Contacts of the strand formed by residues 396 - 400 (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 LEU 396 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35I ILE* 4.3 11.7 - - + -
94I ARG* 4.9 2.0 - - - +
351J PHE* 3.7 38.9 - - + -
354J LEU* 5.2 2.0 - - + -
356J PHE* 4.0 33.9 - - + -
395J THR* 1.3 72.4 - - - +
397J VAL* 1.3 66.6 + - - +
398J GLU* 3.3 39.1 - - + +
428J ARG* 4.6 4.7 - - + +
429J CME 3.9 4.3 - - - +
430J LEU* 4.0 5.1 - - + +
464J GLY 3.6 1.0 - - - +
465J ILE* 3.3 7.3 - - - +
466J SER* 3.0 46.1 + - - +
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Residues in contact with VAL 397 (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 10.8 - - + -
395J THR* 4.7 0.2 - - + -
396J LEU* 1.3 76.4 - - - +
398J GLU* 1.3 59.5 + - - +
428J ARG* 3.2 4.9 - - - +
429J CME 3.0 35.9 + - - +
431J THR* 3.9 27.6 - - + -
437J TYR* 4.4 14.4 - - + -
439J PHE* 3.6 27.4 - - + -
463J PHE* 3.7 24.9 - - + -
464J GLY 3.5 4.9 - - - +
465J ILE* 4.6 10.5 - - + -
525J ILE* 5.2 0.4 - - + -
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Residues in contact with GLU 398 (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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20I GLY 4.3 7.6 - - - +
21I LEU* 3.4 24.2 - - + +
31I ARG* 5.0 7.8 + - - +
35I ILE* 4.9 2.6 - - - +
94I ARG* 2.8 43.8 + - - -
396J LEU* 3.3 27.9 - - + +
397J VAL* 1.3 77.6 - - - +
399J MET* 1.3 61.6 + - - +
400J TRP* 4.3 2.4 - - + -
427J GLY 3.6 6.7 - - - +
428J ARG* 4.2 16.9 + - + +
463J PHE* 3.2 6.9 - - - +
464J GLY* 2.7 41.6 + - - +
473J LYS* 5.1 2.9 + - - -
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Residues in contact with MET 399 (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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363J LEU* 3.7 32.8 - - + -
380J VAL* 5.2 2.0 - - + -
398J GLU* 1.3 77.4 - - - +
400J TRP* 1.3 66.7 + - - +
401J GLN* 4.2 13.9 - - - +
426J VAL* 3.6 4.0 - - - +
427J GLY 3.1 26.4 + - - +
439J PHE* 3.6 53.4 - - + -
441J THR* 4.4 9.9 - - + -
461J ILE* 4.0 21.5 - - + -
462J HIS 3.0 15.3 - - - +
463J PHE* 4.4 13.9 - - + -
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Residues in contact with TRP 400 (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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13I ALA* 3.7 20.6 + - - -
16I TYR* 3.7 15.2 + - + +
17I VAL* 3.8 18.0 - - + +
19I ILE* 3.6 24.0 - - + -
20I GLY* 3.6 27.8 - - - -
21I LEU* 3.8 33.0 - - + -
398J GLU 4.3 1.3 - - - -
399J MET* 1.3 84.7 - - - +
401J GLN* 1.3 63.4 + - - +
408J GLU* 5.2 4.9 - - - -
425J GLY 2.9 14.6 - - - +
426J VAL* 4.5 0.9 - - + -
461J ILE* 3.9 1.0 - - - +
462J HIS* 3.0 72.1 + + + +
463J PHE 4.6 0.7 - - - -
464J GLY* 4.2 15.9 - - - -
475J ILE* 4.1 20.0 - - + -
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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