Contacts of the helix formed by residues 524 - 537 (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 LEU 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522A ASP 5.2 1.6 - - - +
523A ARG* 1.3 74.7 - - - +
525A GLN* 1.3 57.1 + - - +
526A SER* 3.7 16.8 - - - +
527A GLN* 2.7 56.1 + - + +
528A ARG* 3.0 10.3 + - - +
359B ARG* 4.1 22.7 - - - +
363B GLU* 5.6 4.3 - - - +
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Residues in contact with GLN 525 (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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202A TYR* 4.3 6.3 - - + -
328A ARG* 2.7 46.8 + - - +
329A GLU* 3.1 24.0 + - - +
332A ILE* 6.2 0.2 - - - +
353A TYR* 4.1 4.5 - - + -
354A GLY 3.9 11.9 - - - +
355A GLY* 3.4 31.9 - - - +
523A ARG 3.6 2.4 + - - -
524A LEU* 1.3 70.7 - - - +
526A SER* 1.3 62.1 + - - +
528A ARG* 3.2 16.8 + - - +
529A GLU* 3.0 48.7 + - - +
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Residues in contact with SER 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR* 3.4 44.8 + - - +
524A LEU* 3.7 15.6 - - - +
525A GLN* 1.3 81.1 - - - +
527A GLN* 1.3 60.7 + - - +
529A GLU* 3.5 1.7 + - - +
530A GLN* 3.0 29.8 + - - +
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Residues in contact with GLN 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ARG* 3.4 46.9 + - + +
524A LEU* 2.7 59.5 + - + +
526A SER* 1.3 73.4 + - - +
528A ARG* 1.3 61.5 + - - +
530A GLN* 3.9 5.1 - - - +
531A ALA* 2.8 33.3 + - - +
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Residues in contact with ARG 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 3.8 14.1 - - - +
329A GLU* 2.6 49.1 + - - +
518A SER 5.1 1.3 - - - -
519A ILE* 3.8 22.4 - - + +
520A HIS 3.6 22.4 - - - +
521A GLY* 4.3 13.5 + - - -
523A ARG* 4.1 17.7 - - + -
524A LEU 3.0 10.8 + - - +
525A GLN* 3.2 28.5 + - - +
526A SER 3.2 0.2 - - - -
527A GLN* 1.3 78.8 - - - +
529A GLU* 1.3 64.0 + - - +
531A ALA* 3.5 4.9 + - - +
532A LEU* 3.4 22.1 + - - +
548A VAL* 3.6 13.1 - - - +
5E U 2.9 40.2 + - - -
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Residues in contact with GLU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR* 3.0 35.8 + - - +
204A PRO* 3.6 6.4 - - - +
205A PRO* 4.4 4.7 - - + +
329A GLU* 4.9 8.3 - - + +
332A ILE* 5.0 14.5 - - + +
353A TYR* 2.9 31.2 + - - -
525A GLN* 3.0 34.1 + - - +
526A SER 4.0 3.4 - - - +
528A ARG* 1.3 76.8 - - - +
530A GLN* 1.3 62.7 + - - +
532A LEU* 3.0 10.9 + - + +
533A ARG* 3.0 20.4 + - - +
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Residues in contact with GLN 530 (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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526A SER 3.0 19.7 + - - +
527A GLN* 3.9 5.4 - - - +
529A GLU* 1.3 76.0 - - - +
531A ALA* 1.3 58.0 + - - +
533A ARG* 3.1 28.7 + - - +
534A ASP* 2.7 68.6 + - - +
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Residues in contact with ALA 531 (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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517A THR* 3.4 30.8 - - + +
518A SER 3.3 25.8 - - - +
519A ILE* 4.8 4.0 - - + -
523A ARG* 4.0 1.3 - - - +
527A GLN 2.8 19.0 + - - +
528A ARG* 3.7 5.4 - - - +
529A GLU 3.2 0.2 - - - -
530A GLN* 1.3 76.8 - - - +
532A LEU* 1.3 64.3 + - - +
534A ASP* 3.6 5.0 + - - +
535A PHE* 3.2 22.3 + - - +
543A LEU* 4.9 3.2 - - + +
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Residues in contact with LEU 532 (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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329A GLU* 3.5 35.9 - - + +
332A ILE* 5.3 4.7 - - + -
519A ILE* 4.0 13.9 - - + -
528A ARG 3.4 9.6 + - - +
529A GLU* 3.0 10.1 + - - +
531A ALA* 1.3 74.6 - - - +
533A ARG* 1.3 68.6 + - - +
535A PHE* 3.1 4.9 + - + +
536A LYS* 2.9 47.4 + - - +
543A LEU* 3.9 26.0 - - + -
553A LEU* 4.2 21.5 - - + -
555A ILE* 5.3 11.0 - - + -
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Residues in contact with ARG 533 (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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529A GLU 3.0 12.7 + - - +
530A GLN* 3.2 37.9 + - - +
532A LEU* 1.3 78.5 - - - +
534A ASP* 1.3 63.9 + - - +
536A LYS* 3.0 18.1 + - - +
537A ASN* 3.0 38.7 + - - +
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Residues in contact with ASP 534 (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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517A THR* 5.0 1.9 + - - -
530A GLN* 2.7 54.0 + - - +
531A ALA* 3.9 5.9 - - - +
533A ARG* 1.3 80.3 + - - +
535A PHE* 1.3 60.5 + - - +
537A ASN* 3.3 5.0 - - - +
539A SER* 2.8 48.3 + - - -
540A MET* 3.0 31.4 + - + +
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Residues in contact with PHE 535 (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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491A GLY* 3.7 8.5 - - - -
492A THR 3.4 41.3 - - - -
493A ILE* 4.6 0.4 - - + -
531A ALA 3.2 16.2 + - - +
532A LEU* 3.1 8.5 + - + +
534A ASP* 1.3 74.4 - - - +
536A LYS* 1.3 66.8 + - + +
538A GLY 3.4 3.8 + - - -
540A MET* 3.7 19.8 - - + +
541A LYS 3.5 15.0 - - - -
542A VAL 4.1 2.9 - - - -
543A LEU* 3.5 39.0 - - + -
555A ILE* 3.9 18.6 - - + -
557A ASN* 3.1 22.9 + - + +
558A ILE* 3.5 33.2 - - + -
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Residues in contact with LYS 536 (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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332A ILE* 5.9 5.3 - - - +
333A GLN* 6.3 0.6 - - - +
532A LEU* 2.9 35.9 + - - +
533A ARG* 3.5 11.1 - - - +
535A PHE* 1.3 78.3 - - + +
537A ASN* 1.3 57.5 + - + +
538A GLY 3.3 0.2 - - - -
554A ASP 5.4 2.9 - - - -
555A ILE* 4.3 36.1 - - + -
557A ASN* 3.1 20.7 + - - +
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Residues in contact with ASN 537 (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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533A ARG* 3.0 56.9 + - - +
534A ASP* 3.3 1.8 - - - +
536A LYS* 1.3 76.1 - - + +
538A GLY* 1.3 56.6 + - - +
539A SER* 2.5 34.1 + - - -
557A ASN* 4.6 0.4 - - - -
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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