Contacts of the strand formed by residues 435 - 441 (chain F) in PDB entry 1K9V
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 GLY 435 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425F GLU* 3.2 10.9 + - - +
426F VAL 2.8 31.5 + - - -
433F PRO 3.6 0.4 + - - -
434F ASN* 1.3 76.8 - - - +
436F TYR* 1.3 69.5 + - - -
437F TYR* 3.4 10.2 - - - -
485F ILE* 3.4 7.6 - - - -
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Residues in contact with TYR 436 (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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423F TRP* 3.6 30.4 - - + -
424F ASN* 3.2 27.8 - - - -
425F GLU* 3.7 36.0 + - + +
435F GLY* 1.3 74.4 - - - -
437F TYR* 1.3 64.0 + - - +
485F ILE* 3.4 23.8 - - - +
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Residues in contact with TYR 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F TRP* 3.1 9.5 - - - -
424F ASN 3.0 26.8 + - - -
426F VAL* 3.5 22.4 - - + -
428F PHE* 3.5 11.0 - + - -
433F PRO* 2.6 31.3 + - - +
435F GLY 3.4 16.8 - - - -
436F TYR* 1.3 78.4 - - - +
438F TYR* 1.3 61.0 + - - +
439F PHE* 3.3 9.9 - - + -
477F PHE* 3.2 48.5 - + + -
479F PRO* 5.2 0.2 - - + -
482F SER* 3.2 23.3 - - - +
485F ILE* 3.2 43.3 + - + +
486F GLY* 4.4 1.3 - - - -
489F LEU* 4.1 9.0 - - + +
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Residues in contact with TYR 438 (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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421F MET* 3.4 28.3 - - + +
422F GLY* 3.5 33.4 - - - -
423F TRP* 3.7 25.7 - + + -
437F TYR* 1.3 73.1 - - - +
439F PHE* 1.3 58.0 + - - +
440F VAL* 3.3 25.1 - - + +
477F PHE* 3.6 1.0 - - - +
478F HIS* 3.0 30.7 + + - +
481F LYS* 3.6 51.1 - - + +
482F SER* 3.0 9.2 + - - +
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Residues in contact with PHE 439 (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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420F HIS* 3.5 22.9 - - + +
421F MET* 3.3 1.9 - - - -
422F GLY 2.9 30.9 + - - +
424F ASN* 3.6 32.3 - - + -
426F VAL* 3.5 14.8 - - + -
437F TYR 3.3 22.0 - - - -
438F TYR* 1.3 75.0 - - - +
440F VAL* 1.3 72.4 + - - +
441F HIS* 3.8 18.8 - + + -
456F THR* 3.3 30.1 - - + -
463F PHE* 4.1 4.5 - + - -
465F SER* 3.6 20.0 - - - -
476F GLN* 4.3 4.0 - - + -
477F PHE* 3.9 26.2 - + + +
478F HIS* 5.0 0.2 - - - -
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Residues in contact with VAL 440 (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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351F VAL* 5.8 6.6 - - + +
419F PRO* 5.2 8.3 - - + -
420F HIS 3.2 5.2 - - - +
421F MET* 4.2 19.3 - - + +
438F TYR* 3.3 33.2 + - + +
439F PHE* 1.3 82.2 - - - +
441F HIS* 1.3 63.9 + - - +
476F GLN 5.2 0.8 + - - -
478F HIS* 4.2 19.4 + - + +
1001F ACY 3.4 21.8 + - - +
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Residues in contact with HIS 441 (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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413F LEU* 3.7 18.6 - - + +
419F PRO* 4.0 3.2 - - - +
420F HIS* 2.7 71.7 + + - +
439F PHE* 3.8 17.9 - + + -
440F VAL* 1.3 77.1 - - - +
442F THR* 1.3 59.8 + - - +
443F TYR 2.7 25.9 + - - +
463F PHE* 3.4 32.6 - + - -
476F GLN* 3.7 13.6 - - + +
1001F ACY 3.7 22.4 - - + +
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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