Contacts of the helix formed by residues 449 - 459 (chain B) in PDB entry 1FU1
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 GLU 449 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429B GLU* 3.2 35.2 - - - +
430B SER* 3.8 23.5 + - - +
431B GLY* 3.8 5.4 - - - +
448B SER* 1.3 74.4 - - - +
450B SER* 1.3 61.2 + - - +
452B ILE* 3.5 5.2 + - - +
453B SER* 3.2 23.8 + - - +
463B LYS* 4.0 7.6 + - - +
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Residues in contact with SER 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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448B SER* 3.1 9.5 + - - -
449B GLU* 1.3 76.5 - - - +
451B GLU* 1.3 63.1 + - - +
452B ILE 3.1 1.1 - - - -
453B SER* 2.9 8.1 + - - -
454B GLN* 2.8 31.5 + - - +
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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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446B THR 3.6 7.0 - - - +
447B VAL* 3.4 18.6 - - + +
448B SER* 2.9 44.3 + - - +
450B SER* 1.3 77.7 - - - +
452B ILE* 1.3 56.6 + - - +
454B GLN* 3.3 7.4 + - - +
455B GLU* 2.9 31.4 + - - +
511B PHE* 6.1 0.3 - - - +
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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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428B LEU 3.6 24.5 - - - +
429B GLU* 4.4 9.0 - - - +
431B GLY* 4.4 4.0 - - - +
432B PHE* 3.6 22.9 - - + -
447B VAL* 3.6 14.8 - - + -
448B SER 3.1 14.4 + - - +
449B GLU* 3.6 8.3 - - - +
450B SER 3.1 0.8 - - - -
451B GLU* 1.3 77.3 - - - +
453B SER* 1.3 61.0 + - - +
455B GLU* 4.7 0.9 - - - -
456B ALA* 3.2 22.0 + - - +
463B LYS* 4.4 13.0 - - + +
466B TYR* 3.6 25.6 - - + -
467B VAL* 4.6 11.7 - - + -
470B LEU* 4.0 13.7 - - + -
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Residues in contact with SER 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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449B GLU* 3.2 9.8 + - - +
450B SER* 2.9 10.3 + - - -
452B ILE* 1.3 73.8 - - - +
454B GLN* 1.3 66.7 + - - +
456B ALA* 3.3 3.3 + - - +
457B ASP* 3.1 22.9 + - - +
463B LYS* 2.9 44.2 + - - +
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Residues in contact with GLN 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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450B SER 2.8 15.5 + - - +
451B GLU* 3.5 9.2 - - - +
453B SER* 1.3 77.0 - - - +
455B GLU* 1.3 63.3 + - - +
457B ASP* 3.0 14.7 + - - +
458B ASP* 2.7 54.6 + - - +
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Residues in contact with GLU 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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451B GLU 2.9 17.8 + - - +
452B ILE* 4.0 4.5 - - - +
454B GLN* 1.3 75.3 - - - +
456B ALA* 1.3 62.6 + - - +
458B ASP* 3.1 28.4 + - - +
459B MET* 3.3 20.6 + - - +
466B TYR* 3.1 30.1 - - + +
507B ARG* 5.2 4.0 - - - +
508B LEU 4.1 5.2 - - - +
509B GLY* 3.2 23.2 - - - -
510B SER* 3.8 11.3 + - - +
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Residues in contact with ALA 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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452B ILE 3.2 15.8 + - - +
453B SER* 3.6 8.3 - - - +
454B GLN 3.2 0.8 - - - -
455B GLU* 1.3 80.5 - - - +
457B ASP* 1.3 58.7 + - - +
459B MET* 3.4 3.1 + - - -
460B ALA 3.3 1.4 + - - -
461B MET* 2.8 45.7 + - - +
463B LYS* 4.5 12.1 - - + -
466B TYR* 3.6 30.5 - - + -
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Residues in contact with ASP 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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453B SER 3.1 11.7 + - - +
454B GLN* 3.0 20.1 + - - +
456B ALA* 1.3 72.3 - - - +
458B ASP* 1.3 58.6 + - - +
459B MET 2.9 4.5 - - - -
460B ALA* 2.7 28.8 + - - +
461B MET 4.9 0.9 - - - -
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Residues in contact with ASP 458 (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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454B GLN* 2.7 46.5 + - - +
455B GLU* 3.1 24.1 + - - +
457B ASP* 1.3 76.4 - - - +
459B MET* 1.3 60.8 + - + +
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Residues in contact with MET 459 (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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455B GLU* 3.3 22.6 + - + +
456B ALA* 3.9 4.5 - - - +
457B ASP 2.9 1.0 - - - -
458B ASP* 1.3 81.2 - - + +
460B ALA* 1.3 74.1 + - - +
461B MET* 3.0 41.8 + - + +
466B TYR* 4.0 20.9 - - - -
506B PHE* 6.5 0.7 - - + -
507B ARG 4.5 12.6 - - - +
508B LEU* 3.8 26.9 - - + +
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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