Contacts of the helix formed by residues 557 - 563 (chain B) in PDB entry 6DGD
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 ASP 557 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423B PHE 4.2 7.4 - - - -
424B LEU* 3.6 22.0 - - - +
425B ASN* 3.5 23.5 + - - +
555B LEU* 3.2 15.8 - - - +
556B LEU* 1.3 73.6 + - - +
558B VAL* 1.3 59.0 + - - +
559B ASP 3.6 1.1 - - - -
560B GLY 3.9 2.7 - - - -
561B ALA* 2.9 30.9 + - + +
573B PHE* 3.3 31.6 - - - +
576B LEU* 3.5 20.1 - - - +
807B SO4 5.7 1.0 + - - -
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Residues in contact with VAL 558 (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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555B LEU 3.5 15.9 - - - +
556B LEU 3.5 1.8 - - - -
557B ASP* 1.3 73.8 - - - +
559B ASP* 1.3 69.3 + - - +
561B ALA* 2.8 14.0 + - - +
562B LEU* 2.8 35.8 + - + +
573B PHE* 3.9 31.9 - - + -
595B LEU* 4.2 15.5 - - + -
596B GLN 3.3 22.2 + - - +
597B THR* 4.1 9.2 - - + -
605B LEU* 3.8 23.1 - - + -
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Residues in contact with ASP 559 (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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393B LEU* 3.9 5.7 - - - +
434B LEU* 4.7 2.0 - - - -
486B VAL* 3.7 29.6 - - + +
487B GLY* 5.3 1.1 - - - +
556B LEU 5.3 2.1 + - - +
557B ASP 3.6 0.2 - - - -
558B VAL* 1.3 77.0 - - - +
560B GLY* 1.3 63.8 + - - +
562B LEU* 3.4 1.7 + - - -
563B PHE* 3.1 42.2 + - + +
596B GLN 4.4 1.8 + - - +
597B THR* 2.7 31.6 + - - -
598B HIS* 3.0 42.2 + - - +
599B HIS 4.0 1.4 + - - -
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Residues in contact with GLY 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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425B ASN* 3.4 26.3 + - - -
486B VAL* 4.2 20.2 + - - +
487B GLY* 5.6 0.2 - - - -
556B LEU 5.3 1.0 + - - -
557B ASP 3.6 4.0 + - - -
558B VAL 3.1 1.2 - - - -
559B ASP* 1.3 81.6 - - - +
561B ALA* 1.3 61.1 + - - +
563B PHE 4.0 0.5 - - - -
564B SER* 3.2 24.1 + - - -
569B SER* 4.6 0.2 - - - -
807B SO4 5.1 0.7 + - - -
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Residues in contact with ALA 561 (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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425B ASN* 3.4 4.8 - - - +
557B ASP 2.9 17.8 + - - +
558B VAL* 2.8 11.6 + - - +
560B GLY* 1.3 73.5 - - - +
562B LEU* 1.3 65.2 + - + +
563B PHE 3.4 0.2 + - - -
564B SER* 3.5 4.5 + - - -
566B ASP 4.8 0.5 - - - +
569B SER* 3.2 35.7 - - - +
570B ALA* 3.9 6.4 + - - +
573B PHE* 3.5 34.3 - - + -
807B SO4 4.8 2.5 - - - +
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Residues in contact with LEU 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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450B TYR* 3.7 8.3 - - - -
558B VAL* 2.8 59.0 + - + +
559B ASP* 4.1 3.8 - - - +
561B ALA* 1.3 81.1 - - + +
563B PHE* 1.3 70.7 + - + +
564B SER 3.5 1.8 + - - -
570B ALA* 5.1 13.0 - - + -
573B PHE* 5.7 4.0 - - + -
597B THR* 5.1 3.6 - - - +
599B HIS* 5.9 1.6 - - + +
602B HIS* 2.9 54.7 - - + +
604B LEU* 5.3 4.9 - - + -
605B LEU* 4.2 16.6 - - + +
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Residues in contact with PHE 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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432B ALA* 3.5 30.2 + - + +
434B LEU* 4.5 7.6 - - + -
441B ILE* 3.5 31.2 - - + -
450B TYR* 3.2 43.2 - + + +
486B VAL* 4.9 4.9 - - + +
559B ASP* 3.1 37.4 + - + +
560B GLY* 4.0 3.6 - - - -
562B LEU* 1.3 82.4 - - + +
564B SER* 1.3 59.5 + - - +
599B HIS* 3.7 49.1 - + + -
602B HIS* 4.2 23.3 - + - -
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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