Contacts of the strand formed by residues 474 - 480 (chain B) 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 LEU 474 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLU* 4.2 6.3 - - + +
8A THR* 3.5 36.1 - - + +
9A PRO 4.6 2.9 - - - +
10A SER* 3.9 26.9 - - - -
137A ILE* 5.6 0.2 - - + -
138A HIS* 4.6 7.2 - - + -
311B ARG* 4.1 13.2 - - - +
316B HIS* 4.1 13.2 - - + -
464B GLY* 3.6 2.1 - - - -
465B ILE* 3.0 41.6 + - + +
472B THR 3.8 7.4 - - - +
473B LYS* 1.3 79.5 - - - +
475B ILE* 1.3 70.1 + - - +
476B THR* 4.2 7.0 - - + -
525B ILE* 5.1 0.7 - - + -
527B LEU* 4.6 14.8 - - + -
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Residues in contact with ILE 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER* 3.4 10.6 + - - +
11A GLN 3.3 30.4 + - - +
12A THR 4.5 0.9 - - - +
13A ALA* 4.0 24.2 - - + -
17A VAL* 4.8 0.7 - - + -
21A LEU* 3.8 28.5 - - + -
67A PHE* 4.8 0.2 - - + -
131A PHE* 3.6 42.1 - - + -
138A HIS* 4.9 2.4 + - - -
400B TRP* 4.2 12.3 - - + -
462B HIS* 5.7 0.4 - - + -
463B PHE 3.4 11.2 - - - +
464B GLY* 4.2 4.0 - - - -
473B LYS* 4.1 9.9 - - - +
474B LEU* 1.3 79.8 - - - +
476B THR* 1.3 69.5 + - - +
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Residues in contact with THR 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR* 4.1 18.6 - - + -
9A PRO 2.9 24.0 + - - -
10A SER* 4.4 0.2 - - - -
11A GLN* 3.6 12.8 - - - +
462B HIS* 3.5 4.3 + - - +
463B PHE* 2.9 44.4 + - + +
465B ILE* 4.4 12.6 - - + -
474B LEU* 4.6 4.5 - - + -
475B ILE* 1.3 79.7 - - - +
477B GLN* 1.3 75.0 + - - +
504B LEU* 3.5 11.1 - - - +
523B PHE* 4.5 14.1 - - + -
525B ILE* 5.4 0.4 - - + -
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Residues in contact with GLN 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLN* 3.9 13.4 - - + +
12A THR* 3.1 23.0 + - - +
457B ARG* 2.9 24.0 + - - +
460B HIS* 3.2 13.3 - - + -
461B ILE 3.4 7.2 - - - +
462B HIS* 3.4 19.6 - - + +
476B THR* 1.3 86.6 + - - +
478B LEU* 1.3 61.3 + - - +
479B TYR* 3.2 28.8 + - + +
491B ILE* 4.5 2.0 - - - +
504B LEU* 3.6 29.5 - - - +
523B PHE* 4.7 0.3 - - - -
550B DHB 2.8 25.9 + - - -
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Residues in contact with LEU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B VAL* 3.7 26.5 - - + -
460B HIS* 3.1 27.4 - - - +
461B ILE* 2.8 20.8 + - + +
463B PHE* 3.7 16.6 - - + -
476B THR 4.3 0.2 - - - -
477B GLN* 1.3 74.0 - - - +
479B TYR* 1.3 72.9 + - - +
480B PHE* 3.7 30.3 - - + -
504B LEU 3.8 4.3 - - - -
506B ALA* 3.8 15.0 - - + -
523B PHE* 3.6 40.6 - - + -
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Residues in contact with TYR 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLN* 2.8 26.9 + - - -
457B ARG* 3.1 26.7 + - - -
458B PRO* 4.0 15.5 - - + -
459B ALA 3.9 8.7 - - - +
460B HIS* 3.6 26.0 - + + -
477B GLN* 3.2 24.5 + - + +
478B LEU* 1.3 72.9 - - - +
480B PHE* 1.3 65.0 + - - +
486B ILE* 3.7 24.9 - - + -
492B VAL* 3.4 24.3 - - + +
501B VAL* 5.9 0.9 - - + -
504B LEU* 2.9 33.7 + - + +
505B ILE* 4.4 6.5 - - + -
506B ALA* 2.7 34.4 + - - +
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Residues in contact with PHE 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B ILE* 3.8 21.3 - - + -
380B VAL* 5.0 1.3 - - + -
443B LYS* 3.6 28.9 - - + +
444B PRO* 3.8 35.9 - - + -
459B ALA* 3.5 31.9 + - + +
460B HIS* 4.2 2.9 - - - -
461B ILE* 4.0 11.4 - - + -
478B LEU* 3.7 26.0 - - + -
479B TYR* 1.3 77.9 - - - +
481B GLU* 1.3 69.3 + - - +
482B GLY 3.2 0.7 + - - -
483B ASP* 3.1 24.9 + - + +
486B ILE* 3.6 4.5 - - - +
505B ILE* 4.1 4.0 - - - -
506B ALA 4.1 1.6 - - - -
521B TYR* 3.8 29.4 - + + +
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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