Contacts of the helix formed by residues 486 - 490 (chain A) in PDB entry 5IY8
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 LEU 486 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A PRO* 4.0 14.8 - - + -
370A ASP 4.5 3.0 + - - -
371A PRO* 5.4 9.9 - - + -
484A LEU 3.7 2.8 + - - -
485A ASN* 1.3 88.7 + - - +
487A SER* 1.3 56.2 + - - +
489A THR* 2.9 37.4 - - + +
496A PHE* 3.5 32.3 - - + -
538A VAL* 4.0 16.3 - - + +
539A GLN* 4.6 6.7 - - + -
541A THR* 5.4 2.7 - - + -
673A GLN* 5.3 5.2 - - - +
790B GLN* 3.2 53.2 - - + +
791B GLU* 4.6 6.1 - - + -
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Residues in contact with SER 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 3.6 19.3 - - - +
485A ASN* 2.8 3.1 + - - -
486A LEU* 1.3 74.9 - - - +
488A VAL* 1.3 55.6 + - - +
489A THR* 3.0 10.9 + - - +
490A THR* 3.9 3.5 + - - -
491A PRO* 3.9 11.3 - - - +
535A MET* 3.9 9.7 - - - +
536A GLY 3.4 12.9 + - - +
538A VAL* 4.4 10.8 - - - +
669A TYR* 3.3 26.6 - - - -
673A GLN* 3.3 24.7 + - - +
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Residues in contact with VAL 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 3.6 33.4 - - + +
470A MET* 4.1 11.0 - - + -
472A HIS* 4.5 10.5 - - + +
484A LEU* 4.7 6.3 - - + -
485A ASN* 3.3 26.4 + - + +
487A SER* 1.3 71.6 - - - +
489A THR* 1.3 63.0 + - - +
490A THR 3.4 1.3 - - - -
491A PRO* 3.5 22.3 - - + +
492A TYR* 3.6 38.9 + - + -
521A VAL* 4.9 2.7 - - + -
535A MET* 4.8 6.1 - - + -
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Residues in contact with THR 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A LEU* 5.3 3.1 - - - -
485A ASN 4.0 1.4 + - - -
486A LEU* 2.9 28.5 + - + +
487A SER 3.0 2.4 - - - -
488A VAL* 1.3 79.3 - - - +
490A THR* 1.3 64.6 + - - +
492A TYR 3.7 0.3 + - - -
493A ASN* 3.2 5.9 + - - -
494A ALA* 3.0 51.5 + - - +
496A PHE* 4.6 14.7 - - - -
538A VAL* 3.7 22.9 - - + -
539A GLN* 5.9 2.9 - - + -
2002A MG 4.2 4.7 - - - -
791B GLU* 4.7 11.0 - - + +
282U ASP* 4.7 2.0 - - - +
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Residues in contact with THR 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A SER 3.9 2.2 + - - -
489A THR* 1.3 84.8 - - - +
491A PRO* 1.3 74.2 - - - +
493A ASN* 3.4 17.6 + - - +
534A VAL 4.8 9.4 - - - +
535A MET* 5.5 2.0 - - - -
536A GLY 5.7 1.4 + - - -
538A VAL* 3.9 20.5 - - + +
647A THR* 5.5 8.3 - - + -
282U ASP* 4.3 27.7 + - + +
283U GLU* 5.4 5.4 - - - +
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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