Contacts of the helix formed by residues 519 - 530 (chain B) in PDB entry 1Z6T
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 PRO 519 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B LEU* 4.8 12.1 - - + +
514B THR* 4.1 8.9 - - + -
517B VAL 4.8 0.2 - - - +
518B GLY* 1.3 83.8 - - - +
520B ALA* 1.3 67.4 + - + +
521B HIS 3.5 1.6 - - - -
522B LEU* 3.4 7.6 + - + +
523B ILE* 3.0 39.5 + - + +
548B LEU* 4.7 2.9 - - + +
552B GLY* 3.3 27.8 - - - +
555B LEU* 3.6 36.6 - - + +
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Residues in contact with ALA 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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193B SER* 4.8 5.9 - - - -
196B LEU* 3.9 25.6 - - + -
218B LEU 4.0 9.2 - - - +
219B ASN* 5.6 3.1 - - + -
517B VAL 5.0 0.6 + - - +
518B GLY 3.5 2.4 - - - -
519B PRO* 1.3 84.1 - - + +
521B HIS* 1.3 63.1 + - - +
523B ILE* 3.4 9.3 + - - +
524B HIS* 3.1 21.7 + - - +
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Residues in contact with HIS 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B SER* 3.8 26.5 + - - +
196B LEU* 5.2 4.8 - - + +
197B MET* 3.9 38.1 - - + +
485B ASN* 3.2 27.2 + - - -
486B PHE* 6.0 0.7 - + - -
513B LYS* 3.1 32.5 - - - -
517B VAL* 5.5 7.1 + - + +
518B GLY 5.0 1.2 + - - -
519B PRO 3.5 0.2 - - - -
520B ALA* 1.3 74.9 - - - +
522B LEU* 1.3 60.9 + - - +
524B HIS* 3.1 13.2 + + - +
525B GLU* 2.8 51.1 + - + +
529B TYR* 5.2 4.9 - - - -
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Residues in contact with LEU 522 (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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504B MET* 3.8 18.4 - - + -
509B TRP* 4.0 20.0 - - + +
510B ILE* 3.9 36.8 - - + -
513B LYS* 4.2 20.5 - - + +
514B THR* 4.1 14.4 - - + -
518B GLY 5.0 2.6 + - - +
519B PRO* 3.4 12.0 + - + +
520B ALA 3.3 0.2 - - - -
521B HIS* 1.3 78.2 - - - +
523B ILE* 1.3 61.7 + - - +
525B GLU* 3.1 32.3 + - - +
526B PHE* 3.1 30.9 + - + -
548B LEU* 3.9 9.4 - - + -
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Residues in contact with ILE 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 PRO* 3.0 31.3 + - + +
520B ALA* 3.6 9.6 - - - +
522B LEU* 1.3 74.3 - - - +
524B HIS* 1.3 66.0 + - - +
526B PHE* 3.2 8.6 + - - +
527B VAL* 3.2 22.6 + - + +
545B GLN* 4.1 21.3 + - + +
548B LEU* 3.7 45.5 - - + +
549B SER* 4.1 15.5 - - - +
552B GLY* 5.3 1.8 - - - -
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Residues in contact with HIS 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASP* 3.3 26.2 + - + -
193B SER* 3.0 27.8 + - - +
520B ALA 3.1 11.3 + - - +
521B HIS* 3.1 20.6 + + - +
523B ILE* 1.3 82.1 - - - +
525B GLU* 1.3 58.3 + - + +
527B VAL* 3.3 7.9 + - + +
528B GLU* 2.9 61.2 + - + +
529B TYR* 5.9 2.0 - - - -
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Residues in contact with GLU 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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484B TYR 4.2 1.7 - - - +
485B ASN 3.8 8.7 - - - +
488B ALA* 3.5 23.6 - - - +
489B TYR 4.6 0.2 + - - -
504B MET* 3.6 13.2 - - + +
509B TRP* 5.1 2.3 + - - -
513B LYS* 2.9 27.9 + - - +
521B HIS* 2.8 42.0 + - + +
522B LEU* 3.1 25.8 + - - +
524B HIS* 1.3 74.5 - - + +
526B PHE* 1.3 62.7 + - - +
528B GLU* 4.5 2.0 - - - -
529B TYR* 3.1 50.8 + - + +
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Residues in contact with PHE 526 (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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504B MET* 3.5 46.4 - - + -
505B PHE* 3.9 21.5 - + - -
510B ILE* 5.0 2.0 - - + -
522B LEU* 3.1 33.8 + - + -
523B ILE* 3.2 7.6 + - - +
525B GLU* 1.3 76.7 - - - +
527B VAL* 1.3 61.4 + - - +
530B ARG* 3.3 39.8 + - - +
541B SER* 3.7 26.5 + - - -
544B PHE* 3.6 24.7 - + + -
545B GLN* 4.2 10.5 - - + -
548B LEU* 3.5 30.3 - - + -
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Residues in contact with VAL 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 ILE* 3.2 12.2 + - + +
524B HIS* 3.7 12.8 - - + +
526B PHE* 1.3 78.4 - - - +
528B GLU* 1.3 65.4 + - - +
529B TYR 3.4 0.2 + - - -
530B ARG* 3.5 22.8 + - - +
531B HIS 4.9 0.7 + - - -
545B GLN* 2.8 39.7 - - - +
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Residues in contact with GLU 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 HIS* 2.9 45.5 + - + +
525B GLU* 4.1 2.0 - - - +
527B VAL* 1.3 79.6 - - - +
529B TYR* 1.3 83.9 + - + +
531B HIS* 3.1 25.6 + - - -
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Residues in contact with TYR 529 (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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485B ASN 5.3 0.3 + - - -
488B ALA* 3.7 30.3 - - + -
489B TYR* 3.2 39.5 + + - +
492B ALA* 3.6 29.8 - - + -
500B LEU* 4.1 14.9 - - + +
504B MET* 4.8 2.0 - - - -
521B HIS* 5.2 5.0 - - - -
524B HIS* 5.9 1.5 - + - -
525B GLU* 3.1 40.6 + - + +
528B GLU* 1.3 101.8 - - + +
530B ARG* 1.3 65.8 + - - +
531B HIS* 3.1 11.9 + + - -
532B ILE* 3.2 22.2 + - - +
533B LEU* 4.1 4.1 - - - +
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Residues in contact with ARG 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 PHE* 3.3 25.1 + - - +
527B VAL* 3.6 27.0 + - - +
528B GLU 3.5 1.0 - - - -
529B TYR* 1.3 77.3 - - - +
531B HIS* 1.3 57.2 + - - +
533B LEU* 3.0 35.5 + - + +
538B CYS* 3.6 31.9 - - + -
541B SER* 3.0 34.8 + - - +
542B GLU* 3.6 25.3 + - - +
545B GLN* 2.7 46.6 + - - +
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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