Contacts of the helix formed by residues 530 - 545 (chain C) in PDB entry 1NYE
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 530 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493C PHE* 5.9 1.2 - - - -
528C GLY 4.3 0.4 + - - -
529C ILE* 1.3 72.8 - - - +
531C ALA* 1.3 54.9 + - - +
532C SER* 2.7 27.2 + - - +
533C THR* 2.5 50.2 + - - +
534C PHE 3.2 15.6 + - - -
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Residues in contact with ALA 531 (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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529C ILE 3.4 4.0 + - - -
530C ASP* 1.3 69.5 - - - +
532C SER* 1.3 59.7 + - - +
534C PHE* 4.1 9.2 - - - +
535C ASP* 3.3 21.8 + - - +
559C TYR* 4.5 4.2 + - - +
561C LEU* 5.1 13.2 - - + +
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Residues in contact with SER 532 (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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530C ASP* 2.7 18.2 + - - +
531C ALA* 1.3 71.9 - - - +
533C THR* 1.3 67.4 + - - +
534C PHE 3.1 1.1 - - - -
535C ASP* 3.2 15.0 + - - +
536C GLY* 3.3 8.3 + - - -
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Residues in contact with THR 533 (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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493C PHE* 5.3 4.2 - - - -
529C ILE* 3.2 13.6 - - - +
530C ASP* 2.5 33.2 + - - +
532C SER* 1.3 76.7 - - - +
534C PHE* 1.3 60.5 + - - +
536C GLY* 3.0 17.7 + - - +
537C ILE* 3.2 18.5 + - - +
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Residues in contact with PHE 534 (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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484C LEU* 5.0 0.4 - - + -
488C LEU* 4.3 12.6 - - + -
524C VAL* 3.8 17.9 - - + -
526C VAL* 3.6 16.2 - - + -
529C ILE* 3.5 35.2 - - + -
530C ASP 3.2 6.7 + - - +
531C ALA* 4.1 8.7 - - - +
532C SER 3.1 0.6 - - - -
533C THR* 1.3 78.6 + - - +
535C ASP* 1.3 63.0 + - - +
537C ILE* 2.8 23.3 + - + +
538C ILE* 3.2 40.3 + - + -
559C TYR* 3.6 31.2 - + - -
561C LEU* 3.5 36.8 - - + -
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Residues in contact with ASP 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C ALA 3.3 14.4 + - - +
532C SER* 3.2 8.3 + - - +
534C PHE* 1.3 79.7 - - - +
536C GLY* 1.3 60.6 + - - +
538C ILE* 3.1 18.3 - - - +
539C GLN* 2.8 45.1 - - - +
559C TYR* 2.6 34.0 + - - +
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Residues in contact with GLY 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C SER 3.3 6.6 + - - -
533C THR* 3.0 12.0 + - - -
535C ASP* 1.3 80.5 - - - +
537C ILE* 1.3 60.5 + - - +
539C GLN* 4.2 3.9 - - - +
540C LYS* 3.0 29.6 + - - +
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Residues in contact with ILE 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C LEU* 3.7 7.4 - - + -
487C MET* 3.4 39.9 - - + +
488C LEU* 3.4 33.9 - - + +
491C ALA* 4.4 13.2 - - + -
493C PHE* 6.4 0.2 - - + -
529C ILE* 5.9 1.3 - - + -
533C THR* 3.3 16.2 - - - +
534C PHE* 2.8 13.0 + - + +
536C GLY* 1.3 77.4 - - - +
538C ILE* 1.3 58.8 + - - +
539C GLN 2.9 0.7 - - - -
540C LYS* 2.5 34.2 + - + +
541C ALA* 3.0 9.1 + - - +
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Residues in contact with ILE 538 (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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480C PHE* 3.8 10.3 - - + -
484C LEU* 3.3 40.4 - - + -
522C SER* 6.3 0.7 - - - -
524C VAL* 4.7 3.6 - - + -
534C PHE* 3.2 37.9 + - + +
535C ASP* 3.1 33.9 - - - +
537C ILE* 1.3 75.6 - - - +
539C GLN* 1.3 77.3 + - + +
541C ALA 3.2 1.8 + - - +
542C LYS* 2.7 36.8 + - - +
557C LEU* 3.8 22.2 - - + -
559C TYR* 3.9 12.3 - - + -
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Residues in contact with GLN 539 (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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535C ASP* 2.8 42.1 - - - +
536C GLY* 4.2 5.6 - - - +
537C ILE 2.8 2.4 + - - -
538C ILE* 1.3 88.8 - - + +
540C LYS* 1.3 65.4 + - + +
542C LYS* 3.2 36.6 + - - +
543C ALA* 3.3 14.4 + - - +
557C LEU* 4.3 9.1 - - - +
559C TYR* 5.2 1.6 - - - -
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Residues in contact with LYS 540 (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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487C MET* 3.1 29.0 - - + +
536C GLY 3.0 19.3 + - - +
537C ILE* 2.5 18.9 + - + +
539C GLN* 1.3 74.8 - - + +
541C ALA* 1.3 49.5 + - - +
543C ALA* 4.7 0.3 - - - +
544C GLY* 2.8 36.0 + - - -
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Residues in contact with ALA 541 (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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480C PHE* 3.0 17.6 - - + -
483C ALA* 4.0 4.9 - - + -
484C LEU* 3.7 35.7 - - + +
487C MET* 3.7 25.7 - - + +
537C ILE 3.0 5.0 + - - +
538C ILE 3.4 5.4 - - - +
540C LYS* 1.3 75.4 - - - +
542C LYS* 1.3 59.4 + - - +
543C ALA 3.6 0.2 - - - -
544C GLY 4.1 2.7 - - - -
545C CYS* 3.5 21.4 - - - +
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Residues in contact with LYS 542 (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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480C PHE* 3.5 11.8 - - + -
520C LEU* 4.5 8.2 - - + +
538C ILE 2.7 17.4 + - - +
539C GLN* 3.4 28.5 - - - +
540C LYS 3.1 0.8 - - - -
541C ALA* 1.3 80.2 - - - +
543C ALA* 1.3 68.2 - - - +
548C SER* 2.7 29.3 + - - -
555C ILE* 3.7 35.1 + - + +
556C THR* 5.1 1.0 - - - +
557C LEU* 3.8 34.5 - - + +
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Residues in contact with ALA 543 (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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539C GLN 3.3 9.3 + - - +
540C LYS 4.7 0.2 - - - +
542C LYS* 1.3 90.4 - - + +
544C GLY* 1.3 60.7 + - - +
545C CYS 3.7 0.4 - - - -
548C SER* 4.2 9.2 - - - +
549C GLN* 3.7 19.6 + - - +
555C ILE* 6.2 0.7 - - - -
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Residues in contact with GLY 544 (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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540C LYS 2.8 19.3 + - - -
541C ALA* 5.0 0.4 - - - -
543C ALA* 1.3 78.3 - - - +
545C CYS* 1.3 69.4 + - - +
546C PRO* 3.5 2.8 - - - +
549C GLN* 3.3 20.6 + - - +
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Residues in contact with CYS 545 (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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476C HIS* 4.1 5.4 - - - -
479C CYS* 3.5 17.5 - - - -
480C PHE* 4.0 14.1 - - - -
483C ALA* 3.6 17.9 - - + +
541C ALA* 3.5 23.8 + - - +
544C GLY* 1.3 79.4 - - - +
546C PRO* 1.3 77.8 - - + +
548C SER* 3.2 38.4 + - - -
549C GLN* 3.1 17.5 + - - +
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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
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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