Contacts of the strand formed by residues 556 - 560 (chain A) in PDB entry 2DFS
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 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A THR* 5.3 3.5 - - - +
539A GLU* 2.6 45.0 + - - +
549A ILE* 4.1 15.0 - - + -
550A ILE 3.5 4.9 - - - -
551A LYS* 3.9 29.8 - - + +
555A ASP* 1.3 91.0 + - - +
557A VAL* 1.3 65.2 + - - +
558A GLU 4.3 0.2 - - - -
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Residues in contact with VAL 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A PHE* 6.2 1.6 - - + -
443A THR* 3.9 23.6 - - + +
447A ASN* 3.8 22.4 - - - +
455A ASN* 4.3 9.9 - - - +
549A ILE* 3.4 4.5 - - - -
550A ILE 3.0 29.6 + - - -
552A HIS* 3.9 20.2 - - + -
555A ASP* 4.2 6.3 - - + +
556A LYS* 1.3 80.6 - - - +
558A GLU* 1.4 61.5 + - - +
559A TYR* 3.4 41.1 - - + +
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Residues in contact with GLU 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A GLU 5.5 0.9 - - - +
447A ASN* 3.1 28.7 + - - +
541A PRO* 3.5 28.9 - - + +
544A SER* 5.3 1.2 - - - -
547A ALA* 3.5 12.9 - - + +
548A PHE 3.5 6.1 - - - +
549A ILE* 3.8 25.7 - - + +
556A LYS 4.3 0.4 - - - -
557A VAL* 1.4 70.5 - - - +
559A TYR* 1.3 62.4 + - - +
560A GLN* 2.9 27.8 + - - +
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Residues in contact with TYR 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A ASN* 3.5 17.7 - - + +
448A SER 3.7 13.5 - - - -
451A GLN* 4.0 4.5 - - + -
452A PHE* 3.5 41.7 - + + -
455A ASN* 3.0 22.0 + - - +
547A ALA* 3.3 4.3 - - - +
548A PHE* 2.8 67.6 + + + +
550A ILE* 4.0 8.5 - - + -
552A HIS* 2.9 30.8 + - - -
557A VAL* 3.4 33.2 - - + -
558A GLU* 1.3 72.6 - - - +
560A GLN* 1.3 63.1 + - - +
561A CYS 3.8 0.3 + - - -
564A PHE* 4.4 4.7 - - + -
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Residues in contact with GLN 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A ILE* 4.1 36.0 - - + +
447A ASN 2.9 17.9 + - - +
448A SER* 4.4 2.9 - - - -
544A SER* 5.0 2.9 + - - -
546A LYS* 3.9 5.1 - - - +
547A ALA* 3.5 17.3 - - - +
558A GLU* 2.9 39.9 + - - +
559A TYR* 1.3 72.2 - - - +
561A CYS* 1.3 63.8 + - - +
562A GLU* 3.3 12.6 + - + +
564A PHE* 3.2 17.6 - - - -
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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