Contacts of the strand formed by residues 449 - 454 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421D GLN* 3.5 27.8 - - + +
422D VAL 3.0 12.9 + - - +
423D ILE* 3.4 12.5 - - + -
424D ALA 2.9 25.6 + - - +
447D PRO 3.5 2.0 + - - +
448D THR* 1.3 77.3 - - - +
450D PHE* 1.3 65.5 + - - +
451D VAL* 4.1 20.2 - - + -
507D LEU* 5.3 4.0 - - + -
510D ALA* 3.8 45.8 - - + +
511D LEU* 3.9 16.2 - - + -
515D GLY 5.6 0.7 - - - +
517D VAL* 3.3 12.3 - - + +
519D ILE* 4.5 7.0 - - + -
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Residues in contact with PHE 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407D LEU* 3.6 44.6 - - + -
410D ALA* 4.4 0.9 - - + -
411D ILE* 3.8 18.2 - - + -
424D ALA* 3.7 13.5 - - + +
426D ILE* 4.4 2.0 - - + -
438D LEU* 3.9 22.0 - - + -
441D ALA* 4.3 4.5 - - + -
448D THR* 3.5 41.1 - - + -
449D ILE* 1.3 72.2 - - - +
451D VAL* 1.3 59.0 + - - +
452D ILE* 3.8 7.5 + - + -
492D VAL* 5.0 1.1 - - + -
516D PRO* 4.2 13.5 - - + -
517D VAL 2.7 23.1 + - - +
518D LEU* 3.2 17.4 - - + +
519D ILE* 2.8 32.7 + - - +
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Residues in contact with VAL 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D VAL* 4.7 10.8 - - + -
362D LEU* 4.7 10.5 - - + -
423D ILE* 3.7 28.3 - - + -
424D ALA 2.7 12.5 + - - +
425D VAL* 3.5 10.2 - - + +
426D ILE* 2.9 27.2 + - - +
449D ILE* 4.1 10.5 - - + -
450D PHE* 1.3 73.4 - - - +
452D ILE* 1.3 63.7 + - - +
453D MET* 3.7 15.1 + - - -
503D LEU* 5.6 2.2 - - + -
507D LEU* 4.8 7.9 - - + -
519D ILE* 3.6 9.4 - - + +
521D VAL* 3.9 23.6 - - + -
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Residues in contact with ILE 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407D LEU* 5.3 2.9 - - + -
426D ILE* 3.3 30.1 - - + +
427D GLY 4.4 1.1 - - - +
428D ASP* 4.1 17.5 - - + -
431D ALA* 4.2 12.1 - - + -
450D PHE* 4.6 4.9 - - + -
451D VAL* 1.3 75.8 - - - +
453D MET* 1.3 62.5 + - - +
454D ASN* 3.3 3.0 + - + +
483D PHE* 4.1 31.4 - - + -
518D LEU* 3.8 38.8 - - + -
519D ILE 2.8 14.1 + - - +
520D GLU* 3.9 6.2 - - - -
521D VAL* 2.8 35.0 + - - +
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Residues in contact with MET 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D PRO* 3.9 31.0 - - + -
358D VAL* 4.0 25.4 - - + -
359D PHE* 4.7 9.0 - - + -
376D SER* 4.0 19.3 - - - +
379D THR* 4.8 2.0 - - + -
425D VAL* 3.7 28.0 - - + -
426D ILE 2.8 15.3 + - - +
427D GLY* 3.6 3.2 - - - -
428D ASP* 3.0 25.9 + - - +
451D VAL* 4.4 8.7 - - - +
452D ILE* 1.3 68.3 - - - +
454D ASN* 1.3 61.3 + - - +
455D ASN* 3.6 3.4 + - - +
521D VAL* 3.9 4.9 - - - -
523D THR* 3.8 29.3 + - + +
602D TZD 5.6 0.2 + - - -
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Residues in contact with ASN 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D ARG* 2.9 22.8 + - - -
428D ASP* 3.3 19.0 - - + +
452D ILE* 3.3 2.0 + - + +
453D MET* 1.3 71.8 - - - +
455D ASN* 1.3 56.7 + - - +
456D GLY* 3.0 19.8 + - - -
481D ILE 4.1 6.5 + - - -
483D PHE* 3.8 12.7 - - + -
520D GLU* 2.8 36.6 + - + +
521D VAL 2.8 19.1 + - - +
522D SER* 3.8 2.3 + - - +
523D THR* 3.1 16.5 + - - -
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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