Contacts of the strand formed by residues 482 - 487 (chain B) in PDB entry 5FWP
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 482 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B MET* 3.6 7.5 - - - +
480B GLN* 2.7 33.4 + - - +
481B LYS* 1.3 79.2 + - - +
483B ILE* 1.3 54.4 + - - +
484B TYR* 3.5 15.8 + - - -
532B SER* 3.1 25.8 - - - -
534B VAL* 3.4 26.8 - - - +
542B GLU 5.3 0.3 + - - -
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Residues in contact with ILE 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B LEU* 5.1 9.6 - - + +
472B TYR* 3.6 33.7 - - + -
473B VAL* 4.3 11.7 - - + -
476B MET* 4.1 2.2 - - - -
482B SER* 1.3 73.1 - - - +
484B TYR* 1.3 71.0 + - - +
485B TYR* 3.7 2.8 - - + -
511B VAL* 3.9 14.1 - - + -
513B MET* 6.3 0.4 - - + -
528B PHE* 4.3 17.0 - - + -
531B LYS* 4.0 20.6 - - + -
532B SER 2.6 19.4 + - - +
533B LEU* 3.5 30.7 - - + -
534B VAL* 2.8 27.2 + - - +
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Residues in contact with TYR 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B TYR* 3.1 8.1 + - - -
480B GLN* 3.4 16.5 - - + +
481B LYS 5.9 0.2 + - - -
482B SER* 3.5 24.4 + - - -
483B ILE* 1.3 74.9 - - - +
485B TYR* 1.3 61.7 + - - +
503B VAL* 4.6 4.7 - - + -
508B PHE* 3.4 34.9 - + + -
509B GLU 3.6 12.6 - - - +
510B VAL* 3.2 16.0 - - + -
511B VAL* 2.8 25.3 + - - +
534B VAL* 3.5 17.7 - - + -
536B VAL* 4.4 6.7 - - + -
541B LEU* 3.8 19.7 - - + -
542B GLU 2.6 29.1 + - - -
543B LEU* 3.6 21.9 - - + +
544B PRO* 5.1 0.2 - - - +
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Residues in contact with TYR 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ILE* 3.7 9.2 - - + -
484B TYR* 1.3 76.6 - - - +
486B ILE* 1.3 68.6 + - - +
487B THR* 4.0 14.1 - - + -
510B VAL* 4.0 1.8 - - - +
511B VAL* 3.4 27.1 - - + +
513B MET* 3.8 20.2 - - + -
522B VAL* 3.6 29.9 - - + +
533B LEU* 3.9 21.9 - - + -
534B VAL* 3.0 40.1 + - - -
535B SER* 3.4 27.4 + - - -
536B VAL* 3.1 28.6 + - - +
538B LYS* 5.4 5.2 + - - -
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Residues in contact with ILE 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B TYR* 1.3 79.4 - - - +
487B THR* 1.3 76.0 + - - +
494B VAL* 3.7 19.9 - - + +
497B SER* 3.6 33.7 - - - +
500B VAL* 3.8 11.4 - - + -
510B VAL* 4.1 7.2 - - + -
511B VAL 2.9 5.6 + - - +
512B TYR* 3.6 33.2 - - + -
513B MET 3.0 21.5 + - - +
535B SER* 4.8 2.5 - - - -
536B VAL* 3.6 16.6 - - + -
537B THR* 4.0 11.7 - - + -
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Residues in contact with THR 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B TYR* 4.0 14.1 - - + -
486B ILE* 1.3 81.6 - - - +
488B GLY* 1.3 56.4 + - - +
494B VAL* 3.4 11.8 - - - +
513B MET* 3.1 37.5 - - + -
515B GLU 5.8 0.9 - - - -
518B ASP* 4.9 5.6 - - + -
519B GLU* 2.7 32.2 + - - +
522B VAL* 4.9 6.7 - - + -
535B SER* 5.2 1.9 + - - +
537B THR* 5.0 6.0 + - - +
599B THR* 4.7 3.8 + - - +
601B ASN* 2.7 27.3 + - - +
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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
------------------------------------------------------------
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