Contacts of the strand formed by residues 547 - 551 (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 ALA 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A TYR* 3.0 20.1 + - - -
540A LYS* 4.4 0.3 - - - +
541A PRO* 3.3 24.2 - - + +
544A SER* 3.8 6.4 + - - +
546A LYS* 1.3 80.5 - - - +
548A PHE* 1.3 63.4 + - - +
558A GLU* 3.5 13.0 - - - +
559A TYR 3.3 14.4 - - - +
560A GLN* 3.5 26.9 - - - +
561A CYS* 4.0 2.7 - - - -
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Residues in contact with PHE 548 (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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452A PHE* 3.9 14.1 - + - -
505A VAL* 4.2 13.9 - - + -
523A TRP* 3.7 30.7 - + - -
527A LEU* 3.9 8.3 - - + -
528A TYR* 4.7 3.8 - - + -
538A PHE* 3.7 28.7 - + + -
539A GLU 3.8 5.2 - - - +
540A LYS* 5.0 0.2 - - - +
541A PRO* 4.2 1.6 - - - -
547A ALA* 1.3 73.6 - - - +
549A ILE* 1.3 63.5 + - - +
550A ILE* 3.8 28.0 - - + -
557A VAL 3.8 0.7 - - - +
558A GLU* 3.5 0.9 - - - -
559A TYR* 2.8 68.1 + + + +
561A CYS* 3.7 20.6 - - - -
564A PHE* 4.2 8.5 - + - -
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Residues in contact with ILE 549 (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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537A LEU 3.7 0.2 - - - +
538A PHE* 3.4 7.1 - - - -
539A GLU* 2.9 65.1 + - + +
540A LYS 4.3 1.1 - - - +
541A PRO* 4.0 21.5 - - + -
548A PHE* 1.3 76.2 - - - +
550A ILE* 1.3 68.4 + - - +
551A LYS* 4.8 0.9 - - + +
556A LYS* 4.1 26.7 - - + -
557A VAL 3.4 9.9 - - - +
558A GLU* 3.8 32.3 - - + +
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Residues in contact with ILE 550 (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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452A PHE* 4.3 8.1 - - + -
495A CYS* 4.2 11.4 - - - -
498A LEU* 3.9 19.7 - - + -
499A ILE* 5.3 5.2 - - + -
505A VAL* 4.7 5.8 - - + -
537A LEU* 3.4 7.0 - - + +
538A PHE* 3.7 29.2 - - + -
548A PHE* 3.8 26.2 - - + -
549A ILE* 1.3 75.6 - - - +
551A LYS* 1.3 70.3 + - - +
552A HIS* 3.4 31.9 + - + +
556A LYS* 3.5 0.7 - - - -
557A VAL* 3.0 29.8 + - - -
559A TYR* 4.0 11.2 - - + -
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Residues in contact with LYS 551 (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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495A CYS* 3.9 13.3 - - - +
536A ALA 5.1 3.1 - - - +
537A LEU* 3.1 43.5 + - + +
539A GLU* 6.6 0.2 - - - -
549A ILE* 4.2 1.6 - - - +
550A ILE* 1.3 70.8 - - - +
552A HIS* 1.3 80.2 + - - +
553A PHE* 2.8 18.2 + - - +
554A ALA 3.2 16.7 + - - -
555A ASP* 3.9 7.6 - - - +
556A LYS* 3.9 33.7 - - + +
689A GLU* 4.9 4.0 + - - -
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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