Contacts of the helix formed by residues 533 - 547 (chain A) in PDB entry 1VCO
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 SER 533 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A ALA 5.6 0.2 + - - -
460A TYR* 4.5 1.2 + - - -
467A GLU* 4.7 2.4 + - - -
523A PRO* 3.3 41.9 + - - +
526A LYS* 5.9 0.8 - - - +
527A SER* 3.3 19.3 + - - +
532A PRO* 1.3 71.1 - - - +
534A PRO* 1.3 72.0 - - - +
535A PRO* 3.4 8.7 - - - +
536A PHE* 2.9 30.9 + - - +
537A VAL* 3.0 11.0 + - - +
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Residues in contact with PRO 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A LEU* 3.6 35.9 - - + +
460A TYR* 3.4 35.0 - - + +
467A GLU* 5.5 0.7 - - - +
532A PRO 3.4 8.7 - - - +
533A SER* 1.3 82.4 - - - +
535A PRO* 1.3 76.0 - - + +
537A VAL* 2.9 11.8 + - + +
538A GLY* 2.8 23.6 + - - -
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Residues in contact with PRO 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A LEU* 4.0 8.7 - - + +
459A LEU* 4.0 11.9 - - + -
460A TYR* 3.2 30.9 - - + +
515A PHE* 3.9 7.3 - - - -
517A LEU* 4.3 6.7 - - + -
519A LEU* 4.0 30.7 - - + -
523A PRO* 4.4 4.9 - - + -
533A SER* 3.4 11.7 - - - +
534A PRO* 1.3 99.1 - - + +
536A PHE* 1.3 66.0 + - + +
538A GLY 3.7 0.2 + - - -
539A PHE* 3.1 25.3 + - - +
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Residues in contact with PHE 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LEU* 3.6 14.6 - - + -
322A ALA* 3.9 15.5 - - + +
323A LEU* 3.4 36.8 - - + -
326A ALA* 3.7 13.9 - - + -
360A LEU* 4.2 2.0 - - + -
388A LEU* 3.8 15.7 - - + -
390A ILE* 3.9 14.6 - - + -
523A PRO* 3.6 25.4 - - + -
524A GLU* 3.4 33.0 - - + -
533A SER* 2.9 26.8 + - - +
535A PRO* 1.3 77.5 - - + +
537A VAL* 1.3 66.6 + - - +
538A GLY 3.2 0.4 - - - -
539A PHE* 3.6 4.8 - - - +
540A VAL* 2.9 29.6 + - + +
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Residues in contact with VAL 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ALA* 3.8 11.7 - - + -
329A LYS* 3.9 31.9 - - + -
330A ASN* 3.3 17.2 + - - +
459A LEU* 5.9 1.3 - - + -
532A PRO* 3.5 28.5 - - + +
533A SER 3.0 21.3 + - - +
534A PRO* 2.9 11.8 + - + +
536A PHE* 1.3 77.1 - - - +
538A GLY* 1.3 57.2 + - - +
541A GLU* 3.0 27.2 + - + +
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Residues in contact with GLY 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A LEU* 3.5 28.4 - - - +
515A PHE* 3.5 10.0 - - - -
534A PRO 2.8 10.6 + - - -
537A VAL* 1.3 77.3 - - - +
539A PHE* 1.3 54.5 + - - +
541A GLU* 3.1 11.1 + - - +
542A ALA* 2.7 37.1 + - - +
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Residues in contact with PHE 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ILE* 3.8 32.8 - - + -
323A LEU* 4.2 20.6 - - + -
358A GLY* 3.8 9.0 - - - -
359A ILE 3.6 44.2 - - - -
360A LEU* 4.0 9.6 - - + -
386A PRO* 3.8 9.0 - - + +
387A TYR 4.2 1.1 - - - -
388A LEU* 3.4 35.7 - - + -
515A PHE* 3.4 19.8 - + + -
535A PRO 3.1 18.8 + - - +
536A PHE* 3.2 4.2 + - - +
538A GLY* 1.3 75.4 - - - +
540A VAL* 1.3 61.3 + - + +
542A ALA* 3.3 2.4 + - - +
543A ALA* 2.9 26.5 + - - +
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Residues in contact with VAL 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A VAL* 4.6 5.2 - - + -
303A ILE* 5.9 1.1 - - + -
323A LEU* 4.3 16.6 - - + -
326A ALA* 3.5 17.3 - - + -
327A GLY* 4.5 3.1 - - - -
330A ASN* 3.5 32.1 - - + +
332A ALA* 5.1 1.6 - - + -
334A VAL* 4.0 30.5 - - + -
536A PHE 2.9 19.5 + - - +
539A PHE* 1.3 77.7 - - + +
541A GLU* 1.3 57.9 - - - +
543A ALA* 3.2 7.6 + - - +
544A LEU* 2.9 35.2 + - + +
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Residues in contact with GLU 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ASN* 3.8 17.2 - - - +
458A ARG* 3.3 33.5 + - - -
459A LEU* 4.6 1.0 - - - +
537A VAL* 3.0 21.2 + - + +
538A GLY* 3.4 10.6 - - - +
540A VAL* 1.3 76.9 - - - +
542A ALA* 1.3 58.2 + - - +
544A LEU* 3.4 8.1 + - - +
545A ALA* 2.9 27.2 + - + +
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Residues in contact with ALA 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A PRO* 3.7 9.5 - - + +
514A PRO* 5.0 4.2 - - + +
515A PHE* 3.3 39.0 - - + -
538A GLY 2.7 20.1 + - - +
539A PHE 3.7 3.6 - - - +
541A GLU* 1.3 72.0 - - - +
543A ALA* 1.3 54.6 + - - +
545A ALA* 3.1 9.4 + - - +
546A TYR* 2.7 35.3 + - - +
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Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A VAL* 4.5 9.0 - - + -
303A ILE* 3.9 24.0 - - + -
357A SER* 3.3 31.6 - - - +
358A GLY* 4.7 1.3 - - - -
386A PRO* 4.0 1.5 - - + +
539A PHE 2.9 13.2 + - - +
540A VAL* 3.3 12.8 - - - +
542A ALA* 1.3 76.5 - - - +
544A LEU* 1.3 63.4 + - - +
546A TYR* 3.0 5.4 + - - +
547A GLN* 2.8 19.2 + - - +
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Residues in contact with LEU 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ARG* 3.5 51.7 + - + +
301A VAL* 3.1 36.7 - - + +
330A ASN* 3.8 34.3 - - + +
332A ALA* 3.8 21.3 - - + -
540A VAL* 2.9 20.3 + - + +
541A GLU* 3.5 7.6 - - - +
543A ALA* 1.3 74.6 - - - +
545A ALA* 1.3 66.1 + - - +
547A GLN* 3.0 15.2 + - - +
548A GLU 3.2 10.9 + - - -
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Residues in contact with ALA 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A GLU* 2.9 15.8 + - + +
542A ALA* 3.1 14.1 + - - +
544A LEU* 1.3 74.9 - - - +
546A TYR* 1.3 54.1 + - - +
548A GLU* 2.6 37.1 + - - +
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Residues in contact with TYR 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A VAL 3.6 18.1 + - - -
357A SER* 3.4 28.0 - - - +
383A ARG* 4.4 5.1 + - - +
384A LYS* 3.7 24.7 - - + -
385A ILE* 3.9 23.9 - - + +
386A PRO* 3.8 13.9 - - + -
514A PRO* 5.7 2.2 - - + -
542A ALA 2.7 15.0 + - - +
543A ALA 3.0 8.3 + - - +
545A ALA* 1.3 72.5 - - - +
547A GLN* 1.3 59.2 + - - +
548A GLU* 2.9 20.3 + - - +
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Residues in contact with GLN 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ARG* 5.5 3.6 + - - +
300A THR 3.3 21.0 + - - +
301A VAL* 3.2 27.9 - - + +
302A LYS* 4.6 3.0 - - - +
357A SER* 3.6 20.7 + - - +
543A ALA 2.8 10.2 + - - +
544A LEU* 3.0 11.4 + - - +
546A TYR* 1.3 75.8 - - - +
548A GLU* 1.3 72.9 + - - +
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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