Contacts of the helix formed by residues 444 - 453 (chain B) in PDB entry 1FVU
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 SER 444 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A TYR* 3.4 22.8 - - - -
409B TYR* 5.7 0.3 - - - -
442B PHE* 3.4 3.1 - - - +
443B GLN* 1.3 83.8 - - - +
445B LYS* 1.3 63.3 + - - +
446B GLU* 3.2 18.0 + - - +
447B GLU* 3.2 24.3 + - - +
448B ALA* 3.4 12.8 + - - +
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Residues in contact with LYS 445 (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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92A TYR* 3.6 30.7 - - + +
444B SER* 1.3 72.9 - - - +
446B GLU* 1.3 75.9 + - - +
448B ALA* 3.0 4.4 + - - +
449B ASP* 2.8 54.3 + - - +
506B ASN* 4.2 7.0 - - + +
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Residues in contact with GLU 446 (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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409B TYR* 3.3 22.5 + - - +
410B GLU* 5.5 2.0 - - - +
444B SER* 3.2 22.4 - - - +
445B LYS* 1.3 89.4 + - - +
447B GLU* 1.3 61.5 + - - +
449B ASP* 3.1 12.8 + - - +
450B PHE* 3.0 19.1 + - - +
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Residues in contact with GLU 447 (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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409B TYR* 3.7 17.4 + - + -
412B HIS* 5.1 0.3 - - - -
414B TYR* 2.6 35.3 + - + +
441B SER 3.0 12.7 - - - +
442B PHE* 4.1 7.2 - - + -
443B GLN* 2.8 32.6 + - - +
444B SER* 3.2 17.1 + - - +
446B GLU* 1.3 79.4 - - - +
448B ALA* 1.3 61.9 + - - +
450B PHE* 3.3 3.1 + - - +
451B VAL* 3.1 28.6 + - - +
522B GLU* 3.2 1.4 - - - +
1001B MG 2.4 23.8 - - - -
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Residues in contact with ALA 448 (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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92A TYR* 4.7 0.4 - - + +
442B PHE* 3.9 23.2 - - + -
444B SER 3.4 10.0 + - - +
445B LYS 3.0 7.3 + - - +
447B GLU* 1.3 75.1 - - - +
449B ASP* 1.3 67.8 + - - +
451B VAL* 3.2 2.6 + - - +
452B ARG* 3.0 24.1 + - - +
506B ASN* 3.2 42.0 - - - +
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Residues in contact with ASP 449 (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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445B LYS* 2.8 46.5 + - - +
446B GLU* 3.3 13.8 - - - +
448B ALA* 1.3 79.5 - - - +
450B PHE* 1.3 60.5 + - - +
452B ARG* 2.9 48.1 + - - +
453B SER* 3.8 5.9 + - - -
506B ASN* 5.3 2.9 - - - +
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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 SER* 3.8 20.0 - - - -
408B SER 3.4 23.3 - - - -
409B TYR* 3.5 47.6 - + + -
414B TYR* 4.0 19.1 - + - -
446B GLU 3.0 12.2 + - - +
447B GLU 3.6 7.2 - - - +
448B ALA 3.1 0.2 - - - -
449B ASP* 1.3 74.3 - - - +
451B VAL* 1.3 71.5 + - + +
453B SER* 2.6 35.8 + - - -
454B LEU* 4.0 20.2 + - + +
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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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414B TYR* 4.0 28.9 - - + -
440B VAL* 4.1 2.5 - - + -
442B PHE* 3.4 31.0 - - + -
447B GLU 3.1 17.4 + - - +
448B ALA 3.2 5.1 + - - +
450B PHE* 1.3 76.9 - - + +
452B ARG* 1.3 58.0 + - - +
454B LEU* 2.8 33.2 + - + +
455B THR* 3.7 8.7 + - + +
464B VAL* 5.8 3.1 - - + -
503B PRO* 6.4 0.4 - - + -
520B VAL* 3.8 33.0 - - + -
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Residues in contact with ARG 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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448B ALA 3.0 12.4 + - - +
449B ASP* 2.9 44.7 + - - +
450B PHE 3.1 0.4 - - - -
451B VAL* 1.3 76.0 - - - +
453B SER* 1.3 59.9 + - - +
454B LEU 3.1 0.4 - - - -
455B THR* 3.0 22.8 + - - +
456B SER 4.5 2.4 + - - -
503B PRO* 3.2 40.5 + - + +
504B THR* 4.1 16.6 + - - +
505B ASN* 6.0 0.4 - - - +
506B ASN* 5.6 5.5 - - - +
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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 ASP 3.8 4.6 + - - -
450B PHE* 2.6 29.8 + - - -
452B ARG* 1.3 79.9 - - - +
454B LEU* 1.3 69.2 + - - +
455B THR 3.5 0.2 - - - -
456B SER* 4.8 7.8 + - - -
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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