Contacts of the strand formed by residues 442 - 448 (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 ALA 442 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435B THR* 4.4 1.6 - - + -
436B LEU 3.3 9.4 - - - +
437B THR* 4.1 8.7 - - + +
441B SER* 1.3 80.6 - - - +
443B TRP* 1.3 61.7 + - - +
515B LYS* 3.6 2.8 - - - +
516B VAL* 2.6 52.7 + - + +
519B PRO* 4.0 15.7 - - + +
522B VAL* 4.2 19.7 - - + -
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Residues in contact with TRP 443 (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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418B HIS* 4.6 2.2 - + - -
434B ILE 4.1 0.2 - - - +
435B THR* 3.2 3.1 - - - +
436B LEU* 2.8 61.1 + - + +
438B ASP* 4.3 12.1 - - - -
441B SER* 3.6 34.1 - - - -
442B ALA* 1.3 73.9 - - - +
444B THR* 1.3 63.3 + - - +
488B PHE* 3.5 25.5 - + + -
490B LYS* 3.3 53.7 + - + +
493B CAS 4.1 13.1 - - - +
513B LEU* 3.8 22.5 - - + +
514B GLU 3.4 4.5 - - - +
515B LYS* 3.5 45.8 - - + +
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Residues in contact with THR 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B VAL* 3.7 20.2 - - + -
434B ILE 3.5 6.3 - - - +
435B THR* 3.1 25.4 + - - +
443B TRP* 1.3 72.7 - - - +
445B GLY* 1.3 62.0 + - - +
446B THR* 5.6 0.4 - - - +
513B LEU* 3.6 4.7 - - - -
514B GLU* 2.7 44.2 + - - +
516B VAL* 3.1 22.8 - - - +
522B VAL* 5.4 1.6 - - - +
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Residues in contact with GLY 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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433B VAL* 3.4 6.6 - - - +
434B ILE* 3.0 34.5 + - - +
444B THR* 1.3 77.8 - - - +
446B THR* 1.3 66.3 + - - -
511B PHE* 6.3 0.2 - - - -
512B ASN 3.5 19.1 - - - -
513B LEU* 3.3 6.6 - - - +
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Residues in contact with THR 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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432B PHE 3.7 13.2 - - - +
433B VAL* 4.1 18.5 - - + +
434B ILE 4.9 0.2 - - - +
444B THR* 5.6 0.5 - - - +
445B GLY* 1.3 75.3 + - - -
447B VAL* 1.3 75.6 + - - +
448B SER* 4.1 4.3 - - - +
451B GLU* 3.6 8.3 - - - +
511B PHE* 5.0 5.0 - - - +
512B ASN 4.5 3.6 + - - +
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B GLY* 3.1 4.5 - - - -
432B PHE* 2.9 62.8 + - + -
434B ILE* 4.7 3.4 - - + -
446B THR* 1.3 81.2 - - - +
448B SER* 1.3 61.9 + - - +
451B GLU* 3.4 13.2 - - + +
452B ILE* 3.6 25.6 - - + +
470B LEU* 6.0 0.4 - - + -
510B SER 5.5 3.1 - - - +
511B PHE* 3.4 40.6 - - + -
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Residues in contact with SER 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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430B SER 5.3 0.2 - - - -
431B GLY* 4.0 4.7 - - - -
446B THR* 4.1 5.4 - - - +
447B VAL* 1.3 72.1 - - - +
449B GLU* 1.3 62.8 + - - +
450B SER* 3.2 8.7 + - - -
451B GLU* 2.9 40.2 + - - +
452B ILE* 3.1 26.2 + - - +
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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