Contacts of the helix formed by residues 535 - 553 (chain C) in PDB entry 6GYS
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 HIS 535 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520C LEU* 3.7 16.6 - - + -
521C TRP* 3.3 34.1 + + + -
524C VAL* 2.7 34.6 + - + +
525C GLN 3.5 4.9 - - - -
526C LEU* 3.5 30.5 - - + -
533C PHE 3.1 5.5 + - - -
534C TYR* 1.3 73.2 - - - +
536C PRO* 1.3 77.1 - - + +
537C VAL* 3.1 42.8 + - + +
538C PHE* 3.1 20.3 + - + +
539C LYS 3.3 5.4 + - - -
590C PHE* 3.2 14.1 - - - -
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Residues in contact with PRO 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C LEU* 4.9 1.8 - - + -
524C VAL* 4.8 7.4 - - + -
527C LEU* 5.9 4.9 - - + -
534C TYR 4.6 0.7 - - - +
535C HIS* 1.3 95.5 - - + +
537C VAL* 1.3 58.6 + - - +
539C LYS 3.3 0.4 + - - +
540C ILE* 2.9 35.9 + - - +
590C PHE* 3.9 26.5 - - + -
593C ILE* 3.8 44.6 - - + -
594C VAL* 3.4 23.8 - - + +
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Residues in contact with VAL 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C PHE* 4.2 10.3 - - + -
517C LEU* 3.7 41.7 - - + +
520C LEU* 3.9 10.1 - - + -
521C TRP* 3.7 37.7 - - + +
535C HIS* 3.1 27.4 + - + +
536C PRO* 1.3 76.7 - - - +
538C PHE* 1.3 64.6 + - + +
540C ILE* 3.3 5.8 + - - +
541C LEU* 3.0 30.4 + - + +
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Residues in contact with PHE 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR* 4.2 18.4 - - + -
60C ASP* 5.7 4.9 - - - -
61C LEU* 3.7 38.6 - - + -
64C PHE* 5.1 0.2 - - - -
476C PHE* 4.4 3.4 - + - -
521C TRP* 3.5 31.2 - + - -
526C LEU* 3.8 14.1 - - + -
533C PHE* 3.2 34.8 - + + +
535C HIS* 3.1 15.2 + - + +
537C VAL* 1.3 81.5 - - + +
539C LYS* 1.3 58.7 + - - +
541C LEU* 3.2 10.2 + - + +
542C GLN* 2.9 36.1 + - + +
590C PHE* 5.7 0.9 - - + -
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Residues in contact with LYS 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535C HIS 3.3 2.7 + - - +
536C PRO 3.3 1.9 + - - +
537C VAL 3.3 0.4 - - - -
538C PHE* 1.3 76.0 - - - +
540C ILE* 1.3 65.1 + - - +
542C GLN* 3.2 19.6 + - + +
543C ASN* 3.0 55.0 + - - +
590C PHE* 4.2 29.8 - - + +
594C VAL* 3.7 25.6 - - + -
598C GLN* 4.3 0.4 - - - -
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Residues in contact with ILE 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C ARG* 4.3 14.4 - - - +
517C LEU* 4.3 13.5 - - + -
520C LEU* 3.8 17.0 - - + -
536C PRO* 2.9 21.9 + - + +
537C VAL* 3.4 10.3 - - - +
539C LYS* 1.3 76.1 - - - +
541C LEU* 1.3 58.0 + - + +
543C ASN* 3.2 3.5 + - - +
544C ASP* 2.9 45.9 + - - +
594C VAL* 4.3 9.9 - - + -
597C PHE* 3.6 38.8 - - + -
598C GLN* 3.3 26.1 + - + +
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Residues in contact with LEU 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 4.9 2.9 - - + -
64C PHE* 3.2 38.3 - - + -
68C TYR* 3.6 23.4 - - + +
472C PHE* 5.6 5.2 - - + -
476C PHE* 4.8 10.5 - - + -
513C ARG* 5.7 0.4 - - - +
514C LEU* 5.6 2.5 - - + -
517C LEU* 3.7 31.0 - - + -
537C VAL* 3.0 22.4 + - + +
538C PHE* 3.2 14.5 + - + +
540C ILE* 1.3 74.4 - - + +
542C GLN* 1.3 65.5 + - - +
544C ASP* 3.1 27.6 - - - +
545C ILE* 3.7 6.2 - - - +
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Residues in contact with GLN 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 3.2 31.5 - - - -
538C PHE* 2.9 23.2 + - + +
539C LYS* 3.3 30.8 - - + +
540C ILE 3.2 0.2 - - - -
541C LEU* 1.3 76.7 - - - +
543C ASN* 1.3 61.5 + - - +
545C ILE* 3.0 22.4 + - - +
546C LYS* 3.0 32.8 + - + +
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Residues in contact with ASN 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539C LYS* 3.0 46.0 + - - +
542C GLN* 1.3 77.1 - - - +
544C ASP* 1.3 65.4 + - - +
546C LYS* 3.6 14.7 - - - +
547C ILE* 3.0 38.2 + - + +
594C VAL* 4.1 3.8 - - - +
598C GLN* 3.1 34.4 + - - +
603C ILE* 4.2 2.8 - - - +
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Residues in contact with ASP 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 4.3 4.1 + - + -
72C ILE* 3.5 19.5 - - + -
513C ARG* 2.7 42.6 + - - -
540C ILE* 2.9 26.2 + - - +
541C LEU* 3.1 34.9 - - - +
543C ASN* 1.3 78.2 - - - +
545C ILE* 1.3 60.0 + - - +
548C ILE* 3.3 28.4 + - - +
598C GLN* 5.6 0.2 + - - -
603C ILE* 3.3 15.7 - - + +
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Residues in contact with ILE 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 3.6 34.8 - - + -
67C ASN* 3.8 12.3 - - + +
68C TYR* 3.7 21.1 - - + +
71C TRP* 3.7 14.8 - - + -
72C ILE* 3.8 23.3 - - + -
541C LEU 3.7 6.5 - - - +
542C GLN* 3.0 7.2 + - - +
544C ASP* 1.3 75.1 - - - +
546C LYS* 1.3 64.9 + - + +
548C ILE* 3.4 3.2 + - - +
549C GLU* 2.9 53.7 + - - +
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Residues in contact with LYS 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C GLN* 3.0 38.2 + - + +
543C ASN* 3.3 16.5 + - - +
545C ILE* 1.3 83.5 - - + +
547C ILE* 1.3 63.6 + - + +
549C GLU* 3.4 14.6 + - - +
550C LEU* 2.9 28.1 + - - +
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Residues in contact with ILE 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C ASN* 3.0 26.0 + - + +
546C LYS* 1.3 80.9 - - + +
548C ILE* 1.3 57.4 + - - +
550C LEU* 3.2 19.1 + - + +
551C LYS* 3.0 39.7 + - + +
602C ASN* 5.7 0.7 - - - +
603C ILE* 4.1 13.2 - - + -
604C SER* 3.4 24.7 - - - +
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Residues in contact with ILE 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C TRP* 4.2 15.3 - - + +
72C ILE* 3.7 25.4 - - + -
76C GLY* 3.6 25.8 - - - +
80C THR* 5.8 0.3 - - - +
544C ASP 3.3 19.7 + - - +
545C ILE* 3.4 3.8 + - - +
546C LYS 3.3 0.4 - - - -
547C ILE* 1.3 78.4 - - - +
549C GLU* 1.3 52.4 + - - +
551C LYS* 3.3 5.7 + - - +
552C ASN* 2.6 48.7 + - - +
603C ILE* 4.1 13.5 - - + +
604C SER* 5.6 3.8 - - - +
606C ILE* 3.8 30.5 - - + -
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Residues in contact with GLU 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ASN* 4.6 1.6 + - - +
71C TRP* 2.6 60.9 + - + -
545C ILE* 2.9 31.4 + - - +
546C LYS* 3.9 15.6 + - + +
548C ILE* 1.3 75.6 - - - +
550C LEU* 1.3 62.4 + - - +
552C ASN* 3.1 18.0 + - - +
553C ASP* 3.2 11.8 + - - +
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Residues in contact with LEU 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546C LYS 2.9 19.2 + - - +
547C ILE* 3.5 20.9 - - + +
548C ILE 3.2 0.2 - - - -
549C GLU* 1.3 76.8 - - - +
551C LYS* 1.3 74.4 + - + +
553C ASP* 3.2 23.4 + - + +
556C PHE* 3.6 34.9 - - + -
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Residues in contact with LYS 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C THR* 4.8 10.1 - - + +
82C GLN* 3.8 32.6 + - - +
547C ILE* 3.0 29.4 + - + +
548C ILE* 3.7 4.7 - - - +
550C LEU* 1.3 90.5 - - + +
552C ASN* 1.3 60.8 + - - +
553C ASP 3.2 7.8 + - - +
554C GLU* 4.8 3.3 - - - +
556C PHE* 6.4 1.1 - - + -
604C SER* 5.3 9.1 + - - +
607C LEU* 5.2 12.5 - - + +
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Residues in contact with ASN 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C TRP* 3.3 28.0 - - + -
75C ILE* 3.4 10.1 - - - +
80C THR* 2.8 34.2 + - - +
306C PRO* 4.8 4.0 - - + +
307C ARG* 2.3 43.7 + - - +
548C ILE* 2.6 43.1 + - - +
549C GLU* 3.1 10.0 + - - +
551C LYS* 1.3 76.5 - - - +
553C ASP* 1.3 61.4 + - - +
554C GLU* 3.7 2.4 - - - +
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Residues in contact with ASP 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B PHE 4.7 9.4 - - - +
269B VAL* 5.5 1.9 - - - +
282B GLU* 4.6 3.5 - - - +
307C ARG* 5.3 0.4 - - - +
549C GLU 3.2 7.8 + - - +
550C LEU* 3.2 20.1 + - + +
551C LYS* 3.7 7.6 - - - +
552C ASN* 1.3 77.9 - - - +
554C GLU* 1.3 77.2 + - - +
555C MET* 2.8 33.6 + - - +
556C PHE* 3.9 24.3 + - + +
557C SER* 5.2 0.7 + - - -
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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
------------------------------------------------------------
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