Contacts of the helix formed by residues 559 - 563 (chain B) in PDB entry 4DN5
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 THR 559 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A PRO* 4.3 0.7 - - - -
371A SER* 3.4 11.4 + - - +
372A PRO 4.7 5.4 - - - +
373A LYS* 6.2 0.2 - - - -
515B ASP* 2.8 20.6 + - - -
517B LYS* 3.1 35.3 + - + +
557B PRO* 5.1 0.5 - - - +
558B GLY* 1.3 77.5 - - - +
560B GLU* 1.3 67.5 + - - +
561B THR* 3.4 23.6 - - + +
562B HIS* 3.2 24.4 + - - +
563B MET* 3.2 16.8 + - - +
594B HIS* 4.5 5.6 - - + -
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Residues in contact with GLU 560 (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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370A PRO* 4.1 14.3 - - + +
371A SER 3.1 15.8 + - - +
372A PRO* 3.9 24.6 - - + +
559B THR* 1.3 71.6 - - - +
561B THR* 1.3 63.0 + - + +
563B MET* 3.1 31.3 + - - +
603B PRO* 4.3 9.4 - - - +
604B LEU* 3.5 34.8 + - + +
605B CYS* 3.3 34.4 - - - +
608B ILE* 3.4 13.4 - - - +
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Residues in contact with THR 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PRO* 5.4 0.2 - - + -
373A LYS* 4.7 14.6 - - + +
559B THR* 3.4 8.8 - - + +
560B GLU* 1.3 76.9 - - + +
562B HIS* 1.3 70.4 + - - +
563B MET 3.4 0.7 + - - +
584B CYS* 3.9 9.0 - - - -
594B HIS* 2.8 32.0 + - + +
595B PRO* 3.9 11.1 - - - +
596B TRP* 3.4 27.4 + - - -
597B THR* 3.7 21.5 - - + -
604B LEU* 3.7 23.6 - - + -
608B ILE* 5.1 0.2 - - - -
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Residues in contact with HIS 562 (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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515B ASP* 5.9 0.9 - - - +
516B VAL 3.3 16.4 - - - +
517B LYS* 3.5 18.4 - - + +
518B ALA 4.9 0.6 + - - -
559B THR* 3.2 18.1 + - - +
560B GLU 3.1 1.2 - - - -
561B THR* 1.3 95.3 + - - +
563B MET* 1.3 64.1 + - - +
564B ALA 3.4 0.7 + - - -
577B VAL* 5.7 0.3 - - - +
580B TRP* 3.3 9.7 - - - -
581B SER* 2.7 54.8 + - - +
584B CYS* 3.6 19.0 - - + -
585B MET* 3.6 17.2 + - - -
588B HIS* 5.2 3.7 + - + +
594B HIS* 3.3 34.5 - + - -
595B PRO* 4.8 1.1 - - + -
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Residues in contact with MET 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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370A PRO* 4.0 18.6 - - + -
557B PRO* 3.9 36.6 - - + -
559B THR 3.2 16.4 + - - +
560B GLU* 3.1 31.3 + - - +
561B THR 3.4 0.7 - - - +
562B HIS* 1.3 75.8 - - - +
564B ALA* 1.3 63.0 + - - +
567B VAL* 4.7 3.6 - - + +
568B VAL* 3.7 39.3 - - + +
577B VAL* 6.2 0.4 - - - -
580B TRP* 3.1 12.4 + - - -
596B TRP* 5.3 0.3 + - - -
605B CYS* 4.6 11.9 - - - -
608B ILE* 3.7 18.5 - - + +
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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