Contacts of the helix formed by residues 524 - 537 (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 LEU 524 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522D ASP 5.6 1.3 - - - +
523D ARG* 1.3 74.4 - - - +
525D GLN* 1.3 66.5 + - - +
526D SER* 2.8 17.7 - - - +
527D GLN* 2.8 49.2 + - + +
528D ARG* 2.9 10.7 + - - +
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Residues in contact with GLN 525 (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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202D TYR* 4.1 4.5 - - + -
328D ARG* 2.7 46.7 + - - +
329D GLU* 3.1 23.6 + - - +
332D ILE* 4.5 0.8 - - - +
353D TYR* 3.9 10.6 - - + -
354D GLY 3.8 13.5 - - - +
355D GLY* 3.5 23.8 - - - +
523D ARG 3.6 1.8 + - - -
524D LEU* 1.3 71.6 - - - +
526D SER* 1.3 61.4 + - - +
528D ARG* 3.2 15.7 + - - +
529D GLU* 3.1 58.5 + - - +
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Residues in contact with SER 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D TYR* 3.1 44.8 + - - +
524D LEU* 2.8 18.1 - - - +
525D GLN* 1.3 80.9 - - - +
527D GLN* 1.3 58.4 + - - -
529D GLU* 3.4 2.4 + - - +
530D GLN* 3.0 28.7 + - - +
533D ARG* 5.4 0.5 + - - -
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Residues in contact with GLN 527 (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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523D ARG* 3.5 49.1 + - + +
524D LEU* 2.8 58.8 + - + +
526D SER* 1.3 74.0 - - - +
528D ARG* 1.3 57.9 + - - +
530D GLN* 3.7 6.7 - - - +
531D ALA* 3.0 30.1 + - - +
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Residues in contact with ARG 528 (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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328D ARG* 3.9 12.3 - - - +
329D GLU* 2.5 51.6 + - - +
518D SER 5.0 1.1 - - - -
519D ILE* 3.7 29.0 - - + +
520D HIS 3.4 23.5 + - - +
521D GLY* 4.1 16.6 + - - -
523D ARG* 3.9 17.5 - - + -
524D LEU 2.9 12.1 + - - +
525D GLN* 3.2 25.1 + - - +
527D GLN* 1.3 76.6 - - - +
529D GLU* 1.3 64.1 + - - +
531D ALA* 3.4 12.7 + - - +
532D LEU* 3.4 9.7 + - - +
548D VAL* 3.6 12.8 - - - +
5H U 2.9 40.8 + - - -
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Residues in contact with GLU 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D TYR* 2.9 25.1 + - - +
204D PRO* 3.6 6.6 - - - +
205D PRO* 5.0 0.2 - - - +
329D GLU* 4.9 5.8 - - + -
332D ILE* 3.7 16.6 - - + +
353D TYR* 2.7 29.4 + - - -
525D GLN* 3.1 40.7 + - - +
526D SER 3.9 3.6 - - - +
528D ARG* 1.3 73.4 - - - +
530D GLN* 1.3 65.6 + - - +
532D LEU* 3.3 7.7 + - - +
533D ARG* 3.1 39.4 + - - +
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Residues in contact with GLN 530 (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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526D SER 3.0 18.0 + - - +
527D GLN* 3.7 9.0 - - - +
529D GLU* 1.3 76.7 - - - +
531D ALA* 1.3 57.1 + - - +
533D ARG* 2.8 39.0 + - - +
534D ASP* 2.6 65.8 + - - +
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Residues in contact with ALA 531 (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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517D THR* 3.6 28.7 - - + +
518D SER 3.2 28.9 - - - +
519D ILE* 4.7 4.3 - - + -
527D GLN 3.0 15.9 + - - +
528D ARG 3.6 5.6 - - - +
529D GLU 3.3 0.2 - - - -
530D GLN* 1.3 76.9 - - - +
532D LEU* 1.3 63.6 + - - +
534D ASP* 3.3 5.5 + - - +
535D PHE* 3.0 24.4 + - - +
543D LEU* 4.7 3.1 - - + -
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Residues in contact with LEU 532 (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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329D GLU* 3.7 36.8 - - + +
519D ILE* 3.9 20.0 - - + -
528D ARG 3.4 2.4 + - - +
529D GLU* 3.3 9.0 + - - +
530D GLN 3.3 0.6 - - - -
531D ALA* 1.3 76.7 - - - +
533D ARG* 1.3 58.8 + - - +
535D PHE* 3.8 4.3 - - + +
536D LYS* 2.8 51.3 + - - +
543D LEU* 4.0 26.9 - - + -
553D LEU* 4.2 18.6 - - + -
555D ILE* 4.1 19.3 - - + -
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Residues in contact with ARG 533 (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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202D TYR* 5.4 1.0 + - - -
205D PRO* 3.9 29.5 - - - +
526D SER 5.4 0.6 + - - -
529D GLU* 3.1 30.2 + - - +
530D GLN* 2.8 61.2 + - - +
532D LEU* 1.3 76.7 - - - +
534D ASP* 1.3 58.7 + - - +
536D LYS* 3.2 9.0 + - - +
537D ASN* 2.9 42.4 + - + +
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Residues in contact with ASP 534 (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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517D THR* 5.5 1.2 + - - -
530D GLN* 2.6 53.0 + - - +
531D ALA* 3.9 3.9 - - - +
533D ARG* 1.3 75.1 - - - +
535D PHE* 1.3 62.1 + - - +
537D ASN* 2.9 24.5 + - - +
539D SER* 3.0 33.8 + - - +
540D MET* 3.0 34.1 + - + +
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Residues in contact with PHE 535 (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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491D GLY* 3.8 21.1 - - - -
492D THR 3.5 22.7 - - - -
493D ILE* 5.0 0.2 - - - -
517D THR* 5.3 0.4 - - + -
531D ALA 3.0 17.9 + - - +
532D LEU* 3.9 6.3 - - - +
534D ASP* 1.3 73.8 - - - +
536D LYS* 1.3 62.4 + - - +
538D GLY* 3.3 6.1 + - - -
540D MET* 3.7 21.8 - - + +
541D LYS 3.3 24.9 - - - -
542D VAL 4.1 1.6 - - - -
543D LEU* 3.7 31.0 - - + -
555D ILE* 4.1 19.3 - - + -
557D ASN* 2.7 32.7 + - + +
558D ILE* 3.4 29.6 - - + -
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Residues in contact with LYS 536 (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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333D GLN* 5.8 4.3 + - - +
532D LEU* 2.8 42.0 + - - +
533D ARG* 3.6 6.1 - - - +
535D PHE* 1.3 78.7 - - - +
537D ASN* 1.3 57.2 + - - +
538D GLY 3.2 0.2 - - - -
554D ASP 5.2 2.9 - - - -
555D ILE* 4.0 38.1 - - + -
557D ASN* 2.8 21.3 + - - +
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Residues in contact with ASN 537 (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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533D ARG* 2.9 31.4 + - + +
534D ASP* 2.9 18.8 + - - +
536D LYS* 1.3 75.4 - - - +
538D GLY* 1.3 56.2 + - - +
539D SER* 2.8 28.3 + - - -
557D ASN* 4.6 0.2 - - - -
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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