Contacts of the helix formed by residues 569 - 578 (chain B) in PDB entry 2DB3
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 LYS 569 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B ARG* 6.3 0.9 - - - +
406B ASP* 4.5 14.3 + - - +
567B PRO* 3.2 18.2 - - - +
568B SER* 1.3 94.9 + - - +
570B ILE* 1.3 66.0 + - - +
571B ASP* 3.3 11.4 - - + +
572B ASP* 3.2 18.1 + - + +
601B ILE* 3.8 4.5 - - - -
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Residues in contact with ILE 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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569B LYS* 1.3 69.7 - - - +
571B ASP* 1.3 79.8 + - - +
573B TYR* 2.9 37.9 + - + +
574B VAL* 3.1 11.5 + - + +
601B ILE* 3.8 14.8 - - + +
604B ASP* 3.7 51.3 + - + +
605B LEU* 3.9 11.4 - - + +
608B ILE* 3.6 27.6 - - + -
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Residues in contact with ASP 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ASP* 4.9 0.6 - - - +
434B THR* 3.5 37.4 - - + +
435B PHE 5.0 0.9 + - - -
436B PRO* 3.3 28.4 - - - +
459B GLY* 4.8 6.8 - - - +
551B ARG* 4.9 5.8 - - - +
569B LYS* 3.3 8.3 - - + +
570B ILE* 1.3 86.5 - - - +
572B ASP* 1.3 63.7 + - - +
574B VAL* 3.1 6.2 + - - +
575B HIS* 3.1 29.8 + - + -
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Residues in contact with ASP 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B SER* 2.6 27.3 + - - -
550B SER* 3.0 24.6 + - - -
551B ARG* 5.2 5.2 + - - +
567B PRO* 3.5 20.9 - - + +
569B LYS* 3.2 17.6 + - + +
570B ILE 3.1 0.8 - - - -
571B ASP* 1.3 75.8 - - - +
573B TYR* 1.3 64.2 - - - +
575B HIS* 3.5 5.6 + - - +
576B ARG* 3.1 31.8 + - - +
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Residues in contact with TYR 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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467B GLN* 2.9 42.5 + - - +
469B ILE* 3.8 9.6 - - + +
563B ASN* 3.4 17.9 - - - -
566B MET* 4.1 16.6 - - + -
567B PRO* 3.6 16.9 - - + +
569B LYS 3.5 2.6 + - - -
570B ILE* 2.9 28.5 + - + +
572B ASP* 1.3 78.4 - - - +
574B VAL* 1.3 65.7 + - + +
576B ARG* 3.3 4.3 + - - +
577B ILE* 3.0 44.7 + - + +
589B ALA* 5.1 0.7 - - - +
591B SER* 3.2 25.0 + - - -
605B LEU* 3.8 15.8 - - + +
608B ILE* 3.6 23.3 - - + -
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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
----------------------------------------------------------
291B THR* 3.9 12.6 + - + +
433B ALA* 5.0 4.3 - - + +
434B THR* 4.2 12.6 - - + -
459B GLY 3.4 21.1 - - - +
460B GLY 3.7 20.6 - - - +
461B ALA* 4.0 12.2 - - + +
462B CYS 5.3 1.0 + - - +
570B ILE* 3.1 13.5 + - + +
571B ASP* 3.5 9.9 - - - +
573B TYR* 1.3 81.2 - - + +
575B HIS* 1.3 62.5 + - + +
577B ILE* 3.6 9.7 - - - +
578B GLY* 3.3 17.5 + - - -
608B ILE* 3.7 24.5 - - + -
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Residues in contact with HIS 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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291B THR* 4.3 4.7 - - - +
400B GLU* 3.2 25.4 + - - -
432B SER* 4.0 7.4 - - - -
433B ALA* 4.0 18.2 - - + -
434B THR* 2.9 33.0 + - + +
550B SER* 2.9 19.2 - - - +
551B ARG* 3.4 36.8 + - + +
571B ASP 3.1 27.8 + - - +
572B ASP* 4.0 6.7 - - - +
573B TYR 3.3 0.2 - - - -
574B VAL* 1.3 74.2 - - + +
576B ARG* 1.3 64.4 + - - +
578B GLY 3.2 4.0 + - - -
579B ARG* 2.9 36.7 + - - +
2902B ANP 4.7 2.2 + - - -
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Residues in contact with ARG 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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495B PHE* 3.6 38.5 + - + +
496B VAL 3.7 23.2 + - - -
497B GLU* 4.6 9.9 + - - +
547B SER* 3.0 29.0 + - - +
550B SER* 3.5 20.2 - - - -
561B VAL* 3.5 9.5 - - - +
563B ASN* 2.9 25.3 + - - +
565B ASP 2.8 28.7 + - - -
567B PRO* 3.5 17.8 - - - +
572B ASP* 3.1 29.0 + - - +
573B TYR* 3.6 4.0 - - - +
575B HIS* 1.3 76.2 - - - +
577B ILE* 1.3 62.5 + - - +
579B ARG* 3.0 22.2 + - - +
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Residues in contact with ILE 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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461B ALA* 3.8 15.9 - - + -
462B CYS 5.1 1.6 - - - +
465B VAL* 4.0 13.3 - - + +
467B GLN* 3.5 38.4 - - + +
561B VAL* 3.8 9.4 - - + -
563B ASN* 3.8 9.9 - - - +
573B TYR* 3.0 46.1 + - + +
574B VAL* 3.6 11.0 - - - +
576B ARG* 1.3 76.8 - - - +
578B GLY* 1.3 59.0 + - - +
579B ARG 3.1 4.8 + - - -
580B THR* 3.2 26.9 - - - +
589B ALA* 3.8 23.6 - - + -
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Residues in contact with GLY 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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291B THR* 3.3 28.8 - - - -
462B CYS* 5.4 2.9 - - - -
465B VAL* 5.8 0.2 - - - -
574B VAL 3.3 4.2 + - - -
575B HIS 3.2 7.8 + - - -
576B ARG 3.0 1.6 - - - -
577B ILE* 1.3 79.8 - - - +
579B ARG* 1.3 68.2 + - - +
580B THR 3.0 16.0 + - - +
582B ARG* 3.5 19.2 + - - +
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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