Contacts of the strand formed by residues 449 - 454 (chain X) in PDB entry 3F6B
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421X GLN* 3.6 28.9 - - + +
422X VAL 3.0 11.2 + - - +
423X ILE* 3.4 12.0 - - + -
424X ALA 2.8 25.8 + - - -
447X PRO 4.3 2.5 - - - +
448X THR* 1.3 79.5 - - - +
450X PHE* 1.3 63.8 + - - +
451X VAL* 4.1 20.1 + - + -
507X LEU* 5.1 4.9 - - + -
510X ALA* 3.8 42.6 - - + +
511X LEU* 3.9 20.9 - - + -
515X GLY 5.6 0.9 - - - +
517X VAL* 3.3 12.3 - - + +
519X ILE* 4.5 6.7 - - + -
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Residues in contact with PHE 450 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407X LEU* 3.6 44.4 - - + -
410X ALA* 4.5 0.7 - - + -
411X ILE* 3.8 18.6 - - + -
424X ALA* 3.6 7.4 - - + -
426X ILE* 4.4 9.6 - - + -
438X LEU* 3.8 24.2 - - + -
441X ALA* 4.3 3.4 - - + -
448X THR* 3.6 40.8 - - + -
449X ILE* 1.3 73.9 - - - +
451X VAL* 1.3 61.2 + - - +
452X ILE* 3.9 7.5 + - + -
492X VAL* 4.8 2.0 - - + -
516X PRO* 4.3 12.6 - - + -
517X VAL 2.8 22.4 + - - +
518X LEU* 3.3 17.5 - - + +
519X ILE* 2.8 27.7 + - - +
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Residues in contact with VAL 451 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358X VAL* 4.4 10.8 - - + -
362X LEU* 4.7 5.2 - - + -
423X ILE* 3.9 25.8 - - + -
424X ALA 2.7 12.9 + - - +
425X VAL* 3.5 9.9 - - + -
426X ILE 2.9 26.9 + - - +
449X ILE* 4.1 10.5 - - + -
450X PHE* 1.3 76.4 - - - +
452X ILE* 1.3 62.2 + - - +
453X MET* 3.7 17.2 + - - +
503X LEU* 5.4 2.2 - - + -
507X LEU* 4.7 8.5 - - + -
519X ILE* 3.6 13.7 - - + -
521X VAL* 3.7 25.1 - - + -
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Residues in contact with ILE 452 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407X LEU* 5.1 3.8 - - + -
426X ILE* 3.2 23.1 - - + +
427X GLY 4.3 0.7 - - - -
428X ASP* 3.9 24.0 - - + -
431X ALA* 4.1 18.4 - - + -
435X ILE* 6.3 0.4 - - + -
450X PHE* 4.5 10.3 - - + -
451X VAL* 1.3 76.2 - - - +
453X MET* 1.3 60.0 + - - +
454X ASN* 3.3 4.0 + - + +
483X PHE* 4.0 28.0 - - + -
518X LEU* 3.8 40.2 - - + -
519X ILE 2.8 11.8 + - - +
520X GLU* 4.3 5.6 - - - -
521X VAL* 2.8 33.6 + - - +
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Residues in contact with MET 453 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355X PRO* 4.0 35.2 - - + -
358X VAL* 3.9 26.0 - - + -
359X PHE* 4.4 12.3 - - + -
376X SER* 3.7 21.8 - - - +
379X THR* 4.6 1.8 - - + +
425X VAL* 3.6 26.7 - - + -
426X ILE 2.8 15.0 + - - +
427X GLY* 3.7 3.9 - - - -
428X ASP* 3.0 24.2 + - - +
451X VAL* 4.3 7.9 - - - +
452X ILE* 1.3 67.7 - - - +
454X ASN* 1.3 59.9 + - - +
455X ASN* 3.5 5.2 + - - +
521X VAL* 4.0 4.9 - - - -
523X THR* 3.9 23.3 + - + +
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Residues in contact with ASN 454 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352X ARG* 2.9 26.0 + - - -
428X ASP* 3.0 29.0 - - + +
452X ILE* 3.3 1.5 + - + +
453X MET* 1.3 71.2 - - - +
455X ASN* 1.3 56.6 + - - +
456X GLY* 3.1 9.4 + - - -
481X ILE 4.2 6.5 + - - -
483X PHE* 4.0 11.7 - - + -
520X GLU* 2.9 37.0 + - + +
521X VAL 2.8 19.5 + - - +
522X SER* 3.8 1.7 - - - -
523X THR* 3.0 13.3 + - - -
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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