Contacts of the helix formed by residues 533 - 547 (chain A) in PDB entry 3N00
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 THR 533 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A ALA 3.5 3.6 + - - +
532A LEU* 1.3 75.7 - - - +
534A GLU* 1.3 59.0 + - - +
535A GLU* 3.6 8.7 + - - +
536A GLU* 3.2 31.9 + - - +
537A LEU* 2.9 27.1 + - - +
577A ASN* 3.8 20.7 + - + +
584A ARG* 5.6 0.2 - - - +
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Residues in contact with GLU 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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293A ALA* 5.2 4.1 - - - +
296A HIS* 3.8 25.6 + - - +
297A ARG* 3.9 33.2 - - + +
300A PHE 5.7 0.7 - - - +
483A ARG* 5.7 0.3 + - - -
533A THR* 1.3 72.6 - - - +
535A GLU* 1.3 61.3 + - + +
537A LEU* 3.9 20.0 - - - +
538A GLY* 2.8 27.4 + - - -
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Residues in contact with GLU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ILE* 3.8 19.7 - - + +
290A SER* 5.5 1.9 - - - -
293A ALA* 3.7 30.6 - - + +
297A ARG* 4.5 10.2 + - - +
533A THR* 3.3 7.9 + - - +
534A GLU* 1.3 78.2 - - + +
536A GLU* 1.3 62.1 + - - +
538A GLY* 3.4 0.7 + - - -
539A LEU* 3.0 26.9 + - - +
573A LEU* 3.5 29.2 - - + +
577A ASN* 5.1 2.4 + - - +
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Residues in contact with GLU 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU* 3.4 13.6 - - + +
533A THR* 3.2 28.5 + - - +
535A GLU* 1.3 76.0 - - - +
537A LEU* 1.3 53.1 + - - +
539A LEU* 3.3 1.0 + - - -
540A PHE* 2.7 38.3 + - - +
570A LEU* 3.9 10.7 - - + +
573A LEU* 3.9 15.3 - - + -
574A VAL* 3.7 17.8 - - + +
577A ASN* 2.7 39.4 + - - +
584A ARG* 2.6 41.5 + - - -
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Residues in contact with LEU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A HIS* 3.9 21.5 - - + +
482A VAL* 4.0 25.8 - - + +
483A ARG* 4.7 4.0 - - - +
486A SER* 4.6 20.6 - - - -
527A LEU* 4.4 12.6 - - + -
532A LEU* 3.9 27.9 - - + +
533A THR 2.9 17.5 + - - +
534A GLU* 3.9 15.9 - - - +
536A GLU* 1.3 77.2 - - - +
538A GLY* 1.3 50.7 + - - +
540A PHE* 3.6 2.9 - - + +
541A THR* 2.7 44.6 + - - +
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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
----------------------------------------------------------
292A VAL* 3.3 15.8 - - - +
293A ALA* 5.2 1.3 - - - -
296A HIS* 3.5 33.3 + - - -
453A PHE* 3.4 6.6 - - - -
534A GLU 2.8 19.4 + - - -
535A GLU* 3.9 1.6 - - - -
536A GLU 3.3 0.2 - - - -
537A LEU* 1.3 73.8 - - - +
539A LEU* 1.3 57.0 + - - +
541A THR* 3.4 0.9 + - - -
542A ALA 3.2 21.0 + - - -
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Residues in contact with LEU 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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288A VAL* 4.1 6.5 - - + +
289A ILE* 3.9 21.5 - - + +
292A VAL* 3.7 31.1 - - + +
535A GLU 3.0 16.4 + - - +
536A GLU 3.9 2.0 - - - +
538A GLY* 1.3 75.1 - - - +
540A PHE* 1.3 66.1 + - - +
542A ALA* 3.4 3.3 + - + +
543A VAL* 3.0 27.8 + - - +
566A LEU* 4.0 23.3 - - + +
569A ALA* 3.7 12.8 - - + -
570A LEU* 3.6 40.6 - - + +
573A LEU* 4.2 9.4 - - + -
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Residues in contact with PHE 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A VAL* 3.9 25.4 - - + -
523A PHE* 5.1 0.9 - + - -
527A LEU* 4.1 16.8 - - + -
532A LEU* 4.3 11.9 - - + -
536A GLU 2.7 19.5 + - - +
537A LEU* 3.6 5.4 - - + +
539A LEU* 1.3 76.1 - - - +
541A THR* 1.3 64.5 + - - +
543A VAL* 2.9 17.7 + - + +
544A VAL* 2.9 37.0 + - + +
570A LEU* 4.1 20.8 - - + +
588A LEU* 3.5 40.6 - - + -
589A LEU* 5.6 0.2 - - - -
591A LYS* 3.7 24.2 - - + -
592A LEU* 4.3 8.7 - - + -
595A LEU* 4.3 4.3 - - + -
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Residues in contact with THR 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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296A HIS* 4.3 9.1 + - + -
300A PHE* 4.8 9.0 - - + -
453A PHE* 3.8 17.7 - - + -
479A VAL* 3.7 29.0 - - + +
482A VAL* 3.5 23.3 - - + +
483A ARG* 5.1 4.9 - - - -
537A LEU* 2.7 28.9 + - - +
538A GLY* 3.5 7.6 - - - -
540A PHE* 1.3 76.3 - - - +
542A ALA* 1.3 61.4 + - - +
544A VAL* 3.2 10.1 + - - +
545A LEU* 3.2 20.6 + - - +
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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
----------------------------------------------------------
292A VAL* 4.2 11.0 - - + -
453A PHE* 3.8 13.7 - - + -
457A ILE* 3.8 23.3 - - + -
538A GLY 3.2 10.6 + - - +
539A LEU* 3.6 8.5 - - - +
540A PHE 3.2 0.2 - - - -
541A THR* 1.3 76.0 - - - +
543A VAL* 1.3 64.9 + - - +
545A LEU* 3.3 3.0 + - - +
546A VAL* 3.2 27.9 + - - +
566A LEU* 4.1 17.7 - - + -
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Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LEU 3.0 16.9 + - - +
540A PHE* 2.9 15.5 + - + +
542A ALA* 1.3 78.0 - - - +
544A VAL* 1.3 61.0 + - - +
546A VAL* 3.3 7.2 + - - +
547A SER* 2.6 42.4 + - - +
563A GLN* 5.1 0.9 - - + +
566A LEU* 3.8 31.2 - - + +
567A LEU* 3.4 35.2 - - + -
570A LEU* 4.0 12.3 - - + -
589A LEU* 5.4 1.1 - - + -
592A LEU* 4.8 12.1 - - + -
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Residues in contact with VAL 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A GLY 4.9 1.2 - - - +
478A GLU* 3.8 34.6 - - + +
479A VAL* 3.9 15.7 - - + +
482A VAL* 4.2 4.7 - - + -
540A PHE* 2.9 49.5 + - + +
541A THR* 3.2 9.4 + - - +
543A VAL* 1.3 76.1 - - - +
545A LEU* 1.3 64.0 + - - +
547A SER* 3.1 16.3 + - - -
548A ALA* 3.5 9.4 + - - +
592A LEU* 4.0 8.3 - - + -
595A LEU* 3.7 18.2 - - + -
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Residues in contact with LEU 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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450A VAL* 4.6 8.7 - - + -
453A PHE* 5.1 4.7 - - + -
454A ALA* 3.4 34.3 - - + +
457A ILE* 4.1 11.9 - - + -
460A PHE* 4.6 6.5 - - + -
471A LEU* 3.6 28.1 - - + +
472A LEU* 3.9 22.2 - - + +
475A GLY 4.3 11.7 - - - -
476A THR* 4.5 1.1 - - - +
479A VAL* 3.8 16.3 - - + +
541A THR 3.2 8.7 + - - +
542A ALA* 3.3 10.7 + - - +
544A VAL* 1.3 77.4 - - - +
546A VAL* 1.3 66.4 + - + +
547A SER 3.2 0.4 + - - -
548A ALA* 3.6 14.7 - - - +
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Residues in contact with VAL 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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457A ILE* 4.7 6.3 - - + -
460A PHE* 4.6 6.5 - - + -
471A LEU* 4.2 18.2 - - + +
542A ALA 3.2 8.4 + - - +
543A VAL* 3.6 12.1 - - - +
545A LEU* 1.3 83.4 - - + +
547A SER* 1.3 56.4 + - - +
548A ALA 3.3 5.0 + - - +
550A ARG* 5.0 1.7 + - - -
559A VAL* 3.9 19.6 - - - +
562A LEU* 4.0 22.0 - - + -
563A GLN* 3.6 32.4 - - + +
566A LEU* 3.4 31.2 - - + -
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Residues in contact with SER 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A GLU* 5.1 1.3 - - - +
543A VAL* 2.6 35.3 + - - +
544A VAL* 3.1 10.4 + - - -
546A VAL* 1.3 76.7 - - - +
548A ALA* 1.3 56.5 + - - +
550A ARG* 6.0 0.9 - - - +
563A GLN* 3.0 28.9 + - - +
567A LEU* 5.1 0.5 - - - +
592A LEU* 4.3 20.3 - - - +
596A ARG* 2.8 30.1 + - - -
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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