Contacts of the helix formed by residues 533 - 544 (chain B) in PDB entry 3ODX
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 ASP 533 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451B PHE* 4.4 2.9 - - - -
529B LYS* 3.2 49.4 + - - +
530B GLN 3.6 5.1 - - - +
531B ARG 3.4 1.8 - - - -
532B LYS* 1.3 80.8 - - + +
534B PRO* 1.3 67.9 - - - +
535B ARG* 3.1 21.2 + - - +
536B PHE* 3.3 14.7 + - + +
537B CYS 3.0 21.5 + - - -
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Residues in contact with PRO 534 (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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530B GLN 5.0 0.4 - - - +
532B LYS 4.0 5.8 - - - +
533B ASP* 1.3 85.4 - - - +
535B ARG* 1.3 66.3 + - - +
536B PHE 3.1 2.0 - - - -
537B CYS* 3.6 8.2 - - + +
538B ALA* 2.7 27.0 + - - +
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Residues in contact with ARG 535 (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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449B CYS* 2.8 37.4 + - - +
450B LEU 4.8 2.0 + - - -
451B PHE* 3.5 33.6 - - + +
533B ASP* 3.1 15.3 + - - +
534B PRO* 1.3 80.7 - - - +
536B PHE* 1.3 59.4 + - - +
538B ALA* 3.3 6.0 + - - +
539B PHE* 2.9 25.1 + - - +
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Residues in contact with PHE 536 (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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446B MET* 3.5 36.6 - - + -
451B PHE* 3.5 45.3 - + + -
452B PHE* 4.3 8.7 - + - -
526B LEU* 3.7 19.3 - - + -
529B LYS* 3.4 38.6 - - + +
530B GLN* 3.4 24.7 - - + -
533B ASP* 3.3 16.4 + - - +
534B PRO 3.1 0.4 - - - -
535B ARG* 1.3 78.4 - - - +
537B CYS* 1.3 66.5 + - - +
539B PHE* 2.9 14.0 + + - +
540B VAL* 3.0 23.4 + - + +
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Residues in contact with CYS 537 (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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530B GLN* 3.4 43.1 - - - +
533B ASP 3.0 8.2 + - - +
534B PRO* 3.6 10.8 - - + +
536B PHE* 1.3 78.1 - - - +
538B ALA* 1.3 62.9 - - - +
540B VAL* 3.1 2.8 + - - +
541B GLN* 3.0 47.0 + - - +
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Residues in contact with ALA 538 (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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534B PRO 2.7 21.6 + - - +
535B ARG* 3.5 6.7 - - - +
537B CYS* 1.3 71.8 - - - +
539B PHE* 1.3 64.7 + - - +
541B GLN* 3.3 13.3 + - - +
542B GLU* 3.0 26.2 + - - +
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Residues in contact with PHE 539 (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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441B LEU 4.3 13.7 - - - -
442B PHE* 5.0 1.1 - + - -
445B PRO* 3.5 32.8 - - + -
446B MET* 3.6 30.5 - - + -
449B CYS* 4.3 11.4 - - - -
451B PHE* 3.8 30.1 - + + -
535B ARG 2.9 13.9 + - - +
536B PHE* 2.9 11.6 + + - +
538B ALA* 1.3 78.6 - - - +
540B VAL* 1.3 70.1 + - + +
542B GLU* 3.3 14.5 + - - +
543B ALA* 2.9 32.5 + - + +
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Residues in contact with VAL 540 (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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442B PHE* 4.4 8.5 - - + -
446B MET* 4.3 8.1 - - + -
530B GLN* 3.5 27.4 - - + +
536B PHE* 3.0 41.9 + - + +
537B CYS 3.8 5.6 - - - +
539B PHE* 1.3 82.9 - - + +
541B GLN* 1.3 69.2 + - + +
543B ALA* 3.8 4.1 - - - +
544B GLU* 2.9 46.9 + - + +
554B LEU* 4.5 7.4 - - + -
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Residues in contact with GLN 541 (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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537B CYS* 3.0 34.0 + - - +
538B ALA* 3.6 11.7 - - - +
540B VAL* 1.3 75.6 - - + +
542B GLU* 1.3 58.1 + - - +
544B GLU* 2.9 29.8 + - - +
545B SER* 3.2 12.5 + - - -
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Residues in contact with GLU 542 (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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538B ALA 3.0 14.4 + - - +
539B PHE* 3.6 13.2 - - - +
541B GLN* 1.3 79.3 - - - +
543B ALA* 1.3 65.5 + - - +
545B SER* 3.0 24.6 + - - +
546B ARG* 2.8 43.6 + - - +
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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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441B LEU* 3.7 28.6 - - + +
442B PHE* 4.0 14.7 - - + -
539B PHE* 2.9 24.3 + - + +
540B VAL* 3.9 4.9 - - - +
542B GLU* 1.3 83.0 + - - +
544B GLU* 1.3 61.2 + - - +
545B SER 3.2 1.3 + - - -
546B ARG* 3.4 22.9 + - - +
549B CYS* 3.4 13.3 - - - -
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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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442B PHE* 3.9 16.6 - - + -
530B GLN* 5.3 0.9 + - - -
540B VAL* 2.9 30.9 + - + +
541B GLN* 2.9 12.3 + - - +
543B ALA* 1.3 75.1 - - - +
545B SER* 1.3 58.2 + - - +
546B ARG 3.4 0.2 - - - -
549B CYS* 4.0 17.7 - - - +
551B ARG* 5.7 3.8 + - - -
552B LEU 4.6 5.0 - - - +
553B GLN* 3.3 34.7 + - + +
554B LEU* 2.8 34.0 + - - +
555B LYS 4.4 0.7 + - - -
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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