Contacts of the helix formed by residues 565 - 575 (chain B) in PDB entry 3D0G
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 PRO 565 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B LEU* 6.4 2.0 - - + -
95B LEU* 5.8 4.3 - - + -
209B VAL* 3.7 33.0 - - + -
212B VAL* 4.3 18.4 - - + -
215B TYR* 4.6 1.6 - - + +
396B ALA 5.5 0.2 - - - +
564B GLU* 1.3 93.8 - - + +
566B TRP* 1.3 66.3 + - + +
567B THR* 3.0 17.4 + - - +
568B LEU* 3.1 10.8 + - + +
569B ALA* 2.9 19.2 + - - +
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Residues in contact with TRP 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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206B ASP 4.8 1.6 - - - -
207B TYR* 2.7 35.3 + + - +
208B GLU 5.5 0.2 - - - -
209B VAL* 4.3 11.0 - - + +
217B TYR* 3.5 34.3 - + - -
222B LEU* 5.7 0.2 - - + -
396B ALA* 3.8 18.8 + - - +
397B ASN* 3.2 33.9 - - + +
400B PHE* 3.5 13.6 - + + -
521B TYR* 3.6 31.0 - + - -
564B GLU 3.4 2.8 + - - -
565B PRO* 1.3 72.1 - - - +
567B THR* 1.3 81.0 + - + +
569B ALA* 4.0 8.3 - - - -
570B LEU* 2.7 45.6 + - + +
577B LYS 3.9 7.4 - - - -
578B ASN* 3.4 24.9 - - - -
579B MET* 5.3 2.5 - - + -
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Residues in contact with THR 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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209B VAL* 5.0 1.3 - - + -
215B TYR* 2.9 40.1 + - - +
216B ASP 4.7 1.3 - - - +
217B TYR* 4.4 12.1 - - + -
565B PRO* 3.6 10.7 - - - +
566B TRP* 1.3 107.9 - - + +
568B LEU* 1.3 61.7 + - - -
570B LEU* 3.9 0.6 - - - +
571B GLU* 3.1 25.5 + - - +
576B ALA 3.5 6.9 - - - +
577B LYS* 3.5 26.3 - - + +
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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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215B TYR* 3.5 48.4 - - + +
564B GLU* 2.8 30.5 - - - +
565B PRO* 3.1 14.1 + - + +
567B THR* 1.3 78.9 + - - +
569B ALA* 1.3 60.6 + - - +
570B LEU 3.2 0.2 - - - -
571B GLU* 3.0 5.4 + - - +
572B ASN* 2.9 67.7 + - - +
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Residues in contact with ALA 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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396B ALA* 4.3 7.4 - - + -
400B PHE* 4.3 12.3 - - + -
557B MET* 4.5 9.2 - - + +
560B LEU* 5.2 9.9 - - + -
564B GLU* 4.3 15.0 - - + -
565B PRO 2.9 15.5 + - - +
566B TRP* 3.6 9.9 - - - +
568B LEU* 1.3 80.5 - - - +
570B LEU* 1.3 59.4 + - - +
572B ASN* 3.4 14.2 + - - +
573B VAL* 3.0 23.5 + - - +
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Residues in contact with LEU 570 (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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400B PHE* 3.7 10.3 - - + -
521B TYR* 4.0 27.6 - - + -
524B GLN* 4.2 9.2 - - + +
525B PHE* 3.5 31.4 - - + -
566B TRP* 2.7 30.1 + - + +
567B THR 3.9 2.9 - - - +
569B ALA* 1.3 70.2 - - - +
571B GLU* 1.3 60.4 + - - +
573B VAL* 3.0 6.5 + - - +
574B VAL* 2.9 46.3 + - + +
576B ALA 3.7 8.5 - - - +
577B LYS 4.5 0.2 - - - +
578B ASN* 3.4 33.4 - - - +
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Residues in contact with GLU 571 (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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215B TYR* 3.1 27.2 + - + -
567B THR 3.1 15.5 + - - +
568B LEU* 3.0 13.8 + - - +
570B LEU* 1.3 75.6 - - - +
572B ASN* 1.3 62.7 + - - +
575B GLY* 2.7 32.3 + - - -
576B ALA* 3.2 33.4 + - - +
577B LYS* 3.6 28.2 + - - +
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Residues in contact with ASN 572 (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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553B LYS* 4.7 5.9 - - - +
557B MET* 5.9 2.7 - - + -
560B LEU* 5.0 11.8 - - + +
564B GLU* 4.9 0.6 + - - -
568B LEU* 2.9 54.0 + - - +
569B ALA* 3.7 8.9 - - - +
570B LEU 3.2 0.2 - - - -
571B GLU* 1.3 83.0 - - - +
573B VAL* 1.3 60.2 + - + +
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Residues in contact with VAL 573 (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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525B PHE* 3.9 24.7 - - + -
528B ALA* 3.6 4.6 - - + +
529B LEU* 4.8 11.7 - - + -
553B LYS* 3.2 43.9 + - + +
554B LEU* 5.4 3.4 - - + -
557B MET* 3.5 39.9 - - + -
569B ALA 3.0 19.5 - - - +
570B LEU 3.0 4.7 + - - +
572B ASN* 1.3 81.2 - - - +
574B VAL* 1.3 67.8 + - + +
575B GLY 3.7 0.2 - - - -
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Residues in contact with VAL 574 (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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524B GLN* 3.6 32.1 - - + +
525B PHE* 3.6 31.4 - - + +
527B GLU* 5.5 5.2 - - - +
528B ALA* 3.8 13.4 - - + +
531B GLN* 5.7 0.9 - - - +
570B LEU* 2.9 28.8 + - + +
573B VAL* 1.3 81.8 - - + +
575B GLY* 1.3 61.3 + - - +
576B ALA* 3.9 21.4 - - + +
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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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571B GLU* 2.7 32.2 + - - -
573B VAL 3.7 0.4 - - - -
574B VAL* 1.3 72.9 - - - +
576B ALA* 1.3 61.5 + - - +
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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