Contacts of the strand formed by residues 396 - 400 (chain F) 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 396 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E ILE* 4.3 11.2 - - + -
94E ARG* 4.6 3.1 - - - +
351F PHE* 3.5 46.8 - - + -
354F LEU* 5.0 2.9 - - + -
356F PHE* 3.6 37.5 - - + -
395F THR* 1.3 73.1 - - - +
397F VAL* 1.3 60.4 + - - +
398F GLU* 3.6 37.8 - - + +
428F ARG* 4.4 5.4 - - + +
429F CME 3.7 8.5 - - - +
430F LEU* 4.3 0.9 - - + -
464F GLY 3.6 1.6 - - - +
465F ILE* 3.3 6.9 - - - +
466F SER* 2.9 37.9 + - - +
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Residues in contact with VAL 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384F VAL* 4.6 7.2 - - + -
395F THR* 4.2 5.2 - - + +
396F LEU* 1.3 77.2 - - - +
398F GLU* 1.3 61.7 + - - +
428F ARG* 3.2 4.0 - - - +
429F CME 3.0 33.8 + - - +
431F THR* 3.8 28.3 - - + -
437F TYR* 4.4 15.5 - - + -
439F PHE* 3.7 18.5 - - + -
463F PHE* 3.5 39.3 - - + -
464F GLY 3.6 4.9 - - - +
465F ILE* 4.6 7.6 - - + -
525F ILE* 5.2 1.1 - - + -
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Residues in contact with GLU 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLY 4.8 5.9 - - - +
21E LEU* 3.3 24.6 - - + +
31E ARG* 5.4 4.9 + - - -
35E ILE* 4.6 2.8 - - - +
94E ARG* 2.9 41.2 + - - -
396F LEU* 3.6 28.5 - - + +
397F VAL* 1.3 80.2 - - - +
399F MET* 1.3 63.4 + - - +
400F TRP* 4.5 2.9 - - + -
427F GLY 3.6 6.5 - - - +
428F ARG* 4.1 16.3 + - + +
463F PHE* 3.4 4.7 - - - +
464F GLY* 2.9 38.7 + - - +
473F LYS* 5.0 4.0 + - - -
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Residues in contact with MET 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLY 5.3 0.3 - - - +
363F LEU* 3.8 27.6 - - + -
380F VAL* 5.5 1.1 - - + -
398F GLU* 1.3 76.2 - - - +
400F TRP* 1.4 72.7 + - - +
401F GLN* 4.0 16.8 - - - +
426F VAL* 3.6 4.2 - - - +
427F GLY 3.0 31.3 + - - +
439F PHE* 3.5 57.2 - - + -
441F THR* 4.2 9.4 - - + -
461F ILE* 4.0 19.7 - - + -
462F HIS 3.1 13.0 - - - +
463F PHE* 4.4 11.0 - - + -
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Residues in contact with TRP 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ALA* 3.7 18.0 + - - -
16E TYR* 3.7 6.4 + - + +
17E VAL* 3.7 27.9 - - + +
19E ILE* 3.7 24.7 - - + -
20E GLY* 3.6 28.9 - - - -
21E LEU* 3.8 32.1 - - + -
398F GLU 4.5 1.6 - - - -
399F MET* 1.4 84.0 - - - +
401F GLN* 1.3 65.0 + - - +
408F GLU* 5.0 6.1 - - - -
425F GLY 3.1 13.2 - - - +
426F VAL* 4.6 1.1 - - + -
461F ILE* 3.7 1.8 - - - +
462F HIS* 2.9 72.3 + + + +
463F PHE 4.8 0.7 - - - -
464F GLY* 4.4 14.6 - - - -
475F ILE* 4.4 15.3 - - + -
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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