Contacts of the helix formed by residues 519 - 533 (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 ALA 519 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C GLY* 3.4 12.2 + - - +
517C SER* 3.2 2.0 - - - +
518C GLY* 1.3 77.2 - - - +
520C ASP* 1.3 64.5 + - - +
521C VAL 3.2 1.6 - - - -
522C ALA* 3.2 19.8 + - + +
523C ASN 3.4 2.4 + - - -
803C ANP 3.6 14.4 - - - +
465D ARG* 3.4 30.5 - - - +
466D PRO* 3.3 24.5 - - + +
467D GLY* 5.5 0.2 - - - -
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Residues in contact with ASP 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C GLY 4.8 0.7 - - - +
516C PHE* 3.6 40.7 - - + -
517C SER* 3.0 29.0 + - - +
519C ALA* 1.3 74.4 - - - +
521C VAL* 1.3 64.7 + - - +
523C ASN* 3.5 3.5 + - - +
524C VAL* 3.3 26.9 + - - +
552C VAL* 5.9 6.8 - - + +
466D PRO* 3.2 32.8 - - - +
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Residues in contact with VAL 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C ARG* 4.3 22.7 - - + -
486C ILE* 3.7 31.4 - - + +
487C PHE* 3.6 55.2 - - + +
490C HIS* 5.1 0.4 - - + -
516C PHE* 4.5 7.2 - - + -
517C SER 3.4 16.5 + - - +
518C GLY 4.5 0.4 - - - +
519C ALA 3.2 0.4 - - - -
520C ASP* 1.3 78.5 - - - +
522C ALA* 1.3 61.3 + - - +
524C VAL* 3.3 3.3 + - - +
525C CYS* 3.1 24.6 + - - -
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Residues in contact with ALA 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C HIS* 4.4 27.3 - - + +
518C GLY 4.2 5.9 + - - +
519C ALA* 3.2 21.3 + - + +
521C VAL* 1.3 80.2 - - - +
523C ASN* 1.3 59.6 + - - +
525C CYS* 3.9 2.5 + - - +
526C ASN* 3.2 25.3 + - - +
803C ANP 4.4 14.8 - - - +
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Residues in contact with ASN 523 (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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519C ALA 3.4 3.4 + - - -
520C ASP 3.5 5.8 + - - +
521C VAL 3.3 0.8 - - - -
522C ALA* 1.3 80.0 - - - +
524C VAL* 1.3 59.0 + - - +
525C CYS 3.2 0.7 - - - -
526C ASN* 4.2 9.9 + - - +
527C GLU* 2.5 54.0 + - - +
552C VAL* 4.8 13.1 - - + +
466D PRO* 3.2 34.8 - - + +
467D GLY 4.8 0.3 + - - -
470D ASP* 3.4 46.1 + - - +
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Residues in contact with VAL 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C PHE* 4.1 20.4 - - + -
509C LEU* 5.1 1.3 - - + -
513C THR* 4.8 1.1 - - + -
516C PHE* 4.0 21.8 - - + -
520C ASP 3.3 15.9 + - - +
521C VAL* 3.3 8.4 + - - +
523C ASN* 1.3 75.8 - - - +
525C CYS* 1.3 61.3 + - - +
528C ALA* 3.3 24.1 + - - +
545C PHE* 3.7 16.7 - - + +
548C ALA* 3.8 16.9 - - + +
549C ILE* 3.7 31.9 - - + -
552C VAL* 5.0 6.5 - - + -
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Residues in contact with CYS 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C PHE* 3.5 29.4 - - - -
490C HIS* 3.7 45.8 - - + +
491C LEU* 4.1 9.4 - - - -
494C LEU* 3.6 25.9 - - + +
521C VAL* 3.1 20.6 + - - +
522C ALA 4.1 3.4 - - - +
524C VAL* 1.3 80.1 - - - +
526C ASN* 1.3 62.6 + - - +
528C ALA* 4.0 1.2 + - - +
529C ALA 3.9 5.4 + - - -
545C PHE* 4.4 7.2 - - - -
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Residues in contact with ASN 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C LEU* 5.3 2.2 - - - -
522C ALA 3.2 16.6 + - - +
523C ASN* 3.0 12.1 + - - +
525C CYS* 1.3 80.0 - - - +
527C GLU* 1.3 61.9 + - + +
528C ALA 3.1 1.3 - - - -
529C ALA* 2.9 22.0 + - - +
530C LEU* 3.3 15.5 + - - +
338D ALA* 3.9 6.8 - - - +
339D LYS* 3.5 48.6 + - - +
340D ILE 4.3 7.9 + - - -
341D PRO* 4.7 6.5 - - - +
470D ASP* 5.2 2.8 + - - -
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Residues in contact with GLU 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C ASN* 2.5 36.6 + - + +
526C ASN* 1.3 74.6 - - + +
528C ALA* 1.3 55.2 + - - +
529C ALA 3.3 0.4 - - - -
530C LEU* 3.8 13.2 - - + +
531C ILE* 3.2 32.4 + - + +
548C ALA* 3.8 11.3 - - + +
551C ARG* 4.3 13.7 - - - +
552C VAL* 3.8 19.6 - - - +
341D PRO* 6.0 0.9 - - + -
470D ASP* 3.5 21.7 - - + +
471D ARG* 3.1 41.7 + - - +
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Residues in contact with ALA 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C VAL 3.3 20.6 + - - +
525C CYS 4.2 1.1 - - - +
526C ASN 3.1 1.0 - - - -
527C GLU* 1.3 76.9 - - - +
529C ALA* 1.3 59.0 + - - +
530C LEU 3.4 0.2 - - - -
531C ILE 3.7 1.5 + - - +
532C ALA* 3.1 25.3 + - - +
540C ILE* 3.8 6.4 - - + +
544C HIS* 3.3 33.3 - - - +
545C PHE* 3.5 28.0 - - + -
548C ALA* 3.6 2.1 - - + +
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Residues in contact with ALA 529 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C LEU* 4.1 14.6 - - + -
525C CYS 3.9 1.4 + - - -
526C ASN 2.9 11.3 + - - +
528C ALA* 1.3 77.5 - - - +
530C LEU* 1.3 59.7 + - - +
531C ILE 3.2 0.4 - - - -
532C ALA* 3.3 2.7 + - - +
533C ALA* 2.9 31.4 + - - +
540C ILE* 3.7 24.6 - - + +
336D LEU* 4.0 8.7 - - + +
338D ALA* 3.7 22.3 - - + +
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Residues in contact with LEU 530 (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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526C ASN* 3.3 20.0 + - - +
527C GLU* 3.7 15.2 + - + +
528C ALA 3.4 0.2 - - - -
529C ALA* 1.3 76.3 - - - +
531C ILE* 1.3 59.6 + - + +
533C ALA* 4.1 3.5 - - - +
534C ARG* 3.3 24.2 + - - +
322D GLU* 4.1 15.1 - - + +
326D PHE* 5.4 1.6 - - + -
333D TYR* 4.2 28.4 - - + -
338D ALA* 3.8 21.8 - - + -
339D LYS 4.5 4.5 - - - +
341D PRO* 3.7 27.1 - - + -
471D ARG* 3.4 31.2 - - - +
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Residues in contact with ILE 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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527C GLU* 3.2 22.0 + - + +
528C ALA* 3.7 4.5 + - - +
529C ALA 3.2 0.4 - - - -
530C LEU* 1.3 78.2 - - + +
532C ALA* 1.3 63.6 + - - +
533C ALA 3.2 0.2 - - - -
534C ARG* 3.3 38.2 + - - +
535C HIS* 3.0 33.3 + - + +
544C HIS* 4.2 12.3 - - + +
547C GLN* 3.3 61.5 - - + +
548C ALA* 3.9 3.8 - - - +
551C ARG* 5.4 4.7 - - + -
471D ARG* 6.3 0.7 - - - +
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Residues in contact with ALA 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C ALA 3.1 20.5 + - - +
529C ALA 3.6 5.6 - - - +
531C ILE* 1.3 77.8 - - - +
533C ALA* 1.3 56.9 + - - +
535C HIS* 4.0 1.6 + - - +
536C LEU 3.7 2.1 + - - -
537C SER* 2.4 39.5 + - - +
540C ILE* 3.7 23.3 - - + -
544C HIS* 3.3 26.9 + - - +
336D LEU* 3.9 5.6 - - + -
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Residues in contact with ALA 533 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C ALA 2.9 16.8 + - - +
532C ALA* 1.3 75.2 - - - +
534C ARG* 1.3 64.9 + - - +
535C HIS 3.3 0.4 - - - -
536C LEU* 3.4 8.4 + - - +
537C SER 4.6 1.1 - - - +
332D GLN* 3.0 39.2 + - + +
333D TYR* 3.5 32.2 - - + -
336D LEU* 3.7 15.7 - - + -
775D GLY* 4.0 0.5 - - - -
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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
------------------------------------------------------------
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