Contacts of the helix formed by residues 519 - 530 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C LEU* 4.8 13.2 - - + +
514C THR* 4.0 9.1 - - + -
518C GLY* 1.3 84.8 - - - +
520C ALA* 1.3 66.6 + - + +
521C HIS 3.5 0.9 - - - -
522C LEU* 3.4 6.8 + - + +
523C ILE* 3.0 38.9 + - + +
548C LEU* 4.6 2.6 - - + +
552C GLY* 3.3 28.7 - - - +
555C LEU* 3.7 35.9 - - + +
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Residues in contact with ALA 520 (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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193C SER* 4.7 5.7 - - - -
196C LEU* 4.0 25.1 - - + -
218C LEU 4.1 9.2 - - - +
219C ASN* 5.6 3.1 - - + -
517C VAL 5.0 0.8 + - - +
518C GLY 3.5 2.4 - - - -
519C PRO* 1.3 82.2 - - + +
521C HIS* 1.3 63.3 + - - +
523C ILE* 3.3 9.8 + - - +
524C HIS* 3.1 21.5 + - - +
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Residues in contact with HIS 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C SER* 3.7 29.4 + - - +
196C LEU* 5.3 4.6 - - + +
197C MET* 3.9 37.9 - - + +
485C ASN* 3.1 28.9 + - - -
486C PHE* 5.8 0.7 - + - -
513C LYS* 3.0 33.7 - - - -
517C VAL* 5.4 7.5 + - + +
518C GLY 5.0 1.2 + - - -
519C PRO 3.5 0.2 - - - -
520C ALA* 1.3 78.2 - - - +
522C LEU* 1.3 57.4 + - - +
524C HIS* 3.1 10.0 + + - +
525C GLU* 2.8 52.3 + - + +
529C TYR* 5.2 4.5 - - - -
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Residues in contact with LEU 522 (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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504C MET* 3.6 21.5 - - + -
509C TRP* 4.0 18.8 - - + +
510C ILE* 4.1 27.8 - - + -
513C LYS* 3.8 23.4 - - + +
514C THR* 4.0 24.7 - - + -
518C GLY 5.1 1.7 + - - +
519C PRO* 3.4 11.3 + - + +
520C ALA 3.3 0.4 - - - -
521C HIS* 1.3 77.6 - - - +
523C ILE* 1.3 63.3 + - - +
525C GLU* 3.1 23.3 + - - +
526C PHE* 3.1 35.0 + - + -
548C LEU* 4.0 12.1 - - + -
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Residues in contact with ILE 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 PRO* 3.0 26.3 + - + +
520C ALA* 3.6 11.4 - - - +
521C HIS 3.3 0.2 - - - -
522C LEU* 1.3 78.0 - - - +
524C HIS* 1.3 64.7 + - - +
526C PHE* 3.2 15.9 + - - +
527C VAL* 3.2 14.5 + - + +
545C GLN* 3.9 25.1 + - + +
548C LEU* 3.7 31.4 - - + +
549C SER* 4.0 29.6 - - - +
552C GLY* 5.3 1.6 - - - -
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Residues in contact with HIS 524 (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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191C ASP* 3.3 25.9 + - + -
193C SER* 3.1 26.4 + - - +
520C ALA 3.1 11.0 + - - +
521C HIS* 3.1 17.7 + + - +
523C ILE* 1.3 81.7 - - - +
525C GLU* 1.3 60.2 + - + +
527C VAL* 3.3 9.0 + - + +
528C GLU* 2.9 64.2 + - + +
529C TYR* 5.9 1.8 - - - -
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Residues in contact with GLU 525 (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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484C TYR 4.2 1.7 - - - +
485C ASN 3.7 8.7 - - - +
488C ALA* 3.4 23.0 + - - +
489C TYR 4.6 0.2 + - - -
504C MET* 3.6 13.1 - - + +
509C TRP* 5.1 1.9 + - - -
513C LYS* 3.0 27.1 + - - +
521C HIS* 2.8 42.7 + - + +
522C LEU* 3.1 25.7 + - - +
524C HIS* 1.3 70.5 - - + +
526C PHE* 1.3 66.6 + - - +
528C GLU* 4.3 2.5 - - - -
529C TYR* 3.1 51.2 + - + +
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Residues in contact with PHE 526 (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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504C MET* 3.5 46.2 - - + -
505C PHE* 3.8 22.2 - + - -
510C ILE* 5.2 2.7 - - + -
522C LEU* 3.1 32.9 + - + -
523C ILE 3.5 7.2 - - - +
525C GLU* 1.3 76.1 - - - +
527C VAL* 1.3 60.7 + - - +
530C ARG* 3.4 40.0 + - - +
541C SER* 3.5 27.8 + - - -
544C PHE* 3.6 26.2 - + + -
545C GLN* 4.1 11.0 - - + -
548C LEU* 3.6 28.0 - - + -
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Residues in contact with VAL 527 (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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523C ILE* 3.2 11.2 + - + +
524C HIS* 3.7 13.0 - - + +
526C PHE* 1.3 79.2 - - - +
528C GLU* 1.3 64.7 + - - +
529C TYR 3.4 0.3 + - - -
530C ARG* 3.6 22.1 + - - +
531C HIS* 4.9 1.0 + - - -
545C GLN* 2.7 39.9 - - - +
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Residues in contact with GLU 528 (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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524C HIS* 2.9 46.1 + - + +
525C GLU* 4.1 1.8 - - - +
527C VAL* 1.3 81.1 - - - +
529C TYR* 1.3 83.9 + - + +
531C HIS* 3.0 24.9 + - - -
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Residues in contact with TYR 529 (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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485C ASN 5.2 1.0 + - - -
488C ALA* 3.6 26.5 - - + -
489C TYR* 3.2 40.3 + + - +
492C ALA* 3.6 27.4 - - + -
500C LEU* 4.1 15.8 - - + +
504C MET* 4.7 1.8 - - - -
521C HIS* 5.2 4.2 - - - -
524C HIS* 5.9 1.5 - + - -
525C GLU* 3.1 47.6 + - + +
526C PHE 4.3 0.2 - - - -
528C GLU* 1.3 100.9 - - + +
530C ARG* 1.3 65.1 + - - +
531C HIS* 3.2 10.9 + - - -
532C ILE* 3.3 21.5 + - - +
533C LEU* 4.1 4.4 - - - +
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Residues in contact with ARG 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 PHE* 3.4 24.7 + - - +
527C VAL* 3.7 23.8 + - - +
528C GLU 3.5 1.4 - - - -
529C TYR* 1.3 77.1 - - - +
531C HIS* 1.3 57.9 + - - +
533C LEU* 3.0 35.9 + - + +
538C CYS* 3.8 30.3 - - - -
541C SER* 3.0 36.8 + - - +
542C GLU* 3.7 21.2 + - - +
545C GLN* 2.9 48.1 + - - +
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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