Contacts of the helix formed by residues 542 - 553 (chain B) in PDB entry 2DX0
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 SER 542 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543B ALA* 1.3 65.6 + - - +
544B GLU* 3.7 13.6 + - - +
545B LYS* 2.7 62.6 + - - +
546B LEU* 3.0 10.5 + - - +
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Residues in contact with ALA 543 (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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542B SER* 1.3 75.9 + - - +
544B GLU* 1.3 63.5 + - - +
546B LEU* 3.2 13.3 + - - +
547B LEU* 3.1 27.7 + - - +
562B LEU* 3.8 25.3 - - + +
564B ARG* 3.9 26.0 - - + +
576B SER* 5.7 2.5 - - - +
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Residues in contact with GLU 544 (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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542B SER* 3.0 12.1 + - - +
543B ALA* 1.3 79.8 - - - +
545B LYS* 1.3 64.3 + - + +
547B LEU* 3.9 0.4 - - - +
548B GLN* 3.3 19.2 + - - +
576B SER* 3.4 17.3 + - - -
583B VAL* 3.4 42.8 - - + +
585B HIS* 2.8 34.7 + - - -
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Residues in contact with LYS 545 (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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542B SER* 2.7 44.4 + - - +
544B GLU* 1.3 75.2 - - + +
546B LEU* 1.3 62.7 + - - +
547B LEU 3.2 0.4 - - - -
548B GLN* 3.0 9.8 + - + +
549B GLU* 2.9 33.2 + - + +
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Residues in contact with LEU 546 (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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635A VAL* 3.6 32.3 - - + -
542B SER 3.0 9.9 + - - +
543B ALA* 3.2 12.5 + - - +
545B LYS* 1.3 76.9 - - - +
547B LEU* 1.3 62.9 + - - +
549B GLU* 3.4 14.1 + - - +
550B TYR* 3.2 23.6 + - + +
562B LEU* 4.8 11.7 - - + -
564B ARG* 4.6 18.2 - - - +
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Residues in contact with LEU 547 (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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635A VAL* 3.2 31.2 - - + -
543B ALA 3.1 9.5 + - - +
544B GLU 3.9 4.9 - - - +
546B LEU* 1.3 77.2 - - - +
548B GLN* 1.3 67.3 + - - +
550B TYR* 4.7 1.6 - - - -
551B CYS* 2.8 44.0 + - - +
560B THR 3.7 16.4 - - - +
561B PHE* 4.4 0.4 - - - -
562B LEU* 3.3 32.5 - - + -
576B SER* 3.6 27.6 - - - +
577B PHE* 3.9 5.8 - - - +
578B TRP 4.9 0.4 - - - +
583B VAL* 3.8 20.2 - - + -
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Residues in contact with GLN 548 (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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544B GLU 3.3 12.4 + - - +
545B LYS* 3.0 15.0 + - + +
547B LEU* 1.3 77.7 - - - +
549B GLU* 1.3 68.2 + - + +
551B CYS* 4.0 0.3 - - - +
552B ALA* 2.9 31.9 + - + +
578B TRP* 3.3 37.2 - - - -
581B GLY 4.1 7.5 + - - +
582B ARG* 5.6 0.2 - - - -
583B VAL* 4.2 8.6 + - - +
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Residues in contact with GLU 549 (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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545B LYS* 2.9 24.1 + - + +
546B LEU* 3.6 15.4 - - - +
548B GLN* 1.3 80.9 - - + +
550B TYR* 1.3 68.4 + - - +
552B ALA* 4.9 0.9 - - - -
553B GLU* 2.7 50.2 + - - +
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Residues in contact with TYR 550 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633A ASP* 6.0 1.6 - - - +
635A VAL* 3.8 19.1 - - + -
636A PRO* 3.3 39.0 - - + +
546B LEU* 3.2 17.4 + - + +
547B LEU* 4.0 2.5 - - - +
549B GLU* 1.3 79.0 - - - +
551B CYS* 1.3 66.6 + - - +
553B GLU* 3.4 4.6 - - - -
554B THR* 2.5 58.2 + - + +
556B ALA* 4.3 9.4 - - + -
560B THR* 4.2 19.5 - - + -
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Residues in contact with CYS 551 (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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547B LEU* 2.8 32.9 + - - +
549B GLU 2.9 0.4 + - - -
550B TYR* 1.3 72.0 - - - +
552B ALA* 1.3 61.0 + - - +
555B GLY* 3.0 26.9 + - - -
556B ALA* 3.1 26.0 + - + +
560B THR* 3.9 16.2 - - - -
578B TRP* 3.3 55.2 + - + -
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Residues in contact with ALA 552 (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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548B GLN* 2.9 28.9 + - + +
549B GLU* 2.9 5.8 + - - +
551B CYS* 1.3 75.2 - - - +
553B GLU* 1.3 63.3 + - + +
554B THR 3.2 4.2 + - - -
555B GLY* 3.9 5.2 + - - -
578B TRP* 4.6 8.9 - - + -
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Residues in contact with GLU 553 (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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549B GLU* 2.7 52.6 + - - +
550B TYR* 3.4 3.5 + - - +
552B ALA* 1.3 75.5 - - + +
554B THR* 1.3 63.9 + - - +
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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