Contacts of the helix formed by residues 479 - 491 (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 ASP 479 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560B THR* 3.0 27.2 + - - +
561B GLN* 3.3 24.8 + - - +
562B VAL* 3.0 31.6 + - + +
312C GLY 5.3 1.9 - - - +
478C PRO* 1.3 77.4 - - - +
480C ILE* 1.3 63.0 + - - +
481C LYS* 4.1 5.0 - - - +
482C GLY* 3.2 15.1 + - - -
483C ARG* 2.9 32.5 + - - +
612C GLU* 3.8 9.0 - - - +
614C TYR* 4.5 8.3 - - - +
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Residues in contact with ILE 480 (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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562B VAL* 3.8 22.2 - - + +
479C ASP* 1.3 77.8 - - - +
481C LYS* 1.3 60.8 + - + +
483C ARG* 3.5 23.8 - - - +
484C ALA* 3.0 28.1 + - - +
510C ALA* 3.8 18.6 - - + +
511C SER* 4.3 3.4 - - - -
612C GLU* 4.2 6.0 + - - +
756C TYR* 3.6 27.3 - - + -
759C PHE* 3.5 39.3 - - + +
760C VAL* 3.8 17.7 - - + -
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Residues in contact with LYS 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B LYS 5.8 0.6 + - - -
560B THR* 4.1 19.8 + - - +
562B VAL* 4.1 15.0 - - + -
479C ASP* 3.3 6.8 + - - +
480C ILE* 1.3 80.3 - - + +
482C GLY* 1.3 59.5 + - - +
484C ALA* 3.9 2.0 + - - +
485C SER* 3.5 11.1 + - - -
756C TYR* 3.7 20.4 + - - +
760C VAL* 3.6 25.4 - - + -
763C THR* 3.2 19.7 + - - +
765C SER* 2.4 31.3 + - - -
767C ASP* 3.5 23.3 + - - +
768C GLU* 3.1 33.5 + - + +
769C ASP* 5.6 2.4 + - - -
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Residues in contact with GLY 482 (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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312C GLY* 3.7 14.9 - - - -
478C PRO* 3.9 10.5 - - - -
479C ASP* 3.2 20.0 + - - -
481C LYS* 1.3 76.7 - - - +
483C ARG* 1.3 62.8 + - - +
484C ALA 3.3 0.2 - - - -
485C SER* 3.3 2.4 + - - -
486C ILE* 3.1 26.0 + - - +
768C GLU* 3.4 13.2 - - - -
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Residues in contact with ARG 483 (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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478C PRO* 3.6 25.3 + - + +
479C ASP 2.9 14.8 + - - +
480C ILE* 3.5 16.5 - - - +
482C GLY* 1.3 73.3 - - - +
484C ALA* 1.3 60.8 + - - +
486C ILE* 3.1 8.6 + - - +
487C PHE* 2.9 33.8 + - - -
510C ALA* 3.5 30.1 + - + -
513C THR* 2.8 32.0 + - - -
514C PRO* 3.9 4.0 - - - +
515C GLY* 3.4 11.1 - - - +
516C PHE* 4.1 22.1 + - - +
517C SER 5.0 0.4 - - - +
521C VAL* 4.3 14.3 - - + +
612C GLU* 2.5 44.4 + - - -
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Residues in contact with ALA 484 (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 3.0 18.4 + - - +
481C LYS 4.1 3.8 - - - +
482C GLY 3.3 0.4 - - - -
483C ARG* 1.3 76.0 - - - +
485C SER* 1.3 58.8 + - - +
487C PHE* 4.0 0.4 - - - -
488C LYS* 3.3 28.7 + - - +
506C ALA* 3.4 27.7 - - - +
507C ARG* 4.6 3.6 - - + -
510C ALA* 3.6 8.6 - - + +
756C TYR* 3.8 27.6 - - + +
767C ASP* 5.8 2.2 - - - +
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Residues in contact with SER 485 (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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311C ALA* 3.3 22.9 - - - +
481C LYS 3.5 6.0 + - - -
482C GLY 3.3 2.1 + - - -
483C ARG 3.2 0.6 - - - -
484C ALA* 1.3 77.4 - - - +
486C ILE* 1.3 61.5 + - - +
487C PHE 3.3 0.4 - - - -
488C LYS* 3.4 17.1 + - - +
489C VAL* 3.4 17.0 + - - +
767C ASP* 4.1 9.4 + - - -
768C GLU* 3.2 37.6 + - - +
770C THR* 5.6 3.6 - - - +
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Residues in contact with ILE 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C ALA* 3.8 12.6 - - - +
312C GLY* 4.4 0.4 - - - -
478C PRO* 3.8 24.7 - - + -
482C GLY 3.1 16.7 + - - +
483C ARG* 3.1 10.8 + - + +
485C SER* 1.3 73.9 - - - +
487C PHE* 1.3 65.2 + - - +
489C VAL* 3.3 9.7 + - - +
490C HIS* 3.3 19.3 + - + -
517C SER 4.8 1.6 - - - +
518C GLY* 3.9 19.5 - - - +
521C VAL* 3.7 23.6 - - + -
803C ANP 3.4 49.4 - - + +
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Residues in contact with PHE 487 (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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483C ARG* 2.9 27.7 + - + +
484C ALA 3.9 0.2 - - - +
485C SER 3.3 0.2 - - - -
486C ILE* 1.3 76.9 - - - +
488C LYS* 1.3 55.1 + - - +
490C HIS 4.5 0.4 - - - +
491C LEU* 2.7 40.2 + - + +
506C ALA* 3.6 21.8 - - + -
509C LEU* 3.4 55.4 - - + -
510C ALA* 3.7 12.8 - - + -
513C THR* 3.7 21.5 - - + -
521C VAL* 3.6 30.3 - - + -
524C VAL* 4.1 16.4 - - + -
525C CYS* 3.5 24.0 - - - -
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Residues in contact with LYS 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C ALA* 3.3 23.9 + - - +
485C SER* 3.4 16.7 + - - +
486C ILE 3.3 0.8 - - - -
487C PHE* 1.3 76.2 - - - +
489C VAL* 1.3 61.8 + - + +
491C LEU* 4.4 3.5 - - - +
492C ARG* 3.7 20.0 + - - +
502C LYS* 4.6 7.9 - - - +
503C ASP* 3.4 31.9 + - - +
506C ALA* 3.7 15.5 - - + -
507C ARG* 4.6 10.2 - - - +
767C ASP* 3.3 35.2 + - - -
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Residues in contact with VAL 489 (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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308C LYS 3.8 16.4 - - - +
309C ASP* 3.4 33.9 - - + +
311C ALA* 4.1 9.6 - - + -
485C SER 3.4 15.7 - - - +
486C ILE* 3.3 9.5 + - - +
487C PHE 3.2 0.4 - - - -
488C LYS* 1.3 80.8 - - + +
490C HIS* 1.3 75.4 + - + +
492C ARG* 3.4 45.0 + - - +
493C PRO* 3.8 4.5 - - - +
803C ANP 4.7 0.9 - - + -
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Residues in contact with HIS 490 (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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486C ILE* 3.3 26.8 + - + +
487C PHE 3.2 2.0 + - - -
489C VAL* 1.3 87.2 + - + +
491C LEU* 1.3 62.2 + - - +
492C ARG 3.1 1.3 - - - -
493C PRO* 3.4 15.8 - - - +
494C LEU* 3.9 8.1 - - - +
521C VAL* 5.1 0.4 - - + -
522C ALA* 4.4 21.3 - - + +
525C CYS* 3.7 34.2 - - + +
803C ANP 3.0 52.0 + + - -
339D LYS* 5.3 11.9 + - - -
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Residues in contact with LEU 491 (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* 2.7 30.0 + - + +
488C LYS* 4.9 1.8 - - - +
490C HIS* 1.3 71.9 - - - +
492C ARG* 1.3 60.9 + - - +
493C PRO 3.5 0.7 - - - -
494C LEU* 3.3 26.0 + - + +
496C LEU* 4.7 3.9 - - + +
502C LYS* 3.3 41.2 - - + +
505C LEU* 4.1 12.6 - - + -
506C ALA* 3.8 32.1 - - + +
509C LEU* 4.1 9.6 - - + -
525C CYS* 4.2 8.7 - - - -
545C PHE* 3.6 37.2 - - + -
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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