Contacts of the helix formed by residues 515 - 527 (chain B) in PDB entry 1ZY7
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 515 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451B CYS* 3.5 15.3 - - - -
452B GLY* 3.7 11.2 - - - -
481B ARG* 2.8 19.5 + - - +
482B THR* 4.2 0.4 - - - +
483B LYS* 3.7 8.5 - - - +
490B THR* 3.7 18.8 - - - -
513B THR 3.8 0.6 + - - -
514B MET* 1.3 77.4 - - - +
516B CYS* 1.3 58.2 + - - +
517B SER* 3.7 1.6 + - - -
518B ASP* 2.8 33.4 + - - +
519B LYS* 3.0 24.4 + - - +
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Residues in contact with CYS 516 (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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394B HIS* 3.5 15.7 - - - -
396B GLU* 3.4 27.6 - - + +
397B ILE* 3.6 11.9 - - + -
450B PRO* 3.7 9.2 - - + -
451B CYS* 3.4 4.9 - - - -
483B LYS* 3.4 15.3 - - - +
515B SER* 1.3 71.4 - - - +
517B SER* 1.3 60.5 + - - +
519B LYS* 3.2 6.2 + - - -
520B ILE* 2.8 36.3 + - + +
802B ZN 2.3 34.3 - - - -
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Residues in contact with SER 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B PRO* 3.1 10.6 + - - +
451B CYS 2.8 24.3 + - - -
453B ASP* 3.5 17.7 - - - -
454B ALA* 3.0 28.1 + - - +
515B SER* 4.0 1.6 - - - -
516B CYS* 1.3 75.9 - - - +
518B ASP* 1.3 58.6 + - - +
520B ILE 3.5 0.2 + - - -
521B ALA* 3.1 22.2 + - - +
559B ALA* 4.3 0.4 - - - -
560B MET* 3.6 19.0 - - - +
563B ARG* 3.2 17.9 + - - -
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Residues in contact with ASP 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B ASP* 4.9 1.2 + - - +
479B GLN 4.3 0.7 - - - +
480B LEU* 3.3 24.1 - - + +
481B ARG 2.8 34.0 + - - +
514B MET* 3.6 6.5 - - + +
515B SER* 2.8 19.6 + - - +
516B CYS 3.2 0.6 - - - -
517B SER* 1.3 76.1 - - - +
519B LYS* 1.3 59.3 + - - +
521B ALA* 3.3 3.8 + - - +
522B ARG 2.8 24.9 + - - -
563B ARG* 2.9 33.3 + - - +
679B PHE* 5.1 0.2 - - - -
687B TRP* 3.4 21.6 - - + -
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Residues in contact with LYS 519 (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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392B ASP* 2.9 26.1 + - - +
397B ILE* 3.6 26.4 - - + +
483B LYS* 4.5 0.2 - - - +
513B THR* 3.7 2.6 - - - +
514B MET* 3.6 27.6 - - + +
515B SER 3.0 16.7 + - - +
516B CYS 3.2 4.2 + - - +
518B ASP* 1.3 76.3 - - - +
520B ILE* 1.3 57.0 + - - +
522B ARG* 3.2 5.7 - - - +
523B TRP* 2.9 42.6 + - + +
687B TRP* 4.1 12.1 - - + -
902B IHP 2.7 63.0 + - - +
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Residues in contact with ILE 520 (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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396B GLU* 4.5 6.3 - - + -
444B LEU* 4.1 9.4 - - + -
446B ILE* 3.9 17.3 - - + -
450B PRO* 3.8 30.7 - - + -
516B CYS* 2.8 22.9 + - + +
519B LYS* 1.3 73.0 - - + +
521B ALA* 1.3 60.6 + - - +
523B TRP* 2.9 36.7 + - + -
524B ASN* 2.9 31.6 + - - +
542B PHE* 5.4 2.2 - - + -
545B ILE* 3.5 19.5 - - + -
560B MET* 3.4 25.6 - - + -
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Residues in contact with ALA 521 (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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517B SER 3.1 9.8 + - - +
518B ASP 3.5 7.6 - - - +
520B ILE* 1.3 75.3 - - - +
522B ARG* 1.3 64.3 + - - +
524B ASN* 3.0 16.1 + - - +
525B VAL* 3.4 12.5 + - - +
559B ALA 3.5 22.2 - - - +
560B MET* 3.7 17.8 + - - +
563B ARG* 3.8 8.5 - - - +
564B ILE* 4.2 11.4 - - + +
675B LEU* 4.7 0.2 - - - -
679B PHE* 4.1 14.4 - - + -
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Residues in contact with ARG 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B ASP 2.8 14.2 + - - +
519B LYS* 3.2 14.1 - - - +
521B ALA* 1.3 76.1 - - - +
523B TRP* 1.3 66.4 + - + +
525B VAL* 2.9 5.2 + - - +
526B VAL* 2.9 41.3 + - + +
668B TYR* 4.0 7.4 + - - -
672B LYS* 3.8 20.1 - - - +
675B LEU* 3.4 30.9 - - + +
676B PHE* 4.0 15.8 - - - -
687B TRP* 3.4 41.9 - - + +
902B IHP 2.9 60.0 + - - -
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Residues in contact with TRP 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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396B GLU 3.7 22.7 - - - -
397B ILE* 3.7 28.7 - - + -
400B ARG* 3.3 45.6 - - + +
444B LEU* 4.3 8.5 - - + -
519B LYS* 2.9 36.4 + - + +
520B ILE* 2.9 34.5 + - + +
522B ARG* 1.3 88.7 - - + +
524B ASN* 1.3 59.0 + - - +
525B VAL 3.1 0.4 - - - -
526B VAL* 5.2 0.7 - - + -
527B GLY* 3.0 45.6 + - - +
528B ILE* 3.9 11.9 + - + +
541B TYR* 3.4 5.7 - - - -
542B PHE* 3.7 30.2 + + + -
668B TYR* 6.2 0.2 - - - -
902B IHP 5.3 4.1 + - - -
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Residues in contact with ASN 524 (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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520B ILE* 2.9 16.5 + - - +
521B ALA 3.0 9.1 + - - +
523B TRP* 1.3 78.4 - - - +
525B VAL* 1.3 63.4 + - - +
541B TYR* 3.7 3.6 - - - -
542B PHE* 4.8 6.9 + - - +
545B ILE* 4.0 15.1 - - - +
560B MET* 2.9 37.4 + - - +
575B THR 3.1 1.7 - - - +
576B LEU* 3.6 3.5 - - + -
577B ASN* 2.8 71.1 + - - +
579B PRO* 4.0 7.8 - - - +
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Residues in contact with VAL 525 (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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521B ALA 3.8 3.1 - - - +
522B ARG 2.9 6.3 + - - +
523B TRP 3.1 0.2 - - - -
524B ASN* 1.3 85.4 - - - +
526B VAL* 1.3 69.4 + - + +
527B GLY 3.3 3.4 - - - -
541B TYR* 2.7 22.5 + - - -
564B ILE* 3.8 19.7 - - + -
567B ILE* 3.6 28.5 - - + -
570B LEU* 3.8 20.0 - - + -
574B TYR* 3.3 9.0 - - - +
575B THR 3.5 6.9 - - - +
576B LEU* 3.7 22.9 - - + -
671B ALA* 4.3 0.9 - - + +
675B LEU* 3.9 12.1 - - + -
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Residues in contact with VAL 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B ARG* 2.9 37.8 + - + +
523B TRP* 4.6 1.3 - - + -
525B VAL* 1.3 79.8 - - + +
527B GLY* 1.3 63.8 + - - +
529B GLN* 3.0 21.7 + - - -
539B PRO* 4.5 0.6 - - - +
574B TYR* 3.4 18.2 - - + -
668B TYR* 3.4 37.7 - - + +
671B ALA* 3.9 9.2 - - + -
672B LYS* 3.8 37.0 - - + +
675B LEU* 4.6 7.4 - - + -
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Residues in contact with GLY 527 (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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523B TRP* 3.0 35.9 + - - +
525B VAL 3.3 3.0 + - - -
526B VAL* 1.3 88.9 - - - +
528B ILE* 1.3 62.3 + - - -
529B GLN* 3.4 7.6 + - - -
530B GLY 4.6 2.1 + - - -
539B PRO* 4.8 0.2 - - - -
540B ILE 3.1 14.6 - - - -
541B TYR* 3.6 10.2 - - - -
668B TYR* 5.0 0.3 + - - -
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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