - - + +
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Residues in contact with SER 516 (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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414A ILE* 5.1 6.8 - - - +
367B LEU* 3.5 8.8 - - - +
371B ILE* 3.8 15.6 - - - +
373B PHE* 3.5 14.8 - - - -
434B ILE* 3.4 32.8 - - - +
512B LEU* 2.5 23.0 + - - +
515B GLN* 1.3 77.1 - - - +
517B ILE* 1.3 60.2 + - - +
519B GLN* 4.0 7.2 - - - +
520B ALA 3.4 12.8 + - - -
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Residues in contact with ILE 517 (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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432B LEU* 6.5 0.4 - - + -
434B ILE* 3.5 37.2 - - + -
439B ILE* 3.2 30.1 - - + -
461B ILE* 3.3 22.2 - - + -
468B VAL* 6.1 4.0 - - + -
470B LEU* 4.6 10.1 - - + -
513B ILE* 3.5 12.3 + - + +
514B ALA* 2.7 12.3 + - - +
516B SER* 1.3 74.3 - - - +
518B GLY* 1.3 67.9 + - - +
519B GLN 3.2 0.2 - - - -
520B ALA* 3.2 3.7 + - - +
521B PHE* 3.0 53.8 + - + -
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Residues in contact with GLY 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B ALA 2.7 8.6 + - - -
515B GLN 2.5 15.5 + - - -
517B ILE* 1.3 73.2 - - - +
519B GLN* 1.3 63.4 + - - -
521B PHE* 3.1 26.5 - - - +
522B SER* 3.3 11.5 + - - -
757E TYR* 3.8 29.0 - - - -
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Residues in contact with GLN 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B SER* 4.1 22.9 - - - +
367B LEU* 4.4 6.3 - - + -
515B GLN* 2.9 31.1 + - - +
516B SER* 4.1 9.7 - - - +
518B GLY* 1.3 75.1 - - - +
520B ALA* 1.3 50.5 + - - +
521B PHE 2.7 4.2 + - - -
522B SER* 2.7 30.0 + - - +
523B VAL* 2.7 22.7 + - + +
757E TYR* 4.9 7.8 + - - -
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Residues in contact with ALA 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 3.8 12.9 - - + +
434B ILE* 3.9 8.3 - - + -
435B SER 3.3 29.8 - - - +
436B THR* 3.6 13.9 - - - +
455B LEU* 3.1 24.5 - - + +
516B SER 3.4 12.7 + - - +
517B ILE* 3.2 10.1 + - + +
519B GLN* 1.3 77.2 - - - +
521B PHE* 1.3 59.0 + - - +
523B VAL* 3.9 1.3 - - - -
524B ALA* 3.4 10.4 + - - +
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Residues in contact with PHE 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU* 3.3 31.9 - - + -
458B ILE* 3.2 32.1 - - + -
460B TYR 4.5 2.5 - - - -
461B ILE* 3.7 12.8 - - + -
517B ILE* 3.0 37.4 + - + -
518B GLY* 3.1 15.9 - - - +
519B GLN 2.7 0.4 + - - -
520B ALA* 1.3 79.4 - - - +
522B SER* 1.3 59.0 + - - +
524B ALA* 3.4 6.3 + - - +
525B TYR* 3.1 22.0 + - - +
757E TYR* 4.6 4.3 - - + -
758E GLU 3.9 15.0 - - - +
759E ASN* 3.3 44.0 - - + +
760E PRO* 3.8 13.5 - - + +
761E THR* 4.2 0.7 + - - -
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Residues in contact with SER 522 (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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518B GLY 3.5 9.9 + - - -
519B GLN* 2.7 18.0 + - - -
521B PHE* 1.3 71.0 - - - +
523B VAL* 1.3 59.2 + - - -
524B ALA 3.1 2.2 - - - -
525B TYR* 3.0 10.7 - - - +
526B GLN* 3.0 50.8 + - - +
760E PRO* 4.8 8.9 - - - +
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Residues in contact with VAL 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B SER* 3.8 32.3 - - - +
367B LEU* 4.7 2.7 - - + -
368B ILE* 3.9 21.5 - - + -
436B THR* 3.2 29.4 - - + -
519B GLN* 2.7 28.5 + - + +
520B ALA* 4.3 0.4 - - - -
522B SER* 1.3 73.0 - - - +
524B ALA* 1.3 57.5 + - - +
526B GLN* 4.6 6.2 - - - +
527B GLU* 3.0 31.8 + - + +
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Residues in contact with ALA 524 (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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436B THR* 4.4 11.6 - - - +
455B LEU* 3.7 17.0 - - + -
520B ALA 3.4 18.1 + - - +
521B PHE 3.5 6.5 - - - +
522B SER 3.1 0.2 - - - -
523B VAL* 1.3 77.6 - - - +
525B TYR* 1.3 69.1 + - - +
527B GLU* 3.8 5.1 - - - +
528B PHE* 3.1 21.5 + - - +
759E ASN* 5.2 0.9 - - - +
761E THR* 4.3 13.6 + - + +
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Residues in contact with TYR 525 (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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521B PHE 3.1 14.0 + - - +
522B SER* 3.0 15.2 + - - +
524B ALA* 1.3 73.6 - - - +
526B GLN* 1.3 73.7 + - - +
528B PHE* 2.5 31.2 + - + +
529B LEU* 2.9 43.1 + - + +
760E PRO* 3.1 44.9 - - + -
761E THR* 4.3 4.7 - - - -
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Residues in contact with GLN 526 (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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522B SER* 3.0 39.4 + - - +
523B VAL* 4.6 4.6 - - - +
525B TYR* 1.3 98.0 - - - +
527B GLU* 1.3 58.5 + - - +
528B PHE 3.0 0.9 + - - -
529B LEU* 3.3 23.5 + - + +
530B ARG* 2.9 42.8 + - - +
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Residues in contact with GLU 527 (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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368B ILE* 5.0 11.5 - - - +
436B THR* 4.3 19.2 + - - +
523B VAL* 3.0 24.6 + - + +
524B ALA* 3.8 5.9 - - - +
525B TYR 3.0 1.2 + - - -
526B GLN* 1.3 78.6 - - - +
528B PHE* 1.3 56.8 + - - +
530B ARG* 3.9 23.4 - - + +
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Residues in contact with PHE 528 (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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524B ALA 3.1 13.4 + - - +
525B TYR* 2.5 24.2 + - + +
527B GLU* 1.3 71.2 - - - +
529B LEU* 1.3 54.6 + - + +
530B ARG 2.7 15.6 + - - -
531B ALA* 3.1 21.1 + - - +
761E THR* 5.4 10.3 - - + -
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Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B TYR* 2.9 57.2 + - + +
526B GLN* 3.8 26.2 - - + +
528B PHE* 1.3 70.6 - - + +
530B ARG* 1.3 52.8 + - + +
531B ALA* 2.6 27.8 + - - +
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Residues in contact with ARG 530 (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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526B GLN* 2.9 39.8 + - - +
527B GLU* 3.9 21.7 - - + +
528B PHE 2.7 3.5 + - - -
529B LEU* 1.3 74.7 - - - +
531B ALA* 1.3 58.2 + - - +
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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
------------------------------------------------------------
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