Contacts of the helix formed by residues 581 - 589 (chain C) in PDB entry 1Y9D
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 581 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C LYS* 4.4 1.3 - - - -
272C GLU* 3.5 11.0 - - - +
555C LEU* 6.2 0.2 - - + -
557C LEU* 3.6 46.6 - - + +
558C ASP* 4.4 9.0 - - + +
571C LYS* 5.4 1.3 - - - +
579C LEU 4.3 1.1 - - - +
580C GLN* 1.3 97.7 - - + +
582C LEU* 1.3 66.8 + - - +
583C SER* 3.5 22.2 - - - +
584C THR* 3.2 25.7 + - - +
585C TYR* 3.8 5.4 - - - -
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Residues in contact with LEU 582 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C GLU* 2.8 59.2 + - + +
273C ALA* 4.0 7.4 - - - +
276C GLN* 3.7 21.1 - - + +
345C TRP* 5.0 2.0 - - + -
348C ALA* 4.3 12.3 - - + +
349C ASN* 4.3 12.3 - - - +
352C ASN* 3.4 30.1 - - + +
581C PRO* 1.3 66.9 - - - +
583C SER* 1.3 54.4 + - - +
584C THR 2.7 16.8 + - - -
585C TYR* 2.8 17.2 + - + -
586C LEU* 3.1 29.1 + - + +
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Residues in contact with SER 583 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558C ASP* 2.8 28.7 + - - -
581C PRO* 3.5 11.9 - - - +
582C LEU* 1.3 78.0 - - - +
584C THR* 1.3 63.7 + - - +
586C LEU* 3.7 14.0 - - - +
587C LYS* 3.4 22.9 + - - +
593C ASP* 3.3 30.2 - - - +
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Residues in contact with THR 584 (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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580C GLN* 3.7 31.7 + - + +
581C PRO* 3.2 24.3 + - - +
582C LEU 2.7 1.6 + - - -
583C SER* 1.3 78.7 + - - +
585C TYR* 1.3 69.6 + - + +
586C LEU 3.1 0.7 - - - -
587C LYS* 2.9 24.5 + - - +
588C GLN* 3.1 17.8 + - + +
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Residues in contact with TYR 585 (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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348C ALA* 3.4 28.0 - - + +
351C ALA* 3.4 27.8 + - + -
352C ASN* 3.6 38.6 - - + -
355C ASN* 3.1 30.7 + - + +
580C GLN* 3.6 28.9 - - + +
581C PRO 3.8 7.0 - - - -
582C LEU* 2.8 9.6 + - + +
584C THR* 1.3 75.9 - - + +
586C LEU* 1.3 61.1 + - - +
588C GLN* 3.3 30.1 - - - +
589C PHE* 3.2 27.8 + - + +
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Residues in contact with LEU 586 (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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214C ARG* 5.3 1.6 - - - +
276C GLN* 3.8 26.0 - - - +
345C TRP* 4.5 15.7 - - + -
348C ALA* 4.2 11.9 - - + -
582C LEU* 3.1 29.1 + - + +
583C SER* 3.7 17.0 - - - +
584C THR 3.1 0.2 - - - -
585C TYR* 1.3 75.7 - - - +
587C LYS* 1.3 57.8 + - - +
589C PHE 3.4 1.4 + - - -
590C GLY 2.9 8.5 + - - -
591C LEU* 2.6 68.8 + - + +
592C ASP 3.7 17.9 - - - +
593C ASP* 4.2 7.2 - - + -
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Residues in contact with LYS 587 (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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583C SER 3.4 12.0 + - - +
584C THR* 2.9 12.3 + - - +
586C LEU* 1.3 74.3 - - + +
588C GLN* 1.3 67.3 + - - +
589C PHE 3.0 1.6 - - - -
590C GLY* 2.8 16.9 + - - -
591C LEU 4.1 7.6 + - - +
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Residues in contact with GLN 588 (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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351C ALA* 4.8 2.4 - - - +
584C THR* 3.1 14.0 + - + +
585C TYR* 3.3 39.1 - - - +
587C LYS* 1.3 78.2 - - - +
589C PHE* 1.3 92.1 + - + +
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Residues in contact with PHE 589 (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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344C PRO* 3.3 42.6 - - + +
347C GLN* 3.6 46.2 - - + -
348C ALA* 3.8 11.0 - - + -
351C ALA* 4.3 7.2 - - + -
585C TYR 3.2 26.0 + - - +
586C LEU 3.6 1.6 - - - +
587C LYS 2.8 1.6 + - - -
588C GLN* 1.3 112.1 - - + +
590C GLY* 1.3 60.8 + - - +
591C LEU* 3.6 1.8 - - + -
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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