Contacts of the strand formed by residues 517 - 523 (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 LYS 517 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419B GLU 3.1 5.1 - - - +
420B TRP* 4.1 5.6 - - - +
421B MET 3.0 29.3 + - - +
462B ASP* 2.7 36.6 + - - +
463B VAL* 3.7 26.6 - - + +
465B TRP* 3.7 31.3 - - + +
511B ILE* 4.0 15.9 - - + +
515B ARG* 4.2 18.7 - - + +
516B PHE* 1.3 82.8 + - - +
518B ASN* 1.3 72.6 + - - +
519B PHE* 3.6 5.4 - - - -
310C LEU* 5.0 0.6 - - - +
314C LEU* 3.7 17.4 - - - +
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Residues in contact with ASN 518 (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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416B PHE* 3.6 28.7 - - + -
417B PHE 3.5 6.7 - - - +
418B LYS* 3.4 25.7 - - - +
419B GLU 2.9 19.7 + - - -
420B TRP* 3.4 29.9 + - - +
458B MET* 4.0 14.8 - - + +
459B LEU 4.7 1.4 + - - -
462B ASP* 5.8 0.6 + - - -
463B VAL 4.4 3.5 + - - +
464B VAL* 3.3 13.0 - - + -
465B TRP* 3.0 19.2 + - - +
517B LYS* 1.3 76.3 - - - +
519B PHE* 1.3 62.5 + - - +
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Residues in contact with PHE 519 (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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416B PHE* 3.6 5.8 - - - -
417B PHE* 2.8 53.0 + + + +
419B GLU* 3.7 18.2 - - + -
421B MET* 3.9 29.8 - - + -
426B ALA* 3.6 18.2 - - + -
429B PHE* 3.6 34.1 - + - -
430B CYS* 4.0 6.3 - - - -
439B LEU* 3.6 17.3 - - + -
464B VAL* 4.1 3.1 - - - +
465B TRP* 3.8 15.9 - - + +
517B LYS 3.6 7.6 - - - -
518B ASN* 1.3 81.7 - - - +
520B VAL* 1.3 65.3 + - - +
521B CYS* 3.8 15.9 - - - -
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Residues in contact with VAL 520 (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* 4.5 8.1 - - + -
415B ARG 3.4 16.8 - - - +
416B PHE* 4.0 23.1 - - + +
430B CYS* 4.4 0.2 - - - -
439B LEU* 3.4 9.7 - - - +
440B VAL* 2.9 43.2 + - + +
451B VAL* 3.8 28.9 - - + +
454B LEU* 4.7 2.2 - - + -
455B THR* 4.3 6.3 - - + -
464B VAL* 4.5 9.6 - - + -
465B TRP 3.8 4.4 + - - -
519B PHE* 1.3 80.2 - - - +
521B CYS* 1.3 77.2 + - - +
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Residues in contact with CYS 521 (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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406B TRP* 3.8 22.4 - - + -
414B TYR* 3.4 4.9 - - - -
415B ARG 3.0 27.3 + - - +
417B PHE* 3.4 28.5 - - + -
429B PHE* 4.7 0.7 - - - -
430B CYS* 2.0 53.4 - - + -
433B GLN* 4.9 0.4 - - - -
437B ALA* 5.1 0.9 - - + -
438B HIS 3.2 5.8 - - - +
440B VAL 4.3 0.2 - - - -
519B PHE* 3.8 5.8 - - - -
520B VAL* 1.3 79.5 - - - +
522B GLU* 1.3 64.1 + - - +
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Residues in contact with GLU 522 (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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86A ASP* 4.9 4.9 - - - +
406B TRP* 4.3 0.6 - - - -
412B HIS* 3.0 27.7 - - + -
413B CYS 3.2 9.9 - - - +
414B TYR* 3.2 20.6 + - + -
436B GLY 4.3 0.5 - - - +
437B ALA* 3.2 1.3 - - - -
438B HIS* 2.8 32.7 + - - +
439B LEU 4.6 1.7 - - - +
440B VAL* 3.3 13.4 - - - +
441B SER* 2.8 30.9 + - - -
447B GLU* 3.2 4.9 - - - +
521B CYS* 1.3 79.0 - - - +
523B PHE* 1.3 70.9 - - - +
1001B MG 2.5 23.8 - - - -
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Residues in contact with PHE 523 (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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403B PRO* 3.6 28.3 - - + -
406B TRP* 3.5 30.5 - + - -
411B GLY 4.9 0.2 - - - +
412B HIS* 3.6 1.5 - - - -
413B CYS* 3.0 54.5 + - + -
434B GLN* 3.6 34.1 - - + -
435B THR 4.7 0.4 - - - -
436B GLY 3.9 7.2 - - - +
437B ALA* 3.6 18.8 - - + +
522B GLU* 1.3 82.4 - - - +
524B GLN* 1.3 62.1 + - - +
525B ALA* 3.0 30.1 - - - +
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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