Contacts of the helix formed by residues 543 - 559 (chain A) in PDB entry 3OPY
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 LEU 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A LEU* 3.6 20.0 - - + +
320A ALA* 4.0 14.1 - - + +
321A ASP* 3.7 28.5 - - + +
324A ARG* 4.5 10.5 - - + -
353A ILE* 4.9 8.5 - - + +
355A GLY* 5.3 5.6 - - - +
528A SER* 3.1 25.1 + - - +
529A PRO* 4.1 7.8 - - - +
530A VAL* 3.5 27.1 - - + +
541A GLN 3.6 3.0 + - - -
542A PRO* 1.4 69.9 - - - +
544A VAL* 1.3 63.0 + - + +
546A SER* 3.5 0.5 + - - -
547A VAL* 3.1 51.8 + - + +
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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
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321A ASP* 3.4 17.1 + - - +
324A ARG* 3.4 38.8 - - - +
527A PRO* 5.5 7.4 - - + -
528A SER* 5.1 4.0 - - - +
542A PRO* 4.3 14.6 - - + -
543A LEU* 1.3 77.6 - - + +
545A GLU* 1.3 63.8 + - + +
547A VAL* 4.2 1.7 - - - +
548A ALA* 3.2 24.2 + - - +
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Residues in contact with GLU 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A PRO* 3.2 35.9 + - + +
544A VAL* 1.3 78.3 - - + +
546A SER* 1.4 54.6 + - - +
548A ALA* 3.3 6.2 + - - +
549A GLN* 2.8 54.9 + - - +
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Residues in contact with SER 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A MET* 3.7 21.2 - - - +
365A CYS* 3.5 25.5 + - - +
366A GLY* 4.7 1.6 - - - -
530A VAL* 4.3 10.0 - - - +
532A SER* 5.1 0.2 + - - -
541A GLN* 3.8 18.7 - - - +
542A PRO* 3.1 16.5 + - - +
543A LEU 4.0 2.7 - - - -
544A VAL 3.4 0.2 - - - -
545A GLU* 1.4 73.2 - - - +
547A VAL* 1.4 59.1 + - - +
549A GLN* 4.6 6.4 + - - -
550A THR* 3.2 30.1 + - - +
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Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ASP 5.2 0.4 - - - +
317A LEU 3.7 17.5 - - - +
318A THR* 3.4 36.1 - - + +
321A ASP* 4.0 15.3 - - + +
364A MET* 4.0 10.3 - - + -
543A LEU* 3.1 38.9 + - + +
544A VAL 4.2 2.5 - - - +
546A SER* 1.4 72.0 - - - +
548A ALA* 1.3 64.1 + - - +
550A THR* 3.2 10.9 - - + +
551A LYS* 3.1 34.2 + - + +
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Residues in contact with ALA 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A VAL 3.2 19.0 + - - +
545A GLU* 3.5 7.9 - - - +
547A VAL* 1.3 75.5 - - - +
549A GLN* 1.3 64.6 + - + +
551A LYS* 3.3 11.0 + - - +
552A THR* 3.2 27.8 + - + +
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Residues in contact with GLN 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A CYS* 3.5 29.7 - - + +
366A GLY* 4.4 10.3 - - - +
545A GLU* 2.8 44.7 + - - +
546A SER* 4.0 2.7 + - - +
548A ALA* 1.3 73.3 - - + +
550A THR* 1.4 60.8 + - - +
552A THR* 2.7 24.8 + - - -
553A VAL* 3.5 12.8 + - - +
568A LEU* 3.9 9.0 - - + +
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Residues in contact with THR 550 (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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314A ASP* 3.4 25.9 + - + +
318A THR* 5.4 2.5 - - - +
363A ASP* 3.5 22.7 + - - +
364A MET* 3.8 13.2 - - - -
365A CYS* 3.4 18.1 - - - -
546A SER 3.2 18.4 + - - +
547A VAL* 3.2 25.6 - - + +
549A GLN* 1.4 75.4 - - - +
551A LYS* 1.4 61.2 + - + +
553A VAL* 3.4 15.0 - - - +
554A SER* 3.3 15.3 + - - -
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Residues in contact with LYS 551 (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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318A THR* 3.8 31.1 - - - +
321A ASP* 5.8 1.4 + - - -
322A LEU* 6.2 2.6 - - - +
547A VAL* 3.1 26.6 + - + +
548A ALA* 3.5 12.8 - - - +
549A GLN 3.3 0.2 - - - -
550A THR* 1.4 73.9 - - + +
552A THR* 1.3 61.7 + - + +
554A SER* 3.3 9.2 + - - -
555A ALA* 2.9 29.4 + - - +
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Residues in contact with THR 552 (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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548A ALA 3.2 14.5 + - - +
549A GLN* 2.7 22.1 + - - -
551A LYS* 1.3 79.1 - - + +
553A VAL* 1.4 54.6 + - - +
555A ALA* 3.6 8.4 - - + +
556A ALA* 3.0 27.4 + - - +
564A LYS* 3.8 20.8 + - - +
568A LEU* 3.6 18.0 - - - +
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Residues in contact with VAL 553 (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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363A ASP* 3.9 9.9 - - - +
365A CYS* 4.3 11.2 - - - -
406A HIS 5.0 2.0 - - - +
549A GLN 3.6 14.4 - - - +
550A THR* 3.4 12.3 + - - +
551A LYS 3.3 0.8 - - - -
552A THR* 1.4 71.6 - - - +
554A SER* 1.4 71.1 + - - +
556A ALA* 3.2 7.6 + - - +
557A ILE* 3.1 32.0 + - + +
565A ALA* 4.2 8.6 - - + +
568A LEU* 3.8 33.9 - - + +
569A ARG* 3.4 34.5 - - - +
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Residues in contact with SER 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ASP* 4.7 5.7 + - - -
406A HIS* 4.7 16.2 + - - +
550A THR 3.3 12.7 + - - -
551A LYS* 3.3 11.6 + - - -
553A VAL* 1.4 80.5 - - - +
555A ALA* 1.4 55.9 + - - +
557A ILE* 3.6 6.6 + - - +
558A GLU* 3.1 29.2 + - - +
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Residues in contact with ALA 555 (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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551A LYS 2.9 17.1 + - - +
552A THR* 3.6 11.9 - - + +
553A VAL 3.3 0.2 - - - -
554A SER* 1.4 72.6 - - - +
556A ALA* 1.4 54.0 + - - +
558A GLU* 3.2 8.7 + - - +
559A ALA* 2.8 37.5 + - - +
564A LYS* 5.3 4.0 - - - +
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Residues in contact with ALA 556 (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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552A THR 3.0 19.3 + - - +
553A VAL 3.4 5.8 - - - +
555A ALA* 1.4 73.4 - - - +
557A ILE* 1.4 60.3 + - - +
559A ALA* 3.2 11.6 + - - +
561A ASP* 2.9 46.6 + - - +
564A LYS* 3.8 18.8 - - + +
565A ALA* 3.8 20.0 - - + +
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Residues in contact with ILE 557 (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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406A HIS 5.9 3.1 - - - +
426A PRO* 3.3 36.3 - - + +
427A GLU* 3.9 9.2 - - + +
463A ILE* 3.9 27.1 - - + -
467A LEU* 3.3 21.3 - - + +
553A VAL* 3.1 21.2 + - + +
554A SER* 3.8 6.3 - - - +
556A ALA* 1.4 74.3 - - - +
558A GLU* 1.4 55.8 + - - +
560A LYS* 2.8 22.2 + - - -
562A PHE* 3.6 11.5 - - + -
565A ALA* 3.6 21.8 - - + -
569A ARG* 5.9 3.1 - - - +
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Residues in contact with GLU 558 (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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467A LEU* 4.6 12.4 - - - +
554A SER 3.1 18.4 + - - +
555A ALA* 3.5 7.9 - - - +
557A ILE* 1.4 75.1 - - - +
559A ALA* 1.3 55.3 + - - +
560A LYS* 3.4 11.3 + - - +
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Residues in contact with ALA 559 (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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555A ALA 2.8 17.9 + - - +
556A ALA* 3.6 7.6 - - - +
557A ILE 3.2 0.6 - - - -
558A GLU* 1.3 73.6 - - - +
560A LYS* 1.3 65.1 + - - +
561A ASP* 3.1 12.6 + - + +
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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