Contacts of the helix formed by residues 539 - 554 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A ARG* 2.5 48.5 + - - +
514A ILE* 5.0 2.2 - - - +
515A THR* 4.5 6.4 - - - +
529B SER* 3.8 14.8 - - - +
530B LEU* 4.3 14.0 + - - +
531B LEU* 3.9 17.5 - - + +
536B GLU 3.2 15.0 + - - +
538B PHE* 1.3 75.7 - - - +
540B PRO* 1.3 67.1 - - - +
542B TYR* 2.8 23.1 + - + +
543B ARG* 3.1 22.0 + - - +
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Residues in contact with PRO 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A LEU* 4.1 41.2 - - + +
510A TRP* 3.7 27.4 - - + -
511A ARG* 4.3 11.9 - - + +
514A ILE* 4.6 2.7 - - + -
409B PHE* 5.2 2.0 - - + -
538B PHE 3.2 9.8 - - - +
539B ASP* 1.3 88.5 - - - +
541B GLY* 1.3 61.9 + - - +
543B ARG* 3.7 12.5 - - + +
544B CYS* 3.3 28.9 + - - -
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Residues in contact with GLY 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A ARG* 3.4 16.2 - - - +
409B PHE* 3.7 10.9 - - - -
526B LEU* 3.4 32.8 - - - +
539B ASP* 3.2 3.8 + - - -
540B PRO* 1.3 81.1 - - - +
542B TYR* 1.3 63.1 + - - +
543B ARG 3.4 0.2 + - - -
544B CYS* 3.4 4.7 + - - +
545B TYR 3.3 15.2 + - - -
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Residues in contact with TYR 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A ARG* 3.8 1.4 - - - +
533A ARG* 4.8 6.6 + - - -
381B ASN* 5.7 5.2 - - - +
383B PHE* 5.9 1.2 - - - +
526B LEU 3.6 7.6 + - - -
527B ASP* 3.7 33.0 - - - -
528B ILE* 3.9 4.3 - - - +
529B SER* 3.8 26.5 - - - +
536B GLU* 3.3 39.6 + - + -
537B ALA* 5.6 1.1 - - - -
539B ASP* 2.8 21.7 + - + +
541B GLY* 1.3 70.1 - - - -
543B ARG* 1.3 65.8 + - - +
545B TYR* 3.8 10.7 - + - +
546B SER* 3.2 31.8 + - - -
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Residues in contact with ARG 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A HIS* 6.1 1.4 - - - -
394B PRO* 4.1 25.7 + - - +
398B CYS* 3.8 21.4 - - - -
536B GLU 5.2 0.2 + - - -
537B ALA* 3.9 22.9 - - + +
538B PHE* 5.8 0.9 - - - +
539B ASP 3.1 18.6 + - - +
540B PRO* 3.7 12.0 + - + +
541B GLY 3.2 0.4 - - - -
542B TYR* 1.3 79.4 - - - +
544B CYS* 1.3 67.7 + - - +
546B SER* 3.2 10.4 + - - -
547B HIS* 2.9 44.9 + - + +
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Residues in contact with CYS 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A LEU* 4.7 9.0 - - - -
398B CYS* 3.6 34.8 - - + +
402B PHE* 3.9 9.6 - - + -
405B TYR* 3.6 39.5 - - + -
526B LEU* 5.9 1.3 - - + -
540B PRO 3.3 17.8 + - - +
541B GLY* 3.4 4.7 + - - +
542B TYR 3.4 0.2 - - - -
543B ARG* 1.3 85.2 - - - +
545B TYR* 1.3 59.4 + - - +
547B HIS 4.2 1.3 - - - -
548B TYR* 3.4 19.9 + - - +
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Residues in contact with TYR 545 (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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367B HIS* 3.1 40.9 - + - -
370B ASN* 3.4 23.5 + - - +
402B PHE* 3.8 25.1 - + + -
526B LEU* 3.4 25.1 - - + +
527B ASP* 3.6 28.7 - - + -
541B GLY 3.3 7.6 + - - +
542B TYR* 3.4 12.8 + + - +
543B ARG 3.2 1.0 - - - -
544B CYS* 1.3 78.1 - - - +
546B SER* 1.3 68.2 + - - +
548B TYR* 3.4 10.4 - + - +
549B LEU* 3.1 47.5 + - + +
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Residues in contact with SER 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 5.8 0.2 - - - +
384B ASN* 6.2 4.0 - - - -
542B TYR* 3.2 26.2 + - - -
543B ARG* 3.2 11.3 + - - -
545B TYR* 1.3 81.2 - - - +
547B HIS* 1.3 72.5 + - - +
549B LEU* 3.1 5.9 + - - +
550B LYS* 2.8 39.0 + - - +
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Residues in contact with HIS 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B SER* 5.0 2.6 + - - -
394B PRO* 4.4 5.6 - - + +
395B ALA* 3.5 48.8 - - + +
398B CYS* 3.7 21.3 - - + -
543B ARG* 2.9 49.0 + - + +
546B SER* 1.3 86.1 + - - +
548B TYR* 1.3 66.3 + - - +
550B LYS* 4.3 15.3 - - + +
551B ILE* 3.5 15.6 + - - +
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Residues in contact with TYR 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PRO* 3.5 14.3 - - + +
274B LYS* 3.8 18.3 - - + +
275B LEU* 3.1 48.3 + - + +
398B CYS* 4.7 0.8 - - - +
399B TRP* 3.3 43.3 - + - +
402B PHE* 4.0 30.5 - + + -
544B CYS 3.4 16.2 + - - +
545B TYR* 3.4 15.0 - + - +
547B HIS* 1.3 77.0 - - - +
549B LEU* 1.3 91.0 + - + +
551B ILE* 3.0 9.2 + - - +
552B GLU* 3.0 35.3 + - + +
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Residues in contact with LEU 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B PRO* 6.0 0.2 - - + -
275B LEU* 5.4 4.9 - - + -
367B HIS* 5.6 1.3 - - + +
370B ASN* 4.0 23.6 - - + +
371B LEU* 3.7 28.3 - - + +
374B LEU* 3.3 34.3 - - + +
545B TYR* 3.1 43.0 + - + +
546B SER* 3.1 7.3 + - - +
548B TYR* 1.3 97.9 - - + +
550B LYS* 1.3 59.8 + - - +
552B GLU* 3.9 5.7 - - + +
553B VAL* 3.6 15.1 + - - +
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Residues in contact with LYS 550 (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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374B LEU* 4.5 10.0 - - + +
384B ASN* 4.3 26.1 + - - +
385B CYS* 5.1 3.2 - - - +
387B ARG 6.3 0.2 - - - -
388B SER 4.8 7.6 + - - +
389B ILE* 3.8 32.2 - - + +
390B ARG 4.7 19.5 - - - +
391B PRO* 6.3 0.7 - - + -
395B ALA* 5.6 5.6 - - + -
546B SER* 2.8 24.5 + - - +
547B HIS* 4.3 16.8 - - + +
549B LEU* 1.3 76.7 - - - +
551B ILE* 1.3 62.5 + - - +
552B GLU 3.2 0.2 - - - -
553B VAL* 3.3 19.8 - - - +
554B SER* 3.4 10.6 + - - -
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Residues in contact with ILE 551 (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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474A ILE* 6.1 1.3 - - + -
484A ASN* 5.4 5.6 - - - +
81B LEU* 5.2 2.4 - - + +
391B PRO* 4.3 24.5 - - + -
395B ALA* 4.6 6.1 - - + +
396B LEU* 3.7 42.4 - - + +
399B TRP* 3.4 30.7 - - + +
547B HIS 3.5 11.5 + - - +
548B TYR 3.0 12.2 + - - +
550B LYS* 1.3 77.6 - - - +
552B GLU* 1.3 65.7 + - - +
553B VAL 3.3 0.2 - - - -
554B SER* 3.4 13.9 + - - +
555B GLN* 3.3 29.9 - - + +
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Residues in contact with GLU 552 (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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80B PHE 4.6 5.2 - - - +
81B LEU* 3.7 18.8 - - - +
83B HIS* 3.2 26.7 + - + -
272B PRO* 3.3 31.5 - - + +
274B LYS* 5.2 1.6 - - - +
371B LEU* 5.2 8.3 - - + -
399B TRP* 3.3 24.3 + - - -
548B TYR* 3.0 27.2 + - + +
549B LEU* 4.1 11.4 - - + +
550B LYS 3.2 0.6 - - - -
551B ILE* 1.3 80.3 - - - +
553B VAL* 1.3 59.2 + - - +
555B GLN* 4.6 0.7 - - - +
556B SER* 3.2 31.4 + - - +
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Residues in contact with VAL 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 5.2 4.0 - - + -
374B LEU* 4.0 28.5 - - + +
375B TYR* 3.6 23.6 - - + -
389B ILE* 4.8 13.7 - - + -
549B LEU 3.6 13.1 + - - +
550B LYS* 3.3 17.5 - - - +
552B GLU* 1.3 77.2 - - - +
554B SER* 1.3 59.3 + - - +
555B GLN 3.2 6.0 + - - -
556B SER 4.4 0.4 - - - -
557B HIS* 3.5 46.7 + - + +
15D GLU* 5.9 2.2 - - + +
19D LEU* 3.8 5.9 - - - +
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Residues in contact with SER 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LEU* 6.1 0.5 - - - +
389B ILE* 3.7 26.7 - - - -
391B PRO* 4.3 13.8 - - - +
550B LYS 3.4 2.9 + - - -
551B ILE* 3.4 22.9 + - - +
553B VAL* 1.3 79.3 - - - +
555B GLN* 1.3 76.1 + - - +
560B MET* 4.7 4.5 - - - +
19D LEU* 4.3 20.7 - - - +
22D LYS* 5.5 6.5 + - - -
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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