Contacts of the strand formed by residues 460 - 465 (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 HIS 460 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401J GLN* 4.0 7.0 - - - +
402J ALA 4.9 0.5 + - - -
444J PRO* 3.3 23.2 - - - +
445J GLY 5.1 0.2 + - - -
447J TYR* 3.3 33.0 - + - -
457J ARG* 3.4 16.2 + - + -
458J PRO 2.6 23.1 + - - +
459J ALA* 1.3 77.8 - - - +
461J ILE* 1.3 65.1 + - - +
462J HIS* 3.7 12.6 - + - -
477J GLN* 3.2 21.3 - - + +
478J LEU 3.2 13.9 - - - +
479J TYR* 3.7 16.4 - + + -
480J PHE* 4.4 2.0 - - - -
4550J DHB 3.2 4.4 + - - -
4600J FE 2.6 25.4 - - - -
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Residues in contact with ILE 461 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380J VAL* 4.1 20.6 - - + -
399J MET* 4.0 21.1 - - + -
400J TRP 3.9 9.0 - - - +
401J GLN* 4.0 23.1 - - + +
441J THR* 4.7 2.5 - - + -
444J PRO* 4.1 9.2 - - + -
460J HIS* 1.3 83.0 - - - +
462J HIS* 1.3 71.7 + - - +
463J PHE* 3.5 23.7 - - + -
477J GLN* 3.6 1.8 - - - -
478J LEU* 3.0 41.4 + - + -
480J PHE* 3.8 22.4 - - + -
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Residues in contact with HIS 462 (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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12I THR 4.0 3.2 + - - -
13I ALA* 3.7 22.3 + - - -
14I GLY* 4.2 1.8 - - - -
399J MET* 3.0 27.9 - - - +
400J TRP* 3.0 59.1 + + + -
401J GLN* 4.9 4.3 - - - -
408J GLU* 4.7 1.1 + - - -
460J HIS* 3.5 8.3 + + - -
461J ILE* 1.3 74.6 - - - +
463J PHE* 1.3 61.0 - - - +
475J ILE* 5.6 0.6 - - + +
476J THR 3.6 6.4 + - - +
477J GLN* 3.5 24.1 + - + +
4550J DHB 3.5 21.3 - - - -
4600J FE 2.3 30.8 - - - -
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Residues in contact with PHE 463 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380J VAL* 4.1 22.4 - - + -
397J VAL* 3.7 31.2 - - + -
398J GLU 3.2 5.6 - - - -
399J MET* 4.4 7.0 - - + -
400J TRP* 4.2 4.5 - - - -
437J TYR* 3.9 21.5 - + - -
439J PHE* 4.0 7.9 - + - -
461J ILE* 3.5 28.0 - - + -
462J HIS* 1.3 80.6 - - - +
464J GLY* 1.3 58.0 - - - +
465J ILE* 4.0 12.6 - - + -
474J LEU 4.1 0.2 - - - +
475J ILE* 3.2 6.2 - - - +
476J THR* 2.7 46.3 + - + +
478J LEU* 3.6 23.3 - - + -
523J PHE* 4.2 12.6 - + - -
525J ILE* 4.3 11.2 - - + -
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Residues in contact with GLY 464 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21I LEU* 5.7 1.8 - - - -
396J LEU 3.6 1.1 - - - +
397J VAL* 3.5 4.9 - - - +
398J GLU* 2.7 41.0 + - - +
400J TRP* 4.2 6.5 - - - -
463J PHE* 1.3 74.9 - - - +
465J ILE* 1.4 61.2 + - - +
473J LYS* 5.0 6.3 - - - -
474J LEU 3.5 7.2 - - - -
475J ILE* 3.8 13.5 - - - -
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Residues in contact with ILE 465 (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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384J VAL* 4.4 8.1 - - + -
395J THR* 4.3 11.9 - - + -
396J LEU 3.3 9.0 - - - +
397J VAL* 4.6 12.6 - - + -
463J PHE* 4.0 19.7 - - + -
464J GLY* 1.4 78.8 - - - +
466J SER* 1.3 65.3 + - - +
467J GLY 4.3 3.1 - - - +
472J THR 4.1 1.4 - - - +
473J LYS* 3.2 6.4 - - - +
474J LEU* 2.8 50.4 + - + +
476J THR* 4.4 11.0 - - + -
525J ILE* 4.0 35.2 - - + -
527J LEU* 4.1 28.9 - - + -
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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