Contacts of the helix formed by residues 539 - 554 (chain A) in PDB entry 5SY1
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 539 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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529A SER* 3.8 15.8 - - - +
530A LEU* 4.3 13.5 + - - +
531A LEU* 3.9 17.8 - - + +
536A GLU 3.2 15.2 + - - +
538A PHE* 1.3 75.1 - - - +
540A PRO* 1.3 67.0 - - - +
541A GLY 3.9 0.2 - - - -
542A TYR* 2.8 23.5 + - + +
543A ARG* 3.1 22.5 + - - +
511B ARG* 2.6 48.2 + - - +
514B ILE* 4.9 2.0 - - - +
515B THR* 4.5 6.8 - - - +
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Residues in contact with PRO 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PHE* 5.2 3.0 - - + -
538A PHE 3.2 9.4 - - - +
539A ASP* 1.3 90.4 - - - +
541A GLY* 1.3 62.5 + - - +
543A ARG* 3.7 11.6 - - + +
544A CYS* 3.3 28.7 + - - -
507B LEU* 4.1 39.2 - - + +
510B TRP* 3.6 27.8 - - + -
511B ARG* 4.3 12.1 - - + +
514B ILE* 4.6 2.7 - - + -
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Residues in contact with GLY 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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409A PHE* 3.7 11.3 - - - -
526A LEU* 3.4 32.7 - - - +
539A ASP* 3.2 3.6 + - - -
540A PRO* 1.3 81.2 - - - +
542A TYR* 1.3 63.5 + - - +
543A ARG 3.4 0.2 + - - -
544A CYS* 3.4 4.4 + - - +
545A TYR 3.3 14.9 + - - -
511B ARG* 3.5 16.4 - - - +
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Residues in contact with TYR 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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381A ASN* 5.7 5.5 - - - +
383A PHE* 5.9 1.4 - - - +
526A LEU 3.6 8.4 + - - -
527A ASP* 3.7 32.8 - - - -
528A ILE* 3.9 3.8 - - - +
529A SER* 3.8 27.4 - - - +
536A GLU* 3.3 39.1 + - + -
537A ALA* 5.6 1.1 - - - -
539A ASP* 2.8 21.7 + - + +
541A GLY* 1.3 69.6 - - - -
543A ARG* 1.3 64.5 + - - +
545A TYR* 3.4 10.4 + + - +
546A SER* 3.2 32.3 + - - -
511B ARG* 3.8 1.2 - - - +
533B ARG* 4.8 6.2 + - - -
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Residues in contact with ARG 543 (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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394A PRO* 4.1 25.9 + - - +
398A CYS* 3.8 22.0 - - - -
536A GLU 5.2 0.4 + - - -
537A ALA* 3.9 22.9 - - - +
538A PHE* 5.8 0.4 - - - +
539A ASP 3.1 17.5 + - - +
540A PRO* 3.7 12.5 - - + +
541A GLY 3.2 0.4 - - - -
542A TYR* 1.3 79.8 - - - +
544A CYS* 1.3 67.2 + - - +
546A SER* 3.2 9.7 + - - -
547A HIS* 2.9 44.7 + - + +
466B HIS* 6.1 1.0 - - - -
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Residues in contact with CYS 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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398A CYS* 3.6 34.6 - - + +
402A PHE* 3.9 10.7 - - + -
405A TYR* 3.6 39.9 - - + -
526A LEU* 5.9 1.3 - - + -
540A PRO* 3.3 16.9 + - - +
541A GLY* 3.4 3.8 + - - +
542A TYR 3.4 0.2 - - - -
543A ARG* 1.3 86.2 - - - +
545A TYR* 1.3 60.8 + - - +
547A HIS 4.2 1.1 - - - -
548A TYR* 3.4 19.9 + - - +
507B LEU* 4.7 8.7 - - - -
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Residues in contact with TYR 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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367A HIS* 3.1 40.0 - + - -
370A ASN* 3.4 23.0 + - - +
402A PHE* 3.8 23.6 - + + -
526A LEU* 3.4 26.5 - - + +
527A ASP* 3.6 31.0 - - + -
541A GLY 3.3 8.6 + - - +
542A TYR* 3.9 12.8 - + - +
543A ARG 3.2 0.8 - - - -
544A CYS* 1.3 77.9 - - - +
546A SER* 1.3 67.5 + - - +
548A TYR* 3.4 10.5 - + - +
549A LEU* 3.1 48.4 + - + +
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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
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384A ASN* 6.2 4.5 - - - -
542A TYR* 3.2 27.6 + - - -
543A ARG* 3.2 11.3 + - - -
545A TYR* 1.3 80.8 - - - +
547A HIS* 1.3 72.2 + - - +
549A LEU* 3.1 6.2 + - - +
550A LYS* 2.8 38.5 + - - +
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Residues in contact with HIS 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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392A SER* 5.0 2.6 + - - -
394A PRO* 4.4 5.5 - - - +
395A ALA* 3.5 49.0 - - + +
398A CYS* 3.7 21.7 - - + -
543A ARG* 2.9 47.7 + - + +
546A SER* 1.3 86.3 + - - +
548A TYR* 1.3 65.7 + - - +
550A LYS* 4.0 16.5 - - + +
551A ILE* 3.5 15.4 + - - +
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Residues in contact with TYR 548 (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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272A PRO* 3.5 15.0 - - + +
274A LYS* 3.8 18.1 - - + +
275A LEU* 3.1 47.1 + - + +
398A CYS* 4.7 1.4 - - - +
399A TRP* 3.3 44.4 - + - +
402A PHE* 4.0 30.5 - + + -
544A CYS 3.4 16.4 + - - +
545A TYR* 3.4 15.5 - + - +
547A HIS* 1.3 77.2 - - - +
549A LEU* 1.3 90.5 + - + +
551A ILE* 3.0 9.2 + - - +
552A GLU* 3.0 36.1 + - + +
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Residues in contact with LEU 549 (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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272A PRO* 6.0 0.4 - - + -
275A LEU* 5.4 5.2 - - + -
367A HIS* 5.6 0.9 - - + +
370A ASN* 4.0 22.9 - - + +
371A LEU* 3.7 27.7 - - + +
374A LEU* 3.3 33.4 - - + +
545A TYR* 3.1 44.1 + - + +
546A SER* 3.1 7.6 + - - +
548A TYR* 1.3 99.7 - - + +
550A LYS* 1.3 59.9 + - - +
552A GLU* 3.9 5.9 - - + +
553A VAL* 3.6 14.6 + - - +
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Residues in contact with LYS 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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374A LEU* 4.5 10.0 - - + +
384A ASN* 4.3 26.1 + - - +
385A CYS* 5.1 2.8 - - - +
388A SER 4.8 8.2 + - - +
389A ILE* 3.8 33.3 - - + +
390A ARG 4.7 19.7 - - - +
391A PRO* 6.3 0.9 - - + -
395A ALA* 5.6 4.9 - - + -
546A SER* 2.8 22.1 + - - +
547A HIS* 4.3 17.7 - - + +
549A LEU* 1.3 76.9 - - - +
551A ILE* 1.3 63.0 + - - +
552A GLU 3.2 0.2 - - - -
553A VAL* 3.3 19.8 - - - +
554A SER* 3.4 10.9 + - - -
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Residues in contact with ILE 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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81A LEU* 5.2 1.6 - - + +
391A PRO* 4.3 24.5 - - + -
392A SER 5.4 0.2 - - - +
395A ALA* 4.6 6.3 - - + +
396A LEU* 3.7 41.5 - - + +
399A TRP* 3.4 31.2 - - + +
547A HIS 3.5 11.5 + - - +
548A TYR 3.0 11.6 + - - +
550A LYS* 1.3 77.6 - - - +
552A GLU* 1.3 67.9 + - - +
553A VAL 3.3 0.2 - - - -
554A SER* 3.4 13.8 + - - +
555A GLN* 3.3 30.2 - - + +
474B ILE* 5.9 1.1 - - + -
484B ASN* 5.4 4.9 - - - +
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Residues in contact with GLU 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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80A PHE 4.6 5.1 - - - +
81A LEU* 3.7 19.5 - - - +
83A HIS* 3.2 27.0 + - + -
272A PRO* 3.3 31.5 - - + +
274A LYS* 5.2 1.2 - - - +
371A LEU* 5.2 8.5 - - + -
399A TRP* 3.3 24.3 + - - -
548A TYR* 3.0 28.7 + - + +
549A LEU* 4.1 11.0 - - + +
550A LYS 3.2 0.2 - - - -
551A ILE* 1.3 80.1 - - - +
553A VAL* 1.3 59.9 + - - +
554A SER 3.4 0.2 - - - -
555A GLN* 4.5 0.5 - - - +
556A SER* 3.2 31.5 + - - +
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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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371A LEU* 5.2 4.3 - - + -
374A LEU* 4.0 27.8 - - + +
375A TYR* 3.6 24.2 - - + -
389A ILE* 4.8 13.7 - - + -
549A LEU 3.6 12.7 + - - +
550A LYS* 3.3 17.9 - - - +
552A GLU* 1.3 78.1 - - - +
554A SER* 1.3 59.8 + - - +
555A GLN 3.2 5.6 + - - -
556A SER 4.4 0.4 - - - +
557A HIS* 3.6 46.4 + - + +
15C GLU* 6.1 1.6 - - + -
19C LEU* 3.9 5.9 - - + +
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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
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389A ILE* 3.7 26.7 - - - -
391A PRO* 4.3 14.8 - - - +
550A LYS 3.4 3.3 + - - -
551A ILE* 3.4 23.0 + - - +
552A GLU 3.4 0.2 - - - -
553A VAL* 1.3 80.1 - - - +
555A GLN* 1.3 74.9 + - - +
560A MET* 4.7 5.8 - - - +
483B LEU* 5.9 1.0 - - - +
19C LEU* 4.4 20.1 - - - +
22C LYS* 5.8 1.6 + - - -
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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