Contacts of the helix formed by residues 517 - 535 (chain B) 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 SER 517 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B PRO* 6.2 0.9 - - - -
350B PRO 4.0 8.3 + - - -
351B GLY* 3.1 26.0 + - - -
352B THR* 4.6 6.7 - - - -
477B PRO* 5.0 8.1 - - - -
478B PRO* 4.5 12.1 - - - +
515B GLY 3.8 1.0 + - - -
516B PHE* 1.3 77.6 - - - +
518B GLY* 1.3 63.7 + - - +
519B ALA* 3.2 8.2 + - - +
520B ASP* 3.7 16.3 + - - -
521B VAL* 3.3 23.7 + - - +
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Residues in contact with GLY 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B GLY 2.8 14.4 + - - -
352B THR* 4.2 6.0 + - - +
478B PRO* 4.8 4.0 - - - +
486B ILE* 4.3 18.2 - - - +
517B SER* 1.3 72.6 - - - +
519B ALA* 1.3 57.4 + - - +
521B VAL 4.2 1.8 - - - -
522B ALA 3.9 9.4 + - - -
801B ANP 3.1 44.0 + - - -
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Residues in contact with ALA 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B GLY* 2.8 16.4 + - - +
517B SER* 3.2 2.7 - - - +
518B GLY* 1.3 76.8 - - - +
520B ASP* 1.3 60.8 + - - +
521B VAL 3.2 1.8 - - - -
522B ALA* 3.4 3.4 + - - +
523B ASN* 3.1 26.9 + - - +
801B ANP 4.2 5.4 - - - +
465C ARG* 3.4 31.0 - - + +
466C PRO* 3.5 25.5 - - + +
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Residues in contact with ASP 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B PHE* 3.5 46.2 - - + -
517B SER* 3.7 16.6 + - - +
519B ALA* 1.3 76.0 - - - +
521B VAL* 1.3 61.6 + - - +
523B ASN* 3.6 6.4 + - - +
524B VAL* 3.3 28.4 + - - +
552B VAL* 4.6 11.6 - - + +
466C PRO* 3.3 26.7 - - - +
1H ALA 3.8 12.4 + - - -
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Residues in contact with VAL 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ARG* 3.9 28.0 - - + -
486B ILE* 3.7 30.1 - - + +
487B PHE* 3.6 46.8 - - + +
490B HIS* 5.0 0.4 - - + -
516B PHE* 4.3 8.3 - - + -
517B SER 3.3 18.7 + - - +
518B GLY 4.5 1.1 - - - +
519B ALA 3.2 0.6 - - - -
520B ASP* 1.3 76.3 - - - +
522B ALA* 1.3 63.9 + - - +
523B ASN 3.1 1.7 + - - -
524B VAL* 3.4 4.0 + - - +
525B CYS* 3.3 23.1 + - - -
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Residues in contact with ALA 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B HIS* 3.6 41.7 + - + +
518B GLY 3.9 9.2 + - - +
519B ALA* 3.4 8.7 + - - +
521B VAL* 1.3 79.3 - - - +
523B ASN* 1.3 59.4 + - - +
525B CYS* 4.0 2.8 + - - +
526B ASN* 3.5 20.3 + - - +
801B ANP 3.8 14.1 - - - +
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Residues in contact with ASN 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519B ALA 3.1 16.9 + - - +
520B ASP* 3.9 5.6 - - - +
521B VAL 3.1 0.4 - - - -
522B ALA* 1.3 76.3 - - - +
524B VAL* 1.3 55.1 + - - +
525B CYS 3.2 0.2 - - - -
526B ASN* 3.0 6.4 + - - +
527B GLU* 2.6 57.7 + - - +
552B VAL* 4.0 20.7 - - + +
466C PRO* 3.4 29.8 - - + +
470C ASP* 3.3 32.5 + - - +
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Residues in contact with VAL 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B PHE* 4.6 14.4 - - + -
509B LEU* 5.4 0.9 - - + -
513B THR* 5.1 1.8 - - + -
516B PHE* 4.4 13.5 - - + -
520B ASP 3.3 17.2 + - - +
521B VAL* 3.4 5.1 + - - +
523B ASN* 1.3 75.8 - - - +
525B CYS* 1.3 61.6 + - - +
527B GLU* 4.6 0.4 - - - -
528B ALA* 3.1 26.0 + - - +
545B PHE* 4.0 15.3 - - + +
548B ALA* 3.6 29.3 - - + +
549B ILE* 3.7 33.7 - - + -
552B VAL* 4.6 7.2 - - + -
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Residues in contact with CYS 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B PHE* 3.6 28.5 - - - -
490B HIS* 3.4 45.3 - - + +
491B LEU* 4.2 12.1 - - - -
494B LEU* 3.4 28.8 - - + +
521B VAL 3.3 15.7 + - - +
522B ALA 4.2 2.9 - - - +
523B ASN 3.2 0.4 - - - -
524B VAL* 1.3 76.0 - - - +
526B ASN* 1.3 57.5 + - - +
528B ALA 4.5 0.9 - - - -
529B ALA* 4.1 3.8 + - - +
545B PHE* 4.0 10.1 - - - -
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Residues in contact with ASN 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B LEU* 5.6 0.2 - - - -
522B ALA 3.5 16.8 + - - +
523B ASN* 3.0 10.1 + - - +
525B CYS* 1.3 79.5 - - - +
527B GLU* 1.3 65.1 + - - +
528B ALA 3.3 0.4 - - - -
529B ALA* 3.3 4.2 + - - +
530B LEU* 3.1 28.1 + - - +
338C ALA* 4.2 2.6 - - - +
339C LYS* 3.5 49.2 + - - +
340C ILE 4.2 10.1 + - - -
341C PRO* 4.6 6.5 - - - +
470C ASP* 4.9 5.7 + - - -
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Residues in contact with GLU 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ASN* 2.6 46.2 + - - +
526B ASN* 1.3 73.3 + - - +
528B ALA* 1.3 51.2 + - - +
530B LEU* 3.0 11.8 + - - +
531B ILE* 2.7 46.3 + - + +
548B ALA* 3.8 18.2 - - + -
551B ARG* 4.9 13.5 + - + +
552B VAL* 4.9 8.5 - - + -
341C PRO* 5.0 1.6 - - - +
470C ASP* 4.1 8.8 - - - +
471C ARG* 3.3 49.3 + - - +
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Residues in contact with ALA 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B VAL 3.1 18.3 + - - +
525B CYS 5.1 0.2 - - - -
527B GLU* 1.3 77.3 - - - +
529B ALA* 1.3 57.6 + - - +
531B ILE* 3.9 4.5 - - - -
532B ALA* 3.2 23.2 + - - +
540B ILE* 3.6 10.1 - - + +
544B HIS* 3.3 34.6 - - + +
545B PHE* 3.6 27.1 - - + +
548B ALA* 3.6 3.2 - - + +
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Residues in contact with ALA 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B LEU* 3.7 28.9 - - + -
525B CYS 4.1 3.4 + - - +
526B ASN* 3.3 10.5 + - - +
527B GLU 3.1 0.6 - - - -
528B ALA* 1.3 76.9 - - - +
530B LEU* 1.3 63.3 + - - +
532B ALA* 3.3 3.2 + - - +
533B ALA* 3.2 23.7 + - - +
540B ILE* 3.8 14.3 - - + +
336C LEU* 4.3 6.2 - - + +
338C ALA* 3.7 24.7 - - + +
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Residues in contact with LEU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526B ASN* 3.1 23.6 + - - +
527B GLU* 3.0 16.2 + - - +
529B ALA* 1.3 74.9 - - - +
531B ILE* 1.3 64.5 + - + +
533B ALA 3.9 0.5 + - - -
534B ARG* 3.3 22.7 + - - +
322C GLU* 4.1 12.0 - - + +
326C PHE* 5.0 3.6 - - + -
333C TYR* 3.6 33.3 - - + -
338C ALA* 3.9 11.4 - - + -
339C LYS 4.2 7.9 - - - +
341C PRO* 3.8 33.9 - - + -
471C ARG* 3.6 29.6 - - - +
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Residues in contact with ILE 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527B GLU* 2.7 31.3 + - + +
528B ALA* 4.1 4.9 - - - +
530B LEU* 1.3 73.0 - - + +
532B ALA* 1.3 64.5 + - - +
534B ARG* 3.4 37.2 + - + +
535B HIS* 3.5 19.3 - - + +
544B HIS* 4.2 18.6 - - + +
547B GLN* 3.4 31.4 - - + +
548B ALA* 3.9 30.7 - - - +
551B ARG* 5.0 7.9 - - + -
471C ARG* 6.1 0.4 - - - +
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Residues in contact with ALA 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B ALA 3.2 15.7 + - - +
529B ALA 3.5 6.3 - - - +
530B LEU 3.2 0.6 - - - -
531B ILE* 1.3 77.0 - - - +
533B ALA* 1.3 60.2 + - - +
534B ARG 3.3 1.0 + - - -
535B HIS* 3.3 7.3 + - - +
537B SER* 3.1 28.8 + - - -
540B ILE* 3.7 20.0 - - + +
544B HIS* 3.4 32.1 - - + +
336C LEU* 3.9 9.2 - - + -
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Residues in contact with ALA 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B ALA 3.2 6.5 + - - +
530B LEU 4.2 0.4 - - - -
532B ALA* 1.3 77.8 - - - +
534B ARG* 1.3 64.1 + - - +
536B LEU* 3.4 19.4 + - + +
332C GLN* 3.3 33.2 - - + +
333C TYR* 3.6 30.2 + - + -
336C LEU* 3.8 13.4 - - + +
775C GLY* 4.0 9.7 - - - -
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Residues in contact with ARG 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530B LEU 3.3 13.5 + - - +
531B ILE* 3.4 33.7 - - - +
532B ALA 3.2 0.8 - - - -
533B ALA* 1.3 77.4 - - - +
535B HIS* 1.3 70.6 + - - +
536B LEU 3.3 0.2 - - - -
318C LEU* 4.3 23.8 - - - +
319C GLU* 4.0 25.4 + - - +
322C GLU* 2.3 47.3 + - - +
333C TYR* 4.9 2.0 - - - -
471C ARG* 4.1 7.7 - - - +
773C PRO* 3.6 24.3 - - + +
775C GLY* 2.9 24.4 + - - -
776C LEU* 4.1 9.4 - - + -
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Residues in contact with HIS 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B ILE* 3.5 30.8 - - + +
532B ALA 3.3 7.3 + - - +
534B ARG* 1.3 93.7 + - + +
536B LEU* 1.3 69.3 + - - +
537B SER* 3.2 6.9 + - - +
544B HIS* 5.1 9.2 - + - +
547B GLN* 5.5 2.2 + - - -
773C PRO* 4.8 7.8 - - + +
774C GLU* 4.1 27.0 + - - +
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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
------------------------------------------------------------
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