Contacts of the helix formed by residues 519 - 530 (chain C) in PDB entry 5ZR1
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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285B PHE* 3.9 10.8 - - + -
286B GLN* 3.7 21.7 - - - +
483B PHE* 4.2 28.7 - - + -
494C TRP* 3.6 46.0 - - + -
498C LEU* 4.0 7.9 - - + -
518C ALA* 1.3 83.5 - - + +
520C VAL* 1.3 55.1 + - - +
521C LEU 3.3 1.6 - - - +
522C GLY* 2.9 5.6 + - - +
523C GLN 2.8 31.2 + - - -
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Residues in contact with VAL 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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285B PHE* 4.9 7.9 - - + -
517C MET* 4.1 13.7 - - + -
518C ALA 4.4 0.9 - - - +
519C PRO* 1.3 73.5 - - + +
521C LEU* 1.3 58.8 + - + +
523C GLN* 4.3 6.1 - - - +
524C LEU* 2.9 29.3 + - + +
544C PHE* 3.9 21.1 - - + -
583C LEU* 3.3 56.3 - - + +
584C PHE* 5.0 0.2 - - - -
586C GLN* 5.6 3.8 - - + +
587C ALA* 3.7 14.6 - - + -
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Residues in contact with LEU 521 (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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319B VAL* 3.8 22.4 - - + -
320B GLY* 4.8 8.5 - - - +
483B PHE* 4.4 15.9 - - + +
484B GLU 5.1 6.5 - - - +
491C LEU* 3.6 14.5 - - + +
519C PRO* 3.3 1.0 - - - +
520C VAL* 1.3 78.1 - - + +
522C GLY* 1.3 59.4 + - - +
525C PHE* 3.4 10.2 + - - +
587C ALA* 3.8 18.2 - - + -
590C ALA* 3.7 26.9 - - + -
591C PHE* 3.3 41.4 - - + -
594C MET* 4.1 11.0 - - + -
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Residues in contact with GLY 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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483B PHE* 4.4 7.5 - - - -
491C LEU* 3.3 26.1 - - - +
492C LEU* 4.7 3.1 - - - +
494C TRP* 4.2 20.1 + - - -
519C PRO 2.9 8.7 + - - -
521C LEU* 1.3 79.0 - - - +
523C GLN* 1.3 62.4 + - - +
525C PHE 3.7 5.0 + - - -
526C LYS* 3.8 12.5 + - - +
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Residues in contact with GLN 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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517C MET* 5.7 2.5 - - + +
518C ALA* 3.6 29.3 - - + +
519C PRO 2.8 17.9 + - - +
520C VAL* 4.0 7.4 - - - +
521C LEU 3.5 0.2 - - - -
522C GLY* 1.3 74.5 - - - +
524C LEU* 1.3 61.9 + - - +
525C PHE 3.4 0.7 + - - -
526C LYS* 3.4 22.3 - - - +
527C LEU* 3.3 26.1 - - + +
544C PHE* 4.0 15.9 - - + -
547C THR* 3.8 34.5 + - - +
548C LEU* 4.9 7.1 - - + +
380F ARG* 5.0 6.5 - - - +
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Residues in contact with LEU 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C VAL 2.9 18.6 + - - +
523C GLN* 1.3 76.9 - - - +
525C PHE* 1.3 57.6 - - - +
526C LYS 3.4 0.2 - - - -
527C LEU* 3.4 6.1 + - + +
528C TYR* 2.8 26.2 + - - +
540C PHE* 3.6 24.0 - - + -
544C PHE* 3.8 26.0 - - + -
584C PHE* 3.6 20.2 - - + +
587C ALA* 3.8 29.4 - - + -
588C ILE* 3.9 17.7 - - + +
591C PHE* 3.7 27.8 - - + -
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Residues in contact with PHE 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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488C GLU* 3.8 33.4 - - + -
491C LEU* 3.7 30.5 - - + +
492C LEU* 3.6 43.7 - - + -
521C LEU 3.4 18.0 + - - +
522C GLY 4.0 5.2 - - - +
523C GLN 3.2 1.6 - - - -
524C LEU* 1.3 79.8 - - - +
526C LYS* 1.3 56.2 + - - +
528C TYR* 3.2 33.3 + + - +
529C ARG* 2.7 38.6 + - + +
591C PHE* 4.0 5.8 - + + -
596C LEU* 4.4 10.5 - - + -
612C VAL 5.5 1.3 - - - -
614C ARG* 4.7 9.4 - - + -
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Residues in contact with LYS 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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492C LEU* 4.0 19.0 - - + +
522C GLY 3.8 7.3 + - - +
523C GLN* 3.4 29.7 + - - +
525C PHE* 1.3 78.3 - - - +
527C LEU* 1.3 72.7 + - + +
529C ARG* 3.7 7.0 - - - -
530C GLU* 3.4 59.5 + - + +
547C THR* 5.9 1.6 - - - +
375F GLY* 3.3 33.0 - - - +
376F GLU* 4.5 7.4 - - - +
377F LYS 5.5 0.9 - - - +
380F ARG* 5.5 4.5 - - - +
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Residues in contact with LEU 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 GLN* 3.3 32.8 - - + +
524C LEU* 3.4 9.5 + - + +
525C PHE 3.3 0.4 - - - -
526C LYS* 1.3 91.5 - - + +
528C TYR* 1.3 64.6 + - - +
529C ARG 3.6 0.2 + - - -
530C GLU* 3.9 6.8 + - + +
531C ALA* 3.5 17.3 + - - +
540C PHE* 3.4 26.1 - - + +
543C ALA* 3.7 39.3 - - + +
544C PHE* 4.4 8.3 - - + +
547C THR* 3.9 17.3 - - + -
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Residues in contact with TYR 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 LEU 2.8 15.7 + - - +
525C PHE* 3.3 38.8 - + - +
527C LEU* 1.3 78.1 - - - +
529C ARG* 1.3 60.5 + - - +
531C ALA* 3.5 10.4 + - - +
535C ILE* 5.0 7.2 - - + -
540C PHE* 3.6 13.8 - + + -
591C PHE* 4.6 8.1 - + + -
596C LEU* 2.5 40.7 + - + +
597C ILE* 3.8 22.9 - - + -
610C LYS* 2.9 48.8 + - + +
611C CYS 3.3 3.1 + - - -
612C VAL* 3.1 37.8 + - + -
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Residues in contact with ARG 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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240B LEU* 3.6 33.9 - - + +
241B ASP* 3.1 36.2 + - - +
249B GLN* 3.4 18.5 + - - -
492C LEU* 3.7 24.1 - - - +
525C PHE* 2.7 29.0 + - + +
526C LYS* 3.7 6.5 + - - +
527C LEU 3.3 0.2 - - - -
528C TYR* 1.3 77.1 - - - +
530C GLU* 1.3 64.2 + - + +
531C ALA 3.2 3.9 + - - -
610C LYS* 3.6 8.6 + - - +
614C ARG* 3.7 23.7 - - + +
371F GLU* 3.4 30.1 + - - +
372F LEU 5.6 0.8 + - - -
374F ILE* 3.6 22.9 - - - +
375F GLY* 4.9 3.2 - - - +
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Residues in contact with GLU 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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236B ALA* 4.8 13.3 + - - +
237B SER* 5.1 2.3 + - - -
240B LEU* 3.8 32.1 - - + +
249B GLN* 4.7 0.8 + - - -
526C LYS* 3.4 44.3 + - - +
527C LEU* 3.9 8.0 + - + +
528C TYR 3.4 0.4 - - - -
529C ARG* 1.3 82.9 + - + +
531C ALA* 1.3 58.2 + - - +
372F LEU 5.1 5.5 - - - +
375F GLY* 5.9 1.4 - - - -
376F GLU* 5.2 7.1 - - - +
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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