Contacts of the helix formed by residues 569 - 578 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A ARG* 5.2 9.8 - - - +
406A ASP* 3.3 25.1 + - - -
407A MET* 5.3 6.3 - - - +
436A PRO* 6.2 2.0 - - - +
439A ILE* 6.0 1.0 - - - +
567A PRO* 3.4 9.7 - - - +
568A SER* 1.3 93.7 - - - +
570A ILE* 1.3 64.7 + - - +
571A ASP* 4.3 12.1 - - + +
572A ASP* 3.2 19.0 + - + +
573A TYR 3.4 6.8 + - - -
601A ILE* 3.6 3.1 - - - -
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Residues in contact with ILE 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A LYS* 1.3 72.9 - - - +
571A ASP* 1.3 76.7 + - - +
573A TYR* 3.1 23.3 + - + +
574A VAL* 3.0 21.3 + - + +
601A ILE* 3.5 20.4 - - + +
604A ASP* 3.6 31.0 + - + +
605A LEU* 3.7 33.0 - - + +
608A ILE* 3.5 25.8 - - + -
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Residues in contact with ASP 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A ASP* 4.4 2.7 - - - +
434A THR* 3.4 32.2 + - + +
435A PHE 5.3 0.2 - - - -
436A PRO* 3.1 36.4 - - - +
459A GLY* 4.8 7.1 - - - +
551A ARG* 5.2 3.8 - - - +
569A LYS* 3.2 11.5 - - + +
570A ILE* 1.3 87.2 - - - +
572A ASP* 1.3 66.0 + - - +
574A VAL* 3.1 5.1 + - - +
575A HIS* 3.0 30.2 + - + -
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Residues in contact with ASP 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A SER* 2.6 26.8 + - - -
550A SER* 3.0 25.6 + - - -
551A ARG* 5.1 5.7 + - - +
567A PRO* 3.2 22.2 - - + +
569A LYS* 3.2 19.1 + - + +
571A ASP* 1.3 78.8 - - - +
573A TYR* 1.3 63.2 + - - +
575A HIS* 3.4 5.5 + - - -
576A ARG* 3.0 33.8 + - - +
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Residues in contact with TYR 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A GLN* 2.7 35.7 + - - +
469A ILE* 3.8 15.8 - - + +
563A ASN* 3.6 17.5 - - - -
566A MET* 4.0 17.9 - - + -
567A PRO* 3.6 17.6 - - + +
569A LYS 3.4 3.0 + - - -
570A ILE* 3.1 32.8 + - + +
572A ASP* 1.3 79.8 - - - +
574A VAL* 1.3 69.2 + - + +
576A ARG* 3.7 4.3 - - - +
577A ILE* 3.1 42.4 + - + +
589A ALA* 5.3 0.9 + - - +
591A SER* 3.5 22.8 + - - -
601A ILE* 4.9 0.7 - - + -
605A LEU* 3.6 21.1 - - + +
608A ILE* 4.1 7.9 - - + -
609A LEU* 4.3 0.3 - - - +
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Residues in contact with VAL 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A THR* 4.1 11.8 + - + +
433A ALA* 5.1 3.6 - - + +
434A THR* 4.2 14.4 - - + -
459A GLY 3.5 20.9 - - - +
460A GLY 3.9 20.2 - - - +
461A ALA* 4.1 8.7 - - + +
462A CYS 5.4 0.8 + - - +
570A ILE 3.0 18.1 + - - +
571A ASP* 3.1 10.5 + - - +
573A TYR* 1.3 80.7 - - + +
575A HIS* 1.3 63.2 + - - +
577A ILE* 3.6 7.7 - - - +
578A GLY* 3.2 17.2 + - - -
608A ILE* 4.1 28.0 - - + -
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Residues in contact with HIS 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A THR* 4.2 9.8 - - + +
400A GLU* 3.3 27.4 + - - -
432A SER* 4.0 3.1 - - - -
433A ALA* 3.8 27.5 - - + +
434A THR* 2.7 28.6 + - + +
550A SER* 3.2 17.3 - - - +
551A ARG* 3.3 38.9 - - + +
571A ASP 3.0 27.6 + - - -
572A ASP* 4.0 5.8 - - - +
574A VAL* 1.3 73.4 - - - +
576A ARG* 1.3 60.5 + - - +
578A GLY 2.8 15.9 + - - -
579A ARG* 3.1 21.2 + - - +
2901A ANP 4.9 1.2 + - - -
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Residues in contact with ARG 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A PHE* 3.4 37.8 + - + +
496A VAL 3.8 19.8 + - - -
497A GLU* 5.0 6.1 + - - +
547A SER* 3.0 27.9 + - - +
550A SER* 3.4 21.5 + - - -
561A VAL* 3.5 10.6 - - + +
563A ASN* 3.0 25.1 + - - +
565A ASP 2.8 28.3 + - - -
567A PRO* 3.7 17.6 - - - +
572A ASP* 3.0 31.6 + - - +
573A TYR* 3.7 6.1 - - - +
575A HIS* 1.3 76.7 - - - +
577A ILE* 1.3 63.5 + - + +
579A ARG* 3.0 22.1 + - - +
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Residues in contact with ILE 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ALA* 4.0 12.6 - - + -
462A CYS* 5.2 1.8 - - + +
465A VAL* 3.6 25.2 - - + +
467A GLN* 3.3 37.2 - - + +
561A VAL* 4.1 10.2 - - + +
563A ASN* 3.8 13.2 - - - +
573A TYR* 3.1 41.0 + - + +
574A VAL 3.6 11.2 - - - +
576A ARG* 1.3 75.3 - - - +
578A GLY* 1.3 63.1 + - - +
579A ARG 3.1 1.8 + - - -
580A THR* 3.4 18.8 + - - +
589A ALA* 3.8 22.1 - - + +
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Residues in contact with GLY 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A THR* 3.3 27.0 + - - -
462A CYS* 5.7 1.3 - - - -
465A VAL* 5.2 1.8 - - - -
574A VAL 3.2 9.0 + - - -
575A HIS 2.8 14.0 + - - -
577A ILE* 1.3 76.4 - - - +
579A ARG* 1.3 66.9 + - - +
580A THR 3.0 15.4 + - - +
582A ARG* 3.6 18.2 + - - +
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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