Contacts of the helix formed by residues 497 - 503 (chain J) in PDB entry 1YKN
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 ASN 497 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314J ASN 5.0 9.0 + - - +
315J TRP* 3.6 22.8 - - + +
495J ILE* 3.4 8.1 - - - +
496J ALA* 1.3 78.8 - - + +
498J PRO* 1.3 73.7 - - - +
499J GLU* 2.8 52.4 + - - +
500J ALA* 2.9 22.0 + - + +
501J VAL 3.3 6.6 + - - -
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Residues in contact with PRO 498 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496J ALA 3.6 7.5 - - - +
497J ASN* 1.3 89.3 - - - +
499J GLU* 1.3 68.2 + - + +
500J ALA 3.2 0.4 - - - -
501J VAL* 3.1 14.9 + - + +
502J GLN* 3.1 26.0 + - - +
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Residues in contact with GLU 499 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315J TRP* 3.9 18.3 - - + -
497J ASN* 2.8 25.7 + - - +
498J PRO* 1.3 76.9 - - + +
500J ALA* 1.3 58.7 + - - +
502J GLN* 3.3 24.0 + - + +
503J GLN* 3.6 7.1 + - - +
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Residues in contact with ALA 500 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I PRO* 3.6 15.8 - - + +
315J TRP* 3.5 47.9 - - + +
495J ILE* 3.5 16.6 - - + -
497J ASN* 2.9 13.2 + - + +
499J GLU* 1.3 73.0 - - - +
501J VAL* 1.4 67.1 + - - +
503J GLN* 3.2 17.6 + - - +
504J LEU* 4.1 1.7 + - - +
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Residues in contact with VAL 501 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479J TYR* 5.8 1.6 - - + -
486J ILE* 4.1 16.4 - - + -
492J VAL* 3.8 31.0 - - + -
493J LYS* 6.0 0.2 - - - -
495J ILE* 4.1 29.4 - - + +
497J ASN 3.3 10.2 + - - +
498J PRO* 3.1 15.1 + - + +
500J ALA* 1.4 75.4 - - - +
502J GLN* 1.4 64.3 + - - +
504J LEU* 3.0 23.3 + - + +
505J ILE* 3.9 13.8 + - + +
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Residues in contact with GLN 502 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498J PRO 3.1 18.3 + - - +
499J GLU* 3.4 13.7 - - - +
500J ALA 3.2 0.6 - - - -
501J VAL* 1.4 79.0 - - - +
503J GLN* 1.3 61.8 + - + +
504J LEU 3.0 2.0 + - - -
505J ILE* 3.3 31.3 + - - +
507J LYS* 3.3 38.6 + - - +
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Residues in contact with GLN 503 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I PRO* 3.0 48.5 + - + +
7I GLU 3.5 9.9 + - - -
8I THR* 3.6 20.4 + - - +
9I PRO* 4.0 8.1 - - + -
315J TRP* 3.3 15.2 - - + +
499J GLU 3.6 7.6 + - - +
500J ALA 3.2 14.6 + - - +
502J GLN* 1.3 79.6 - - + +
504J LEU* 1.3 60.8 + - - +
505J ILE 3.3 1.1 - - - -
523J PHE* 3.7 13.5 - - - -
524J ASP 4.7 7.1 - - - +
526J VAL* 4.0 10.6 - - - +
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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