Contacts of the strand formed by residues 449 - 457 (chain B) in PDB entry 1FO4
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 VAL 449 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440B VAL* 4.4 1.3 - - + -
441B LEU 4.0 0.4 - - - -
442B PHE* 3.8 10.8 - - + -
443B GLN* 4.9 0.9 + - - -
448B GLN* 1.3 70.7 - - - +
450B LYS* 1.3 61.2 + - - +
451B GLU 3.7 21.5 - - - +
452B LEU* 3.9 19.3 - - + -
473B GLN* 3.5 19.3 - - + +
474B LEU* 4.0 6.3 - - + -
475B SER* 2.6 32.9 + - - -
476B LYS 2.7 16.4 + - - +
478B TRP* 3.7 33.0 - - + +
482B LEU* 4.0 15.3 - - + -
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Residues in contact with LYS 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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413B ARG* 6.1 0.4 - - - +
441B LEU* 2.6 42.7 + - + +
442B PHE 4.1 8.7 - - - +
443B GLN* 3.4 34.2 + - - +
444B PRO* 5.9 1.1 - - + -
448B GLN 3.3 1.2 + - - -
449B VAL* 1.3 75.0 - - - +
451B GLU* 1.3 71.8 + - + +
474B LEU* 3.3 18.9 - - - +
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Residues in contact with GLU 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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413B ARG* 4.0 7.1 + - - -
439B ARG* 3.0 36.7 + - - +
440B VAL* 3.3 7.9 - - - +
441B LEU* 2.8 55.3 + - + +
449B VAL* 3.7 2.1 - - - +
450B LYS* 1.3 93.8 + - + +
452B LEU* 1.3 63.2 + - - +
474B LEU* 3.9 3.4 - - - -
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Residues in contact with LEU 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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439B ARG* 3.4 16.6 - - - +
440B VAL* 3.9 19.1 - - + -
449B VAL* 3.9 12.1 - - + -
451B GLU* 1.3 75.3 - - - +
453B ALA* 1.3 61.4 + - - +
454B LEU* 4.2 12.1 - - + -
467B LEU* 5.8 1.7 - - - +
470B THR* 3.1 48.3 + - + +
473B GLN* 4.1 27.8 - - + -
474B LEU* 3.9 6.5 - - + +
478B TRP* 4.1 17.9 - - + -
482B LEU* 5.4 0.4 - - + -
486B VAL* 5.0 8.1 - - + -
516B PHE* 5.0 0.9 - - + -
519B PHE* 4.1 11.9 - - + -
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Residues in contact with ALA 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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366B MET 5.2 0.9 - - - +
367B ALA* 3.8 30.2 - - - +
437B GLY 3.8 1.0 - - - +
438B MET* 3.2 4.7 - - - -
439B ARG* 2.8 51.7 + - + +
452B LEU* 1.3 74.8 - - - +
454B LEU* 1.3 64.0 + - - +
455B CYS* 4.0 5.6 - - - -
465B SER* 5.2 4.3 - - - +
467B LEU* 6.5 0.7 - - - -
470B THR* 4.3 0.9 - - - -
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Residues in contact with LEU 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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437B GLY 3.8 2.9 - - - -
438B MET* 3.6 25.6 - - + -
452B LEU* 4.2 7.4 - - + -
453B ALA* 1.3 79.7 - - - +
455B CYS* 1.3 63.0 + - - +
456B TYR* 3.8 20.8 - - + +
465B SER* 3.6 2.6 + - - -
466B ALA* 3.0 27.7 + - + +
469B THR* 5.2 1.3 - - + -
470B THR* 3.5 28.0 - - + +
486B VAL* 4.1 13.5 - - + -
490B LEU* 4.4 13.9 - - + -
516B PHE* 3.6 37.0 - - + -
519B PHE* 3.9 10.8 - - + -
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Residues in contact with CYS 455 (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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363B PRO* 3.5 23.7 - - + +
366B MET* 3.5 38.6 - - - -
367B ALA* 3.6 19.7 - - - -
436B CYS* 3.1 6.4 - - - +
437B GLY 2.9 37.8 + - - +
453B ALA* 4.6 3.6 - - - -
454B LEU* 1.3 78.4 - - - +
456B TYR* 1.3 61.4 + - - +
463B THR* 4.8 0.4 - - + -
464B ILE 3.1 9.0 - - - +
465B SER* 3.8 13.2 - - - -
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Residues in contact with TYR 456 (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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363B PRO* 4.2 4.9 - - - -
434B VAL* 4.0 17.0 - - + -
435B THR 3.3 3.6 - - - +
436B CYS* 3.8 14.6 - - + -
438B MET* 3.0 26.7 - - + +
454B LEU* 3.8 27.5 - - + +
455B CYS* 1.3 76.6 - - - +
457B GLY* 1.3 63.4 + - - +
459B MET* 4.3 13.9 + - + -
462B ARG 4.3 0.9 - - - +
463B THR* 3.6 4.2 - - - +
464B ILE* 2.8 42.4 + - + +
466B ALA* 4.7 2.0 - - + -
490B LEU* 3.6 17.8 - - + +
494B LEU* 3.8 24.7 - - + -
512B THR* 2.8 48.2 + - + -
515B PHE* 4.6 1.6 - - + -
516B PHE* 4.2 0.3 - - - +
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Residues in contact with GLY 457 (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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357B PRO 3.2 12.8 - - - -
358B ILE* 4.7 0.4 - - - -
359B SER 4.6 0.4 - - - -
363B PRO* 4.0 7.3 - - - +
434B VAL* 3.6 7.3 - - - +
435B THR* 2.7 46.0 + - - +
456B TYR* 1.3 74.6 - - - +
458B GLY* 1.3 63.2 + - - -
459B MET* 3.3 3.2 + - - +
462B ARG 5.1 0.4 - - - -
463B THR* 4.8 3.1 - - - -
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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