Contacts of the helix formed by residues 501 - 512 (chain C) in PDB entry 6NYY
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 GLU 501 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499C THR 3.7 1.2 - - - -
500C LEU* 1.3 76.2 - - - +
502C LYS* 1.3 65.3 + - - +
503C ASP* 3.1 26.2 + - + +
504C LYS* 3.5 31.1 + - + +
505C LEU* 3.2 21.0 + - - +
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Residues in contact with LYS 502 (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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488C LYS* 4.6 6.6 - - - +
491C LEU* 3.3 36.0 + - + +
492C ARG* 2.7 34.2 + - + +
494C LEU 3.6 17.8 + - - -
495C LYS* 5.4 0.2 - - - +
496C LEU* 3.7 31.4 - - + +
500C LEU 3.6 0.9 + - - +
501C GLU* 1.3 74.3 - - - +
503C ASP* 1.3 60.7 + - - +
505C LEU* 4.2 3.6 - - - -
506C ALA* 3.8 16.8 + - - +
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Residues in contact with ASP 503 (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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488C LYS* 3.4 30.7 + - - +
501C GLU* 3.1 20.7 - - + +
502C LYS* 1.3 76.0 - - - +
504C LYS* 1.3 66.7 + - - +
505C LEU 3.2 1.6 + - - -
506C ALA* 3.4 13.9 + - - +
507C ARG* 2.5 45.7 + - - +
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Residues in contact with LYS 504 (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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501C GLU* 3.5 30.7 + - + +
503C ASP* 1.3 77.2 - - - +
505C LEU* 1.3 63.3 + - - +
507C ARG* 3.6 22.4 + - - +
508C LYS* 3.4 17.8 + - - +
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Residues in contact with LEU 505 (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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491C LEU* 4.1 8.5 - - + -
496C LEU* 3.7 23.1 - - + -
500C LEU* 3.8 28.5 - - + -
501C GLU 3.2 16.8 + - - +
502C LYS* 4.6 0.4 - - - +
503C ASP 3.2 0.6 - - - -
504C LYS* 1.3 76.7 - - - +
506C ALA* 1.3 54.5 + - - +
508C LYS* 3.0 12.0 + - + +
509C LEU* 2.8 51.8 + - + +
542C GLN* 4.4 19.1 - - + -
545C PHE* 3.6 33.7 - - + -
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Residues in contact with ALA 506 (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 ALA* 3.4 27.5 - - - +
487C PHE* 3.6 22.1 - - + -
488C LYS* 3.7 16.4 - - + -
491C LEU* 3.8 6.2 - - + +
502C LYS 3.8 9.3 + - - +
503C ASP 3.4 11.1 + - - +
504C LYS 3.4 0.2 - - - -
505C LEU* 1.3 79.0 - - - +
507C ARG* 1.3 60.1 + - - +
509C LEU 4.4 0.4 - - - +
510C ALA* 3.2 24.9 + - - +
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Residues in contact with ARG 507 (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 ALA* 4.6 5.4 - - + -
488C LYS* 4.6 11.7 - - - +
503C ASP* 2.5 47.6 + - - +
504C LYS* 3.6 20.1 + - - +
505C LEU 3.2 0.6 - - - -
506C ALA* 1.3 77.6 - - + +
508C LYS* 1.3 61.6 + - - +
510C ALA 3.7 0.2 + - - -
511C SER* 3.0 25.8 + - - -
756C TYR* 3.3 49.1 - - + +
757C GLU* 3.6 23.0 + - - +
766C LEU* 4.4 20.7 + - - +
767C ASP* 4.7 9.5 + - - +
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Residues in contact with LYS 508 (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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504C LYS 3.4 9.6 + - - +
505C LEU* 3.0 16.5 + - + +
507C ARG* 1.3 80.1 - - - +
509C LEU* 1.3 63.0 + - + +
511C SER* 3.2 18.7 + - - +
512C LEU* 3.4 40.2 + - + +
542C GLN* 3.5 31.2 - - - +
546C GLU* 5.3 2.2 - - - -
754C SER* 5.6 3.0 + - - -
755C THR* 5.0 19.1 - - + +
756C TYR* 5.3 1.3 - - - +
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Residues in contact with LEU 509 (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 PHE* 3.4 38.4 - - + -
491C LEU* 4.1 5.8 - - + -
505C LEU* 2.8 44.6 + - + +
507C ARG 3.3 0.4 - - - -
508C LYS* 1.3 73.9 - - + +
510C ALA* 1.3 63.5 + - - +
512C LEU* 3.5 11.2 + - + +
513C THR* 2.8 29.6 + - - +
524C VAL* 5.1 1.1 - - + -
542C GLN* 5.9 2.9 - - + -
545C PHE* 3.7 49.8 - - + -
546C GLU* 6.0 0.4 - - + -
549C ILE* 4.6 13.7 - - + -
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Residues in contact with ALA 510 (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 ILE* 3.8 18.1 - - + +
483C ARG* 3.5 30.7 + - + +
484C ALA* 3.6 29.2 - - + +
487C PHE* 3.7 3.3 - - + -
506C ALA 3.2 18.7 + - - +
507C ARG 3.7 2.7 + - - +
508C LYS 3.4 0.2 - - - -
509C LEU* 1.3 73.7 - - - +
511C SER* 1.3 65.1 + - - +
513C THR* 3.5 14.3 + - - -
756C TYR* 4.7 0.2 - - + -
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Residues in contact with SER 511 (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 ILE* 4.3 8.4 - - - +
507C ARG 3.0 14.3 + - - -
508C LYS* 3.2 15.5 + - - -
509C LEU 3.2 0.2 - - - -
510C ALA* 1.3 80.4 - - - +
512C LEU* 1.3 65.3 + - - +
513C THR 3.1 1.8 + - - -
514C PRO* 3.9 6.8 - - - +
609C LEU* 3.4 19.3 - - - +
754C SER 3.7 19.5 - - - -
755C THR* 3.5 2.1 - - - -
756C TYR* 3.1 27.6 + - - +
759C PHE* 4.3 7.9 - - - -
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Residues in contact with LEU 512 (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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508C LYS* 3.4 40.9 + - + +
509C LEU* 3.5 10.0 + - + +
510C ALA 3.4 0.4 - - - -
511C SER* 1.3 79.8 - - - +
513C THR* 1.3 59.8 + - - +
514C PRO* 3.5 9.5 - - - +
542C GLN* 5.3 1.8 - - + +
546C GLU* 4.1 31.6 - - + +
549C ILE* 3.7 31.1 - - + +
553C ILE* 5.1 2.8 - - - +
592C LEU* 4.5 31.2 - - + +
607C GLN* 5.6 0.9 + - - -
609C LEU* 3.9 12.0 - - + +
754C SER 6.0 0.4 - - - +
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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