Contacts of the helix formed by residues 505 - 510 (chain D) in PDB entry 1Y8Q
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 LYS 505 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456D VAL 4.2 0.4 - - - +
457D HIS* 3.9 7.9 - - - +
458D LYS* 3.4 53.7 + - - +
459D VAL 3.5 5.4 - - - -
460D THR* 4.2 14.6 - - + +
503D HIS* 4.4 11.4 + - + -
504D LYS* 1.3 77.2 - - - +
506D LEU* 1.3 63.0 + - - +
507D SER* 3.1 15.5 - - - +
508D GLU* 3.0 33.7 + - + +
509D PHE* 3.3 9.2 - - - -
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Residues in contact with LEU 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454D LEU* 3.5 32.3 - - + -
456D VAL* 3.5 17.2 + - + +
459D VAL* 2.9 34.1 + - + +
460D THR 4.0 0.7 - - - +
461D VAL* 3.9 25.6 - - + -
464D LEU* 3.8 29.6 - - + -
490D LEU* 5.1 1.3 - - + -
505D LYS* 1.3 68.2 - - - +
507D SER* 1.3 63.8 + - - +
509D PHE* 3.3 10.5 + - - +
511D ILE* 2.9 52.6 + - + +
517D LEU* 6.1 1.1 - - + -
532D ILE* 6.4 0.2 - - + -
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Residues in contact with SER 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456D VAL* 3.2 24.2 + - - -
457D HIS* 3.9 33.6 - - - -
505D LYS* 3.7 13.5 - - - +
506D LEU* 1.3 73.6 - - - +
508D GLU* 1.3 59.5 + - - +
509D PHE 2.9 5.2 - - - -
510D GLY* 2.7 26.7 + - - -
511D ILE 4.0 5.8 - - - -
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Residues in contact with GLU 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D LYS* 3.2 46.1 + - + +
505D LYS* 3.0 43.2 + - + +
507D SER* 1.3 78.3 - - - +
509D PHE* 1.3 58.4 + - - +
510D GLY 3.4 1.1 + - - -
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Residues in contact with PHE 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D VAL* 3.5 22.9 - - + -
482D ILE* 3.8 16.4 - - + +
488D THR* 4.8 13.5 - - + +
489D ILE 5.1 1.3 - - - -
490D LEU* 3.4 31.6 - - + -
501D ASN* 3.5 48.2 - - + -
504D LYS* 3.6 28.7 - - + -
505D LYS 3.3 19.3 - - - -
506D LEU* 3.8 10.3 - - - +
507D SER 2.8 1.4 + - - -
508D GLU* 1.3 79.6 - - - +
510D GLY* 1.3 62.0 + - - +
511D ILE* 3.3 1.3 - - + -
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Residues in contact with GLY 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D ILE* 5.8 2.2 - - - +
507D SER 2.7 13.0 + - - -
508D GLU 3.4 1.4 + - - -
509D PHE* 1.3 79.4 - - - +
511D ILE* 1.3 58.2 + - - +
512D ARG* 3.2 34.8 + - - +
515D SER* 5.0 0.2 - - - -
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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