Contacts of the strand formed by residues 410 - 415 (chain B) in PDB entry 4KXY
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 ILE 410 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B VAL* 4.0 21.1 - - + +
373B ALA* 3.7 39.0 - - + +
374B VAL* 3.8 18.8 - - + +
377B ALA* 4.1 3.4 - - + -
384B PRO* 4.2 6.5 - - + +
386B CYS* 5.6 1.1 - - - -
400B ILE* 5.7 0.9 - - + -
403B ALA* 4.2 8.7 - - + -
408B SER* 3.4 17.5 - - - +
409B ASN* 1.3 78.9 - - - +
411B ASN* 1.3 65.7 + - - +
412B LEU* 3.9 20.6 - - + +
466B GLY 3.2 5.5 + - - +
467B ILE* 3.8 17.6 - - + -
468B CYS 3.1 23.7 + - - +
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Residues in contact with ASN 411 (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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383B VAL* 3.8 15.0 - - - +
384B PRO 3.0 25.0 + - - +
385B PHE* 3.3 45.7 - - + -
386B CYS* 2.8 28.8 + - - +
409B ASN 4.8 3.3 + - - -
410B ILE* 1.3 77.7 - - - +
412B LEU* 1.3 62.1 + - - +
461B ALA* 3.2 24.2 + - + +
462B ALA 5.2 0.2 + - - -
464B THR 4.7 1.4 - - - +
466B GLY 5.2 0.2 - - - +
468B CYS* 3.3 22.0 - - + +
470B ILE* 5.9 1.3 - - + -
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Residues in contact with LEU 412 (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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370B VAL* 4.1 10.8 - - + -
385B PHE* 6.0 0.9 - - - -
386B CYS* 3.2 8.5 - - + +
393B PHE* 3.6 35.7 - - + -
400B ILE* 4.0 23.8 - - + -
410B ILE* 3.9 24.0 - - + +
411B ASN* 1.3 80.5 - - - +
413B CYS* 1.3 59.2 + - - +
414B GLY 4.1 0.7 - - - -
437B PHE* 3.9 13.0 - - + -
467B ILE* 3.6 24.2 - - + -
468B CYS 2.8 19.0 + - - +
469B PHE* 3.2 9.5 - - + -
470B ILE* 2.9 26.5 + - - +
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Residues in contact with CYS 413 (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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321B TYR* 3.4 53.6 + - + +
346B THR* 6.2 1.1 - - - -
385B PHE* 5.6 1.1 - - + -
386B CYS 2.9 8.4 + - - +
387B SER* 3.2 24.8 - - - -
388B THR 3.3 5.2 + - - +
393B PHE* 3.4 3.5 - - - -
411B ASN 4.3 0.2 - - - -
412B LEU* 1.3 72.5 - - - +
414B GLY* 1.3 59.1 + - - +
415B SER* 4.1 1.5 + - - -
470B ILE* 3.3 14.6 - - + +
472B THR* 3.5 36.6 - - - -
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Residues in contact with GLY 414 (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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388B THR 3.2 6.7 - - - -
390B ALA* 3.6 25.4 - - - +
393B PHE* 3.8 6.7 - - - -
413B CYS* 1.3 71.9 - - - +
415B SER* 1.3 63.2 + - - -
469B PHE* 3.6 8.0 - - - -
470B ILE 3.0 7.5 + - - -
471B ARG* 3.6 6.4 - - - +
472B THR* 2.9 26.3 + - - +
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Residues in contact with SER 415 (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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318B ARG* 4.3 10.1 - - - -
346B THR* 3.6 22.7 - - - +
388B THR 2.9 17.3 + - - -
389B PHE* 3.7 5.4 - - - -
390B ALA* 2.8 21.9 + - - +
413B CYS* 4.1 2.1 - - - -
414B GLY* 1.3 72.5 - - - -
416B HIS* 1.3 95.8 + - - +
417B CYS 3.2 3.4 + - - -
472B THR* 3.1 21.7 + - - -
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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