Contacts of the helix formed by residues 3548 - 3564 (chain C) in PDB entry 5Y3R
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 GLY3548 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3545C THR 4.3 0.9 - - - +
3546C SER 3.1 3.9 + - - -
3547C THR* 1.3 85.9 + - - +
3549C HIS* 1.3 69.3 + - - +
3550C LYS 3.7 0.9 - - - -
3551C ASN* 3.2 17.9 + - - -
3552C LYS* 3.1 23.2 + - - +
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Residues in contact with HIS3549 (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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3548C GLY* 1.3 71.0 - - - +
3550C LYS* 1.3 81.5 + - + +
3551C ASN* 4.5 0.2 + - - -
3552C LYS* 3.2 3.3 + - - +
3553C GLU* 3.0 48.5 + - + +
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Residues in contact with LYS3550 (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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3514C VAL* 4.4 15.5 - - + -
3515C GLN* 5.6 7.0 - - - +
3549C HIS* 1.3 86.1 - - + +
3551C ASN* 1.3 69.6 + - - +
3553C GLU* 3.1 10.3 + - - +
3554C PHE* 3.0 69.7 + - + -
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Residues in contact with ASN3551 (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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3510C GLN 4.3 9.8 + - - +
3511C ALA* 3.0 44.2 + - - +
3513C ALA 5.3 0.8 - - - +
3514C VAL* 4.0 17.7 - - - +
3545C THR* 5.3 3.1 - - + -
3547C THR* 4.2 5.7 + - - +
3548C GLY* 3.2 29.2 + - - +
3550C LYS* 1.3 82.6 - - - +
3552C LYS* 1.3 65.6 + - - +
3553C GLU 2.9 0.7 + - - -
3555C VAL* 2.9 33.7 + - + +
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Residues in contact with LYS3552 (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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3540C TYR* 4.7 7.3 + - + +
3544C ASP* 4.2 24.4 + - - -
3545C THR* 3.0 39.2 + - - +
3546C SER* 4.7 8.1 - - - +
3548C GLY 3.1 12.4 + - - +
3549C HIS* 3.7 3.1 - - - +
3551C ASN* 1.3 78.7 - - - +
3553C GLU* 1.3 64.4 + - - +
3555C VAL* 4.9 2.2 - - - -
3556C ALA* 2.7 49.8 + - + +
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Residues in contact with GLU3553 (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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3549C HIS* 3.0 43.7 + - + +
3550C LYS* 3.3 10.3 - - - +
3551C ASN 2.9 1.8 + - - -
3552C LYS* 1.3 93.5 + - - +
3554C PHE* 1.3 72.6 + - + +
3556C ALA* 3.8 2.1 - - - +
3557C ARG* 2.9 26.9 + - - +
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Residues in contact with PHE3554 (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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3514C VAL* 3.3 28.7 - - + -
3550C LYS* 3.0 53.4 + - + -
3553C GLU* 1.3 86.7 - - + +
3555C VAL* 1.3 62.9 + - - +
3557C ARG* 2.9 49.9 + - - +
3558C ILE* 2.9 14.0 + - - +
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Residues in contact with VAL3555 (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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3506C LEU* 4.1 34.1 - - + +
3507C ASP* 5.6 2.2 - - - -
3513C ALA* 3.5 30.5 - - + -
3514C VAL* 3.6 6.1 - - + -
3518C VAL* 3.6 10.3 - - + -
3540C TYR* 6.2 5.4 - - + -
3545C THR* 6.0 2.7 - - - +
3551C ASN* 2.9 19.9 + - + +
3552C LYS* 4.6 1.8 - - - +
3554C PHE* 1.3 74.8 - - - +
3556C ALA* 1.3 58.3 + - - +
3558C ILE* 2.5 32.9 + - + +
3559C LYS* 2.8 11.4 + - + +
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Residues in contact with ALA3556 (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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3540C TYR* 4.1 23.3 - - + +
3552C LYS* 2.7 34.1 + - + +
3553C GLU* 3.8 2.9 - - - +
3555C VAL* 1.3 76.1 - - - +
3557C ARG* 1.3 62.5 + - - +
3559C LYS* 3.1 14.1 - - + +
3560C SER* 2.9 26.1 + - - -
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Residues in contact with ARG3557 (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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3514C VAL* 5.4 1.0 - - - +
3518C VAL* 3.9 11.1 - - - +
3553C GLU 2.9 15.0 + - - +
3554C PHE* 2.9 39.2 + - + +
3556C ALA* 1.3 75.1 - - - +
3558C ILE* 1.3 79.1 + - - +
3560C SER* 3.0 8.2 + - - +
3561C LYS* 2.9 66.4 + - + +
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Residues in contact with ILE3558 (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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3506C LEU* 5.5 3.1 - - + -
3518C VAL* 3.5 26.7 - - + -
3521C ILE* 4.6 12.3 - - + -
3522C THR* 3.5 19.3 - - + -
3525C TYR* 4.6 0.7 - - + -
3554C PHE 2.9 10.6 + - - +
3555C VAL* 2.5 24.6 + - + +
3557C ARG* 1.3 109.3 - - - +
3559C LYS* 1.3 61.9 + - - +
3561C LYS* 3.0 19.2 + - + +
3562C LEU* 2.9 43.7 + - + +
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Residues in contact with LYS3559 (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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3536C SER* 5.9 4.7 - - - +
3537C SER* 5.5 10.1 - - - +
3540C TYR* 3.6 45.6 - - + -
3555C VAL* 2.8 6.5 + - + +
3556C ALA* 3.1 19.1 - - - +
3558C ILE* 1.3 76.4 - - - +
3560C SER* 1.3 59.9 + - - +
3562C LEU* 3.3 13.9 - - + +
3563C ASP* 2.4 79.0 + - - +
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Residues in contact with SER3560 (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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3556C ALA 2.9 12.6 + - - -
3557C ARG* 3.6 10.0 - - - -
3559C LYS* 1.3 78.1 - - - +
3561C LYS* 1.3 64.5 + - - +
3563C ASP* 3.3 22.2 + - - +
3564C GLN* 4.0 4.5 + - - +
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Residues in contact with LYS3561 (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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3518C VAL* 5.5 0.2 - - - +
3522C THR* 3.4 20.7 - - - +
3557C ARG* 2.9 59.6 + - + +
3558C ILE* 3.2 21.8 - - + +
3560C SER* 1.3 78.7 - - - +
3562C LEU* 1.3 61.5 + - + +
3564C GLN* 4.1 11.1 + - - +
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Residues in contact with LEU3562 (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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3521C ILE* 5.1 0.7 - - + -
3525C TYR* 3.1 34.3 - - + +
3533C PHE* 3.3 54.1 - - + -
3536C SER* 5.5 6.7 - - - +
3558C ILE* 2.9 41.8 + - + +
3559C LYS* 3.3 19.3 - - + +
3561C LYS* 1.3 76.2 - - + +
3563C ASP* 1.3 77.9 + - - +
3564C GLN 3.0 11.3 - - - +
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Residues in contact with ASP3563 (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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3533C PHE* 5.7 1.0 - - - +
3537C SER* 5.7 0.7 + - - -
3559C LYS* 2.4 71.3 + - - +
3560C SER* 3.3 12.2 + - - +
3562C LEU* 1.3 82.8 - - - +
3564C GLN* 1.3 53.7 + - - +
3566C GLY* 2.6 30.7 + - - -
3567C VAL* 2.9 11.3 + - - -
3570C ASP* 4.9 5.9 - - - +
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Residues in contact with GLN3564 (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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3533C PHE* 4.8 2.3 - - - -
3560C SER 4.0 5.0 + - - +
3561C LYS 4.5 8.7 - - - +
3562C LEU* 3.0 14.3 - - - +
3563C ASP* 1.3 77.2 - - - +
3565C GLY* 1.3 78.1 + - - +
3566C GLY 3.1 0.7 + - - -
3567C VAL* 3.1 23.5 - - - +
3699C LEU* 4.7 2.6 - - - +
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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