Contacts of the strand formed by residues 511 - 517 (chain B) in PDB entry 3QFR
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 LEU 511 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A LYS* 5.1 10.8 - - - +
286B LEU* 3.7 46.9 - - + +
287B ALA 3.6 2.7 - - - -
288B ALA* 4.4 12.3 - - + +
496B TRP* 4.1 3.3 - - - -
500B LYS* 3.0 24.3 - - - +
509B ARG* 3.7 29.8 + - + +
510B ALA* 1.3 78.1 - - - +
512B VAL* 1.3 58.6 + - - +
513B PRO* 4.2 3.1 - - - +
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Residues in contact with VAL 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 4.0 0.9 - - - -
287B ALA 2.9 33.2 + - - +
289B VAL* 3.4 27.1 - - + -
308B LEU* 4.1 17.0 - - + -
325B VAL* 3.3 34.1 - - + -
496B TRP* 3.8 16.8 - - + -
497B LEU* 4.5 8.3 - - + -
500B LYS* 3.7 13.7 - - + -
511B LEU* 1.3 80.3 - - - +
513B PRO* 1.3 67.2 - - - +
514B MET* 3.0 6.8 + - - +
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Residues in contact with PRO 513 (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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272B TYR* 3.4 36.3 - - + +
284B PRO* 3.9 13.2 - - + -
285B PHE 3.7 7.2 - - - +
286B LEU* 3.2 25.1 - - + -
325B VAL* 3.4 4.2 - - - +
326B TYR* 2.8 41.7 + - + +
496B TRP* 3.7 20.4 - - + -
511B LEU 4.2 1.3 - - - +
512B VAL* 1.3 80.5 - - - +
514B MET* 1.3 58.6 + - - +
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Residues in contact with MET 514 (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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279B PHE* 5.1 0.2 - - - +
284B PRO* 3.2 4.1 - - - +
285B PHE* 2.6 53.8 + - - +
287B ALA* 3.8 10.3 - - + -
308B LEU* 3.9 12.1 - - + -
310B ILE* 3.5 31.9 - - + -
315B ILE* 4.5 4.3 - - + -
323B VAL* 4.3 15.5 - - + -
324B ALA 3.2 14.8 - - - +
325B VAL* 3.6 13.9 - - + -
472B VAL* 4.1 19.5 - - + -
512B VAL 3.5 11.2 - - - +
513B PRO* 1.3 74.4 - - - +
515B PHE* 1.3 73.0 + - - +
516B VAL* 4.4 12.3 - - + -
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Residues in contact with PHE 515 (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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279B PHE 4.4 2.7 - - - +
280B ASP* 3.6 33.0 - - + +
281B ALA* 3.5 31.9 - - + -
284B PRO* 4.2 0.9 - - + -
315B ILE* 5.1 4.9 - - - -
323B VAL* 3.9 0.5 - - - -
324B ALA* 3.0 53.4 + - + +
326B TYR* 3.7 32.1 - + - -
456B ALA* 4.1 13.7 - - + -
458B TYR* 4.5 13.9 - + - -
514B MET* 1.3 92.5 - - - +
516B VAL* 1.3 73.2 + - - +
517B ARG* 5.0 6.7 - - + -
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Residues in contact with VAL 516 (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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279B PHE 5.3 2.5 + - - +
280B ASP* 5.5 3.8 - - - +
315B ILE* 3.9 29.4 - - + +
316B ARG 4.5 3.1 - - - +
317B TYR* 3.8 25.8 - - + -
321B ASP* 4.0 17.0 - - + +
322B HIS 3.4 9.9 - - - +
323B VAL* 4.9 1.8 - - - -
461B ILE* 4.3 15.5 - - + -
472B VAL* 4.7 5.6 - - + -
514B MET* 4.4 13.9 - - + -
515B PHE* 1.3 86.3 - - - +
517B ARG* 1.3 66.6 + - - +
518B LYS* 4.6 2.5 - - + +
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Residues in contact with ARG 517 (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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90B GLN* 3.5 20.0 + - - +
143B TYR* 4.4 22.9 - - - +
144B GLY* 5.6 3.2 - - - +
150B ASP* 3.3 29.5 + - - +
321B ASP* 4.1 0.9 - - - -
322B HIS* 2.9 62.6 + - + +
458B TYR* 4.1 25.7 - - + -
515B PHE* 5.0 7.4 - - + +
516B VAL* 1.3 79.9 - - - +
518B LYS* 1.3 78.9 + - - +
519B SER* 3.6 3.9 + - - +
751B FMN 5.7 5.0 - - - +
752B FAD 6.0 0.4 - - - +
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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