Contacts of the strand formed by residues 504 - 511 (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 VAL 504 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500B ASN* 3.2 4.5 - - - +
501B LEU 2.7 39.8 + - - +
502B LYS* 3.0 10.3 - - + +
503B ASP* 1.3 83.7 - - + +
505B SER* 1.3 65.4 + - - +
506B PHE* 3.3 26.5 - - + -
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Residues in contact with SER 505 (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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485B THR* 4.6 7.4 - - - -
498B GLU* 2.8 36.1 + - - +
499B LYS 3.5 5.2 - - - -
500B ASN* 3.9 17.4 - - - +
503B ASP 4.4 0.2 + - - -
504B VAL* 1.3 83.0 - - - +
506B PHE* 1.3 62.8 + - - +
507B ARG 4.2 0.3 + - - -
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Residues in contact with PHE 506 (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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459B MET* 6.5 0.9 - - + -
498B GLU* 2.8 16.2 - - - +
499B LYS* 2.9 23.7 + - + +
501B LEU* 3.7 27.6 - - + -
502B LYS* 5.9 0.4 - - + -
504B VAL* 3.3 40.8 - - + -
505B SER* 1.3 73.8 - - - +
507B ARG* 1.3 68.0 + - - +
508B LEU* 3.1 1.9 + - - +
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Residues in contact with ARG 507 (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* 5.2 3.1 - - - +
459B MET* 4.5 13.3 - - - +
494B TYR* 3.0 34.2 + - - -
496B PHE* 3.5 46.6 - - + -
497B PHE 4.2 2.0 - - - +
498B GLU* 3.4 19.5 + - - +
505B SER 4.2 0.2 + - - -
506B PHE* 1.3 72.9 - - - +
508B LEU* 1.3 61.3 + - - +
509B GLY* 3.7 17.9 - - - +
510B SER* 4.6 4.5 - - - -
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Residues in contact with LEU 508 (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* 4.1 4.7 - - - +
459B MET* 3.8 27.0 - - + +
461B MET* 4.8 2.0 - - + -
466B TYR* 2.9 33.0 + - + -
469B GLU* 3.6 36.1 - - + +
470B LEU* 5.5 0.2 - - + -
473B ALA* 4.2 2.5 - - + -
484B TYR* 3.5 33.9 - - + -
497B PHE* 2.9 36.4 + - + +
499B LYS* 4.2 18.6 - - + +
506B PHE 3.1 2.5 + - - +
507B ARG* 1.3 74.1 - - - +
509B GLY* 1.3 57.5 + - - +
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Residues in contact with GLY 509 (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* 3.2 15.0 - - - -
466B TYR* 3.9 4.9 - - - -
496B PHE* 3.3 2.8 - - - +
497B PHE* 3.0 43.8 + - - +
507B ARG* 3.5 8.2 - - - +
508B LEU* 1.3 82.4 - - - +
510B SER* 1.3 63.8 + - - -
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Residues in contact with SER 510 (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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447B VAL* 4.9 3.6 - - - +
455B GLU* 3.8 9.9 + - - +
494B TYR* 2.8 36.6 + - - -
495B PHE 3.3 10.1 - - - -
496B PHE* 3.6 6.5 - - - +
497B PHE* 4.1 1.8 - - - -
507B ARG* 4.6 5.0 - - - -
509B GLY* 1.3 76.4 - - - -
511B PHE* 1.3 76.8 + - - +
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Residues in contact with PHE 511 (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* 4.9 2.0 - + - -
434B ILE* 3.4 32.8 - - + -
446B THR 5.0 4.7 - - - +
447B VAL* 3.4 34.1 - - + -
451B GLU* 6.1 0.4 - - - +
474B LEU* 4.7 8.5 - - + -
494B TYR* 3.9 4.9 - - - -
495B PHE* 2.9 74.5 + + + +
497B PHE* 4.5 14.4 - + - -
510B SER* 1.3 87.8 - - - +
512B ASN* 1.3 68.5 + - - +
513B LEU* 3.8 24.0 - - + -
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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