Contacts of the helix formed by residues 453 - 469 (chain B) in PDB entry 1S0V
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 GLY 453 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451B PRO 4.1 0.9 - - - -
452B ILE* 1.3 92.3 - - - +
454B LYS* 1.3 54.2 - - - -
455B GLU 3.3 3.4 - - - -
456B GLY 3.1 1.9 + - - -
457B TYR* 2.6 35.5 + - - +
526B LEU* 3.2 18.4 + - - -
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Residues in contact with LYS 454 (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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453B GLY* 1.3 69.6 - - - +
455B GLU* 1.3 104.2 + - + +
457B TYR* 3.7 4.2 - - - +
458B TYR* 3.3 23.3 + - - +
526B LEU* 3.1 30.0 - - + +
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Residues in contact with GLU 455 (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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453B GLY 3.3 0.4 - - - -
454B LYS* 1.3 101.3 + - + +
456B GLY* 1.3 66.1 + - - +
457B TYR 3.0 3.0 + - - -
458B TYR* 3.0 26.3 - - - +
459B TRP* 3.0 25.5 + - + -
822B ALA* 3.5 33.6 - - + +
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Residues in contact with GLY 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B ILE* 3.6 15.0 + - - +
453B GLY 3.1 7.7 + - - -
455B GLU* 1.3 80.3 - - - +
457B TYR* 1.3 56.6 + - - +
459B TRP* 3.8 3.7 - - - +
460B LEU* 2.9 21.8 + - - +
818B PRO* 3.3 40.2 - - - +
819B ALA* 4.4 1.3 - - - +
822B ALA* 6.0 0.2 - - - -
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Residues in contact with TYR 457 (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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452B ILE* 3.7 6.9 - - + +
453B GLY 2.6 20.0 + - - +
454B LYS* 3.7 6.7 - - - +
455B GLU 3.0 0.4 - - - -
456B GLY* 1.3 69.1 - - - +
458B TYR* 1.3 57.9 + - - +
459B TRP 3.0 1.6 - - - -
460B LEU* 2.8 11.9 + - + +
461B LYS* 2.6 66.3 + - + +
518B TYR* 3.0 41.3 + + - -
521B VAL* 3.1 45.3 - - + +
522B GLN* 3.8 11.4 + - - -
526B LEU* 4.2 14.8 - - + -
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Residues in contact with TYR 458 (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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454B LYS* 3.3 13.1 + - - +
455B GLU* 3.0 17.7 - - - +
457B TYR* 1.3 78.9 - - - +
459B TRP* 1.3 80.9 + + - +
461B LYS* 3.3 20.9 - - - +
462B ILE* 3.0 37.7 + - + +
475B PHE* 3.4 33.8 - + - +
476B PRO* 4.3 6.3 - - + +
479B ILE* 3.8 22.6 - - + +
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Residues in contact with TRP 459 (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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455B GLU* 3.0 41.0 + - + -
456B GLY* 3.8 5.6 - - - +
458B TYR* 1.3 89.6 - + - +
460B LEU* 1.3 68.0 + - - +
461B LYS 3.0 1.3 - - - -
462B ILE* 2.6 41.7 + - + +
463B HIS 2.8 10.4 + - - -
475B PHE* 4.0 19.3 - + - -
534B LEU* 2.9 19.1 - - + +
536B PHE* 3.0 29.6 - + - -
821B ALA* 4.2 7.2 - - + -
822B ALA* 3.8 25.3 + - - +
825B PHE* 3.0 48.7 - + + -
882B PHE* 5.4 1.6 - + - -
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Residues in contact with LEU 460 (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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452B ILE* 4.1 11.2 - - + -
456B GLY 2.9 16.8 + - - +
457B TYR* 2.8 19.4 + - + +
459B TRP* 1.3 69.8 - - - +
461B LYS* 1.3 63.3 + - - +
463B HIS* 3.2 1.9 + - - +
464B GLY 3.1 15.6 + - - -
514B PHE* 3.1 26.2 - - + +
517B GLU* 3.6 44.6 - - + +
518B TYR* 4.2 4.5 - - + +
521B VAL* 4.4 5.8 - - + -
530B CYS* 3.9 12.3 - - - -
532B LEU* 4.6 7.9 - - + -
534B LEU* 2.9 25.5 - - + +
818B PRO* 4.7 1.6 - - + -
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Residues in contact with LYS 461 (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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457B TYR* 2.6 47.3 + - + +
458B TYR* 3.3 34.4 - - - +
460B LEU* 1.3 71.8 - - - +
462B ILE* 1.3 65.4 + - - +
464B GLY* 2.9 12.1 + - - -
465B ALA* 3.0 10.9 + - - +
479B ILE* 3.5 23.5 - - + +
482B ILE* 3.6 36.6 - - + +
483B GLU* 2.8 30.7 + - - +
514B PHE* 3.9 6.7 - - - -
518B TYR* 4.5 11.2 - - + -
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Residues in contact with ILE 462 (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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458B TYR* 3.0 34.6 + - + +
459B TRP* 2.6 41.5 + - + +
461B LYS* 1.3 73.4 - - - +
463B HIS* 1.3 60.5 + - - +
465B ALA* 3.5 7.4 + - - +
466B ASN* 3.2 28.4 + - - +
475B PHE* 3.6 23.8 - - + -
478B ARG* 3.5 44.6 - - + +
479B ILE* 3.9 9.9 - - + -
536B PHE* 4.9 4.9 - - + -
882B PHE* 5.6 1.1 - - + -
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Residues in contact with HIS 463 (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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459B TRP 2.8 5.8 + - - +
460B LEU 3.6 1.1 - - - +
462B ILE* 1.3 78.7 - - + +
464B GLY* 1.3 58.1 + - - +
466B ASN* 3.3 15.9 + - + +
467B CYS* 2.7 50.5 - - - -
510B CYS* 4.9 16.9 - - + +
514B PHE* 4.7 6.2 - - + +
532B LEU* 3.6 20.2 - - + +
533B PRO 4.2 8.9 + - - -
534B LEU* 3.0 38.2 - - + +
535B ALA* 4.0 26.3 + - + +
536B PHE* 6.4 0.7 - - + -
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Residues in contact with GLY 464 (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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460B LEU 3.1 3.8 + - - -
461B LYS 2.9 4.5 + - - -
463B HIS* 1.3 78.6 - - - +
465B ALA* 1.3 66.6 + - - +
467B CYS* 3.5 2.9 + - - -
468B ALA* 3.4 12.8 + - - +
482B ILE* 3.8 6.2 - - - +
511B PHE* 3.6 14.1 - - - -
514B PHE* 3.1 40.8 - - - -
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Residues in contact with ALA 465 (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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461B LYS 3.0 9.0 + - - +
462B ILE 3.8 5.6 - - - +
463B HIS 3.3 0.4 - - - -
464B GLY* 1.3 76.0 - - - +
466B ASN* 1.3 51.4 + - - +
468B ALA* 2.7 29.7 + - - +
469B GLY 2.8 16.1 + - - -
470B VAL* 3.3 16.9 + - + -
478B ARG* 3.4 46.0 - - + -
481B PHE* 4.3 2.7 - - + -
482B ILE* 3.7 7.0 - - + +
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Residues in contact with ASN 466 (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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462B ILE* 3.2 19.9 + - - +
463B HIS* 3.3 17.5 + - + +
464B GLY 3.3 1.0 - - - -
465B ALA* 1.3 77.2 - - - +
467B CYS* 1.3 59.8 - - - +
469B GLY* 4.1 4.3 + - - -
471B ASP* 4.1 27.8 - - + +
478B ARG* 3.2 30.9 + - - +
506B ASP* 5.5 1.4 - - - +
507B SER* 5.1 1.6 + - - -
535B ALA 4.8 10.1 + - - -
536B PHE* 5.7 0.8 - - - -
537B ASP* 5.7 3.1 + - - +
882B PHE* 4.0 21.0 - - - -
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Residues in contact with CYS 467 (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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463B HIS* 2.7 52.7 - - - -
464B GLY* 3.8 6.7 - - - -
465B ALA 3.1 0.2 - - - -
466B ASN* 1.3 77.2 - - - +
468B ALA* 1.3 68.4 + - - +
469B GLY 3.3 0.2 - - - -
505B GLN* 3.9 2.7 - - - +
506B ASP* 3.0 9.2 + - - +
507B SER* 3.0 41.2 + - - +
510B CYS* 4.6 4.5 - - - -
511B PHE* 3.8 33.0 - - + +
514B PHE* 4.9 1.1 - - - -
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Residues in contact with ALA 468 (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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464B GLY 3.4 7.9 + - - +
465B ALA 2.8 10.3 - - - +
467B CYS* 1.3 80.9 - - - +
469B GLY* 1.3 53.9 + - - +
470B VAL* 3.8 2.0 - - + +
481B PHE* 3.2 37.9 - - + -
505B GLN* 4.1 20.6 - - - +
506B ASP* 2.7 28.6 + - - +
511B PHE* 4.3 6.0 - - + -
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Residues in contact with GLY 469 (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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465B ALA 2.8 3.6 + - - -
466B ASN 4.7 2.9 - - - -
467B CYS 3.3 2.5 - - - +
468B ALA* 1.3 79.0 - - - +
470B VAL* 1.3 54.0 + - - +
471B ASP* 2.3 37.0 + - - +
472B LYS* 4.3 2.4 + - - +
506B ASP* 4.1 14.4 - - - -
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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