Contacts of the strand formed by residues 449 - 454 (chain B) in PDB entry 4K9N
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 449 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421B GLN* 3.5 27.6 - - + +
422B VAL 3.0 13.1 + - - +
423B ILE* 3.3 12.1 - - + -
424B ALA 2.8 26.5 + - - +
447B PRO 4.4 2.0 - - - +
448B THR* 1.3 77.0 - - - +
450B PHE* 1.3 64.4 + - - +
451B VAL* 4.2 20.2 - - + -
507B LEU* 5.3 3.8 - - + -
510B ALA* 3.7 45.5 - - + +
511B LEU* 4.0 17.9 - - + +
517B VAL* 3.4 13.0 - - + +
519B ILE* 4.5 5.8 - - + -
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Residues in contact with PHE 450 (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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407B LEU* 3.5 42.8 - - + -
410B ALA* 4.4 1.1 - - + -
411B ILE* 3.7 18.6 - - + -
424B ALA* 3.6 14.8 - - + +
426B ILE* 4.4 1.3 - - + -
438B LEU* 3.7 25.8 - - + -
441B ALA* 4.4 2.9 - - + -
448B THR* 3.5 39.7 - - + -
449B ILE* 1.3 71.4 - - - +
451B VAL* 1.3 61.1 + - - +
452B ILE* 3.9 8.3 - - + -
492B VAL* 5.0 1.6 - - + -
516B PRO* 4.4 12.8 - - + -
517B VAL 2.8 23.0 + - - +
518B LEU* 3.2 17.9 - - + +
519B ILE* 2.8 28.8 + - - +
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Residues in contact with VAL 451 (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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358B VAL* 4.6 10.5 - - + -
362B LEU* 4.8 4.3 - - + -
423B ILE* 3.9 25.4 - - + -
424B ALA 2.7 13.1 + - - +
425B VAL* 3.5 9.6 - - + +
426B ILE* 2.9 27.9 + - - +
449B ILE* 4.2 9.6 - - + -
450B PHE* 1.3 74.6 - - - +
452B ILE* 1.3 63.0 + - - +
453B MET* 3.7 16.8 + - - -
503B LEU* 5.7 2.2 - - + -
507B LEU* 4.7 9.0 - - + -
519B ILE* 3.6 15.5 - - + -
521B VAL* 3.7 24.7 - - + -
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Residues in contact with ILE 452 (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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407B LEU* 5.3 3.4 - - + -
426B ILE* 3.2 20.4 - - + +
427B GLY 4.5 0.7 - - - +
428B ASP* 4.0 21.5 - - + -
431B ALA* 4.1 18.6 - - + -
450B PHE* 4.5 9.2 - - + -
451B VAL* 1.3 77.9 - - - +
453B MET* 1.3 62.5 + - - +
454B ASN* 3.3 4.4 + - + +
483B PHE* 4.0 29.2 - - + -
518B LEU* 3.8 38.8 - - + -
519B ILE 2.8 12.0 + - - +
520B GLU* 3.9 6.0 - - + -
521B VAL* 2.8 33.3 + - - +
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Residues in contact with MET 453 (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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355B PRO* 3.9 36.6 - - + -
358B VAL* 3.9 28.5 - - + -
359B PHE* 4.4 12.6 - - + -
376B SER* 3.9 18.6 - - - +
379B THR* 4.8 1.1 - - + -
425B VAL* 3.7 23.8 - - + -
426B ILE 2.8 15.9 + - - +
427B GLY* 3.7 3.0 - - - -
428B ASP* 3.1 24.6 + - - +
451B VAL* 4.3 8.5 - - - +
452B ILE* 1.3 69.6 - - - +
454B ASN* 1.3 60.1 + - - +
455B ASN* 3.5 3.3 + - - +
521B VAL* 3.9 4.3 - - - -
523B THR* 3.9 24.8 + - + +
601B MG 4.2 2.1 - - - -
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Residues in contact with ASN 454 (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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352B ARG* 2.8 24.9 + - - -
428B ASP* 3.3 19.1 - - + +
452B ILE* 3.3 1.7 + - + +
453B MET* 1.3 69.6 - - - +
455B ASN* 1.3 57.2 + - - +
456B GLY* 3.1 18.4 + - - -
478B VAL 5.6 0.3 - - - +
481B ILE* 4.0 7.7 + - - +
483B PHE* 3.7 13.2 - - + -
520B GLU* 2.9 37.0 + - + +
521B VAL 2.8 18.2 + - - +
522B SER* 4.8 2.2 - - - +
523B THR* 3.0 12.5 + - - -
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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