Contacts of the strand formed by residues 562 - 569 (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 LYS 562 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B PHE* 3.4 4.3 - - - +
509B ALA* 2.9 35.6 + - - +
510B LYS 3.2 21.3 - - - +
511B ALA* 4.2 2.9 - - + -
512B THR* 4.5 7.9 - - - +
515B ASP* 3.4 33.6 + - - +
561B GLY* 1.3 79.0 - - - +
563B GLY* 1.3 60.2 + - - +
579B TRP* 3.1 30.2 - - - +
580B ASN* 3.7 9.0 - - + +
581B ILE* 4.1 8.7 - - + +
608B PHE 5.0 1.4 + - - -
609B ASN* 3.5 34.1 + - - +
610B ILE* 3.6 21.2 - - + +
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Residues in contact with GLY 563 (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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507B VAL 3.2 13.0 - - - -
508B PHE* 4.0 10.5 - - - -
562B LYS* 1.3 77.0 - - - +
564B VAL* 1.3 61.6 + - - -
565B ILE* 5.5 0.8 - - - +
577B VAL 4.0 0.2 - - - +
578B LEU* 3.6 2.1 - - - -
579B TRP* 2.8 37.7 + - - +
581B ILE* 3.6 13.3 - - - +
610B ILE* 4.5 3.4 - - - -
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Residues in contact with VAL 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B VAL 3.9 0.7 - - - +
506B GLY* 3.3 1.7 - - - -
507B VAL* 2.8 41.6 + - + +
508B PHE* 5.1 0.4 - - - -
563B GLY* 1.3 74.6 - - - +
565B ILE* 1.3 67.4 + - - +
566B PHE* 3.8 29.2 - - + -
576B ILE* 3.8 13.2 - - + -
577B VAL 3.4 2.9 - - - -
578B LEU* 3.7 25.1 - - + -
605B ALA* 3.8 30.3 - - + -
608B PHE* 4.1 12.8 - - + -
610B ILE* 4.7 6.1 - - + -
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Residues in contact with ILE 565 (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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344B LEU* 4.7 0.2 - - + -
345B PRO* 3.6 32.1 - - + -
348B LEU* 3.7 26.9 - - + -
504B THR* 4.0 20.0 - - - -
505B VAL 3.4 6.7 - - - +
506B GLY* 4.1 9.4 - - - -
508B PHE* 4.2 11.7 - - + -
563B GLY 5.9 0.4 - - - +
564B VAL* 1.3 80.2 - - - +
566B PHE* 1.3 62.3 + - - +
567B TYR* 3.5 27.8 - - + +
576B ILE* 3.3 7.8 - - - +
577B VAL* 2.8 49.9 + - + +
579B TRP* 5.8 1.1 - - + -
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Residues in contact with PHE 566 (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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503B PRO 3.9 0.2 - - - +
504B THR* 3.1 8.1 - - - -
505B VAL 2.8 45.5 + - - +
507B VAL* 4.2 6.5 - - + -
564B VAL* 3.8 36.6 - - + -
565B ILE* 1.3 74.1 - - - +
567B TYR* 1.3 61.0 + - - +
568B LEU* 4.2 3.3 - - + +
573B VAL* 4.0 22.0 - - + -
575B GLY 3.7 2.9 - - - -
576B ILE* 4.0 20.6 - - + -
591B ILE* 4.7 0.4 - - + -
601B LEU* 3.7 48.7 - - + -
604B VAL* 3.7 33.2 - - + -
605B ALA* 4.2 4.3 - - - -
608B PHE* 4.3 8.1 - + - -
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Residues in contact with TYR 567 (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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343B ILE 2.7 26.7 + - - -
344B LEU* 3.9 1.2 - - - +
345B PRO* 3.7 14.9 - - - +
497B LEU 3.5 18.6 - - - +
498B VAL* 3.6 8.5 - - + -
499B ASP 3.3 39.7 - - - -
500B SER* 4.3 0.4 - - - -
502B LEU* 4.1 8.7 - - + -
503B PRO 3.5 2.5 - - - -
504B THR* 3.3 19.3 - - + -
565B ILE* 3.5 24.5 - - + +
566B PHE* 1.3 76.1 - - - +
568B LEU* 1.3 60.3 + - - +
573B VAL* 3.5 3.6 - - - -
574B VAL* 2.9 27.7 + - - +
575B GLY 2.6 27.3 + - - +
576B ILE 4.2 0.2 - - - -
577B VAL* 3.6 29.6 - - + +
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Residues in contact with LEU 568 (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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502B LEU* 3.7 7.7 - - - +
503B PRO* 2.9 52.9 + - + +
504B THR 4.9 0.2 - - - -
505B VAL* 4.1 24.7 - - + -
566B PHE* 4.3 6.3 - - + +
567B TYR* 1.3 79.5 - - - +
569B ARG* 1.3 61.9 + - - +
570B ASP 4.2 0.2 - - - -
571B LYS* 4.6 21.1 - - + +
572B VAL 3.3 14.4 - - - +
573B VAL* 3.9 20.6 - - + -
574B VAL* 4.1 2.5 - - - -
601B LEU* 4.2 16.4 - - + -
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Residues in contact with ARG 569 (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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446B LYS 4.7 3.8 + - - -
447B LEU* 3.3 30.5 + - - +
497B LEU* 3.5 26.9 - - - +
502B LEU* 4.6 14.8 - - + -
568B LEU* 1.3 74.7 - - - +
570B ASP* 1.3 84.8 + - - +
572B VAL* 3.0 22.3 + - - +
574B VAL* 3.9 26.0 - - + +
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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