Contacts of the helix formed by residues 574 - 579 (chain B) in PDB entry 5DO7
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 GLY 574 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453B PHE* 4.2 10.5 - - - -
570B PHE 2.9 10.2 + - - -
571B TYR* 2.8 22.2 + - - +
572B LEU 2.9 14.4 - - - +
573B ALA* 1.3 70.0 - - - +
575B GLY* 1.3 69.4 + - - +
576B PHE 3.6 1.3 - - - -
577B MET 4.1 0.9 + - - -
578B ILE* 3.6 5.7 + - - +
596B LEU 4.8 0.2 - - - -
597B ARG* 3.6 22.8 - - - +
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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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417A GLN* 4.9 0.7 - - - -
453B PHE* 4.7 0.8 - - - -
573B ALA 3.5 3.0 + - - -
574B GLY* 1.3 73.0 - - - +
576B PHE* 1.3 56.4 + - - +
578B ILE 3.2 0.2 + - - -
579B ASN* 2.8 33.6 + - - -
580B LEU* 3.9 17.6 + - - -
597B ARG* 4.0 11.4 - - - +
600B PHE* 3.9 21.9 - - - -
633B MET* 5.3 2.7 - - - -
634B GLU* 5.1 3.4 - - - -
635B LEU* 5.8 0.9 - - - -
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Residues in contact with PHE 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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417A GLN* 2.9 38.1 + - + +
420A VAL* 5.2 14.5 - - + +
548A PHE 5.3 3.8 - - - -
549A LEU* 3.3 37.2 - - + -
446B MET 4.2 11.9 - - - -
449B ALA* 4.4 8.1 - - + -
450B ALA* 3.9 27.1 - - + -
453B PHE* 3.9 31.4 - + + -
574B GLY 3.6 0.6 - - - -
575B GLY* 1.3 71.5 - - - +
577B MET* 1.3 81.0 + - + +
578B ILE 2.9 4.5 + - - -
600B PHE* 3.8 19.2 - - + -
633B MET* 5.5 1.6 - - - -
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Residues in contact with MET 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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417A GLN 3.6 8.0 - - - +
418A ASP* 4.9 1.0 - - - +
420A VAL* 5.8 1.3 - - + -
421A GLY* 3.5 36.6 - - - +
424A TYR* 3.5 33.2 - - + -
425A GLN* 3.6 6.5 - - - +
549A LEU* 5.5 3.1 - - + -
453B PHE* 3.4 29.8 - - + -
454B MET* 5.4 3.1 - - - -
571B TYR* 3.0 53.2 - - + +
572B LEU* 5.5 5.6 - - + +
574B GLY 4.1 2.6 + - - -
575B GLY 3.4 0.8 + - - -
576B PHE* 1.3 94.7 - - + +
578B ILE* 1.3 61.8 + - + +
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Residues in contact with ILE 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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403A PHE* 4.3 11.7 - - + -
404A VAL* 3.3 46.7 - - + +
417A GLN* 4.6 2.7 - - - -
418A ASP* 2.9 20.6 - - - +
572B LEU* 2.8 42.2 - - + +
573B ALA* 4.5 2.5 - - - +
574B GLY 3.6 7.3 + - - +
575B GLY 3.2 0.2 + - - -
576B PHE 2.9 2.4 + - - -
577B MET* 1.3 81.9 - - - +
579B ASN* 1.3 75.8 + - - +
580B LEU* 3.0 15.6 + - - +
582B SER 4.7 3.0 - - - +
583B LEU* 4.3 17.5 - - + -
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Residues in contact with ASN 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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413A LYS* 3.9 18.6 - - - +
414A GLY* 3.6 10.5 - - - -
417A GLN* 3.5 31.7 - - + +
418A ASP* 2.6 37.0 + - - -
575B GLY 2.8 18.3 + - - -
578B ILE* 1.3 67.2 + - - +
580B LEU* 1.3 52.9 + - - +
581B SER* 2.8 19.6 + - - -
582B SER* 3.4 27.3 + - - -
633B MET* 5.5 0.4 - - - -
634B GLU* 3.5 17.5 - - - +
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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