Contacts of the strand formed by residues 572 - 579 (chain B) in PDB entry 5FS9
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 572 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568B LEU* 3.3 4.7 - - - -
569B ARG 3.0 31.2 + - - +
570B ASP* 3.1 12.5 + - + +
571B LYS* 1.3 79.4 - - - +
573B VAL* 1.3 73.3 + - - +
574B VAL* 3.4 6.9 + - + +
595B GLY* 3.5 45.8 - - - +
596B GLU 4.1 4.0 - - - +
597B GLN* 4.0 17.0 - - + +
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Residues in contact with VAL 573 (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 LEU* 5.8 0.2 - - - +
566B PHE* 4.0 19.5 - - + -
567B TYR 3.5 5.8 - - - +
568B LEU* 3.9 16.6 - - + -
571B LYS 5.7 0.2 - - - +
572B VAL* 1.3 82.1 - - - +
574B VAL* 1.3 61.7 + - - +
575B GLY 3.5 22.7 - - - +
576B ILE* 3.6 24.2 - - + -
591B ILE* 4.1 13.1 - - + +
592B ILE* 3.9 23.1 - - + +
596B GLU 4.5 2.8 + - - -
598B HIS* 4.1 22.2 - - + +
601B LEU* 4.1 5.8 - - + -
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Residues in contact with VAL 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LEU* 4.1 23.3 - - + +
496B GLY* 3.4 6.4 - - - -
497B LEU* 2.8 52.2 + - + +
502B LEU* 4.2 6.1 - - + -
567B TYR 2.9 17.1 + - - +
568B LEU 4.1 1.1 - - - -
569B ARG* 3.9 47.8 - - + +
572B VAL* 4.0 10.5 - - + +
573B VAL* 1.3 79.2 - - - +
575B GLY* 1.3 56.0 + - - +
592B ILE* 4.0 7.8 - - - +
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Residues in contact with GLY 575 (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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495B ILE 3.2 11.7 - - - -
497B LEU 3.3 15.5 - - - -
567B TYR* 2.6 40.6 + - - -
573B VAL* 3.5 3.2 - - - +
574B VAL* 1.3 82.8 - - - +
576B ILE* 1.3 67.4 + - - +
592B ILE* 3.9 2.9 - - - -
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Residues in contact with ILE 576 (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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494B ALA* 3.1 4.9 - - - +
495B ILE* 2.8 43.4 + - + +
498B VAL* 4.0 2.0 - - - +
564B VAL* 3.8 19.7 - - + -
565B ILE 3.3 9.0 - - - +
566B PHE* 4.0 13.5 - - + -
567B TYR* 4.3 0.4 - - - -
573B VAL* 3.6 19.3 - - + -
575B GLY* 1.3 80.5 - - - +
577B VAL* 1.3 69.6 + - - +
578B LEU* 4.0 13.2 - - + +
585B MET* 5.7 0.6 - - + +
588B ALA* 3.7 38.1 - - + +
591B ILE* 4.2 17.9 - - + -
592B ILE* 4.2 3.3 - - + +
608B PHE* 4.3 1.8 - - + -
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Residues in contact with VAL 577 (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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310B PHE* 6.2 1.3 - - + -
343B ILE* 4.9 1.6 - - + -
344B LEU* 3.9 23.6 - - + -
348B LEU* 4.8 4.7 - - + -
492B TYR* 4.9 7.6 - - + -
493B GLU 3.2 8.1 - - - +
494B ALA* 4.0 10.1 - - + -
498B VAL* 3.6 17.0 - - + -
563B GLY 4.0 0.2 - - - +
564B VAL* 3.4 3.3 - - - -
565B ILE* 2.8 49.0 + - + +
567B TYR* 3.6 31.6 - - + +
576B ILE* 1.3 77.8 - - - +
578B LEU* 1.3 72.8 + - - +
579B TRP 4.7 0.4 - - - +
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Residues in contact with LEU 578 (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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492B TYR* 3.3 6.1 - - - +
493B GLU* 2.8 55.1 + - + +
563B GLY 3.6 2.0 - - - +
564B VAL* 3.7 26.7 - - + -
576B ILE* 4.0 7.4 - - + -
577B VAL* 1.3 77.3 - - - +
579B TRP* 1.3 60.4 + - - +
580B ASN 4.0 0.7 + - - -
581B ILE* 3.9 32.0 + - + +
584B ARG* 4.4 14.1 - - + -
585B MET* 4.5 11.7 - - + -
588B ALA* 4.8 3.4 - - + -
608B PHE* 3.6 40.4 - - + -
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Residues in contact with TRP 579 (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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347B TYR* 4.4 7.4 - + - -
348B LEU* 3.4 33.7 - - + +
351B TRP* 3.5 56.0 - + - -
490B VAL* 4.0 3.0 - - + +
491B GLY 3.7 11.2 - - - -
492B TYR* 3.7 19.3 - + + +
508B PHE* 3.8 25.4 - + + -
560B TYR 3.7 11.4 - - - -
561B GLY* 3.6 26.0 - - - -
562B LYS* 3.1 34.9 - - - +
563B GLY 2.8 33.3 + - - +
565B ILE* 5.8 0.4 - - + -
577B VAL* 5.3 0.4 - - + -
578B LEU* 1.3 71.5 - - - +
580B ASN* 1.3 80.4 + - - +
581B ILE* 3.2 1.2 + - - +
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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