Contacts of the helix formed by residues 569 - 578 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403D ARG* 5.5 8.7 - - - +
406D ASP* 4.2 13.8 + - - +
407D MET* 4.2 22.8 - - - +
567D PRO* 3.5 6.4 - - - +
568D SER* 1.3 92.7 + - - +
570D ILE* 1.3 66.1 + - - +
571D ASP* 4.3 10.1 - - + +
572D ASP* 3.1 26.5 + - + +
573D TYR 3.4 4.2 + - - -
601D ILE* 3.6 3.8 - - - -
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Residues in contact with ILE 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D MET* 5.6 0.4 - - + -
569D LYS* 1.3 69.6 - - - +
571D ASP* 1.3 80.2 + - - +
573D TYR* 3.1 35.1 + - + +
574D VAL* 3.1 13.1 + - + +
601D ILE* 3.6 16.3 - - + +
604D ASP* 3.7 35.6 + - + +
605D LEU* 3.8 31.4 - - + +
608D ILE* 4.0 26.5 - - + -
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Residues in contact with ASP 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D ASP* 4.6 2.6 - - - +
434D THR* 3.5 35.6 + - + +
435D PHE 5.2 0.5 + - - -
436D PRO* 3.2 29.9 - - - +
459D GLY* 4.9 7.1 - - - +
551D ARG* 5.2 3.6 - - - +
569D LYS* 3.2 7.4 - - + +
570D ILE* 1.3 91.6 - - - +
572D ASP* 1.3 63.0 + - - +
574D VAL* 3.2 6.3 + - - +
575D HIS* 3.0 29.8 + - + -
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Residues in contact with ASP 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547D SER* 2.7 25.6 + - - -
550D SER* 2.9 26.5 + - - -
551D ARG* 5.0 4.9 - - - +
567D PRO* 3.2 22.1 - - + +
569D LYS* 3.1 19.1 + - + +
571D ASP* 1.3 78.3 - - - +
573D TYR* 1.3 59.0 + - - +
575D HIS* 3.3 6.0 + - - +
576D ARG* 2.9 37.4 + - - +
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Residues in contact with TYR 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D GLN* 2.7 36.9 + - - +
469D ILE* 3.7 16.6 - - - +
563D ASN* 3.6 16.8 - - - -
566D MET* 4.1 16.8 - - + -
567D PRO* 3.6 17.6 - - + +
569D LYS 3.4 2.2 + - - -
570D ILE* 3.1 32.4 + - + +
572D ASP* 1.3 76.7 - - - +
574D VAL* 1.3 63.7 + - + +
576D ARG* 3.2 5.7 + - - +
577D ILE* 2.9 52.5 + - + +
589D ALA* 5.3 1.0 - - - +
591D SER* 3.3 25.0 + - - -
601D ILE* 5.2 0.2 - - + -
605D LEU* 3.6 19.1 - - + +
608D ILE* 3.8 11.9 - - + -
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Residues in contact with VAL 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D THR* 3.9 12.6 + - + +
433D ALA* 5.1 3.6 - - + +
434D THR* 4.0 15.0 - - + -
459D GLY 3.5 21.1 - - - +
460D GLY 3.7 20.0 - - - +
461D ALA* 4.3 10.5 - - - +
462D CYS 5.4 1.2 + - - +
570D ILE 3.5 12.6 - - - +
571D ASP* 3.3 10.8 - - - +
573D TYR* 1.3 87.0 - - + +
575D HIS* 1.3 61.8 + - + +
577D ILE* 3.6 8.5 - - - +
578D GLY* 3.3 17.8 + - - -
608D ILE* 3.7 24.0 - - + -
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Residues in contact with HIS 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D THR* 4.3 6.2 - - - +
400D GLU* 3.3 28.1 + - - -
432D SER* 3.9 3.1 - - - -
433D ALA* 3.6 27.2 - - + +
434D THR* 2.6 33.3 + - + +
550D SER* 3.1 15.9 - - - +
551D ARG* 3.3 33.8 + - + +
571D ASP 3.0 28.8 + - - -
572D ASP* 3.8 6.7 - - - +
574D VAL* 1.3 73.4 - - - +
576D ARG* 1.3 64.3 + - - +
578D GLY 3.1 4.3 + - - -
579D ARG* 2.8 32.4 + - - +
2904D ANP 4.9 1.7 + - - -
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Residues in contact with ARG 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D PHE* 3.5 38.3 - - + +
496D VAL 3.7 21.2 + - - -
497D GLU* 4.8 7.3 + - - +
547D SER* 2.9 27.7 + - - +
550D SER* 3.3 21.3 - - - -
561D VAL* 3.5 12.7 - - + +
563D ASN* 2.9 28.8 + - - +
565D ASP 2.9 24.2 + - - -
567D PRO* 3.5 22.5 - - - +
572D ASP* 2.9 26.3 + - - +
573D TYR* 3.5 6.3 - - - +
575D HIS* 1.3 77.1 - - - +
577D ILE* 1.3 62.3 + - + +
579D ARG* 3.1 20.8 + - - +
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Residues in contact with ILE 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D ALA* 3.8 15.5 - - + -
462D CYS 5.1 0.9 - - - +
465D VAL* 3.7 23.9 - - + +
467D GLN* 3.5 35.7 - - + +
561D VAL* 4.0 9.1 - - + +
563D ASN* 3.8 11.4 - - - +
573D TYR* 2.9 47.1 + - + +
574D VAL 3.6 8.5 - - - +
576D ARG* 1.3 71.9 - - - +
578D GLY* 1.3 63.2 + - - +
579D ARG 3.0 2.5 + - - -
580D THR* 3.3 21.0 + - - +
589D ALA* 3.7 24.9 - - + -
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Residues in contact with GLY 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D THR* 3.3 29.6 + - - -
462D CYS* 5.4 2.9 - - - -
465D VAL* 5.9 0.7 - - - -
574D VAL 3.3 3.0 + - - -
575D HIS 3.1 8.4 + - - -
576D ARG 3.0 2.0 - - - -
577D ILE* 1.3 80.5 - - - +
579D ARG* 1.3 73.0 + - - +
580D THR 2.9 16.7 + - - +
582D ARG* 3.6 13.3 + - - +
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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