Contacts of the helix formed by residues 519 - 533 (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 GLN 519 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515B PHE* 4.8 1.6 - - + +
516B CYS* 3.2 20.0 - - - +
517B SER 3.2 4.6 + - - +
518B ARG* 1.3 74.8 - - - +
520B SER* 1.3 70.3 + - - +
521B PHE 3.1 0.4 - - - -
522B ALA* 3.0 6.4 + - - +
523B LEU* 3.0 36.0 + - + +
558B ILE* 4.0 22.0 - - + +
559B PRO* 3.2 37.9 + - + +
562B MET* 3.8 27.3 - - - +
606B VAL* 6.0 1.4 - - + +
610B GLU* 5.2 3.8 - - - +
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Residues in contact with SER 520 (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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517B SER 4.8 1.4 + - - -
519B GLN* 1.3 79.1 + - - +
521B PHE* 1.3 65.8 + - - +
523B LEU* 3.8 9.3 - - - +
524B GLU* 3.0 29.4 + - - +
610B GLU* 3.2 39.7 + - - +
613B LEU* 5.3 3.6 - - - +
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Residues in contact with PHE 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B GLU* 6.3 1.8 - - + -
459B ASN* 3.6 39.0 - - - -
460B ILE* 4.1 7.2 - - + -
517B SER 5.4 0.2 - - - +
518B ARG* 3.2 37.7 - - + -
519B GLN 4.0 0.6 - - - +
520B SER* 1.3 80.4 + - - +
522B ALA* 1.3 72.2 + - - +
523B LEU 3.1 0.2 + - - -
524B GLU* 3.2 12.8 + - - +
525B GLN* 3.0 59.9 + - + +
613B LEU* 3.6 30.1 - - + -
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Residues in contact with ALA 522 (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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460B ILE* 3.4 30.0 - - + +
518B ARG 3.2 19.7 + - - +
519B GLN 3.0 6.0 + - - +
521B PHE* 1.3 88.9 - - - +
523B LEU* 1.3 63.7 + - - +
525B GLN* 3.4 3.2 - - - +
526B LEU* 3.1 27.3 + - - +
558B ILE* 4.1 20.2 - - + -
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Residues in contact with LEU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B GLN* 3.0 33.4 + - + +
520B SER* 3.8 7.4 - - - +
522B ALA* 1.3 77.2 - - + +
524B GLU* 1.3 69.0 + - - +
526B LEU* 2.8 19.7 + - + +
527B LYS* 2.9 15.3 + - - +
555B LYS* 4.0 35.9 - - + +
558B ILE* 4.1 25.1 - - + -
559B PRO* 5.1 4.0 - - + -
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Residues in contact with GLU 524 (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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520B SER* 3.0 17.1 + - - +
521B PHE* 3.3 18.7 - - - +
523B LEU* 1.3 76.7 - - - +
525B GLN* 1.3 58.6 + - + +
527B LYS* 3.1 9.8 + - - +
528B ALA* 2.8 35.4 + - + +
613B LEU* 5.6 2.6 - - - +
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Residues in contact with GLN 525 (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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452B PHE* 4.3 15.1 - - - -
456B GLU* 5.1 8.3 + - - +
460B ILE* 4.2 16.4 - - + +
521B PHE* 3.0 49.6 + - + +
522B ALA 3.4 9.2 - - - +
524B GLU* 1.3 85.7 - - - +
526B LEU* 1.3 62.1 + - - +
528B ALA* 3.5 8.8 - - - +
529B LYS* 3.1 23.0 + - - +
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Residues in contact with LEU 526 (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* 4.2 17.0 - - + -
452B PHE* 4.5 4.5 - - + -
460B ILE* 4.3 26.7 - - + -
461B PHE* 4.8 2.2 - - + -
522B ALA 3.1 17.0 + - - +
523B LEU* 2.8 17.8 + - + +
525B GLN* 1.3 70.5 - - - +
527B LYS* 1.3 53.2 + - - +
529B LYS* 3.1 3.4 + - - -
530B GLN* 2.7 49.1 + - - +
536B PHE* 3.7 23.2 - - + -
554B LEU* 4.0 17.0 - - + -
558B ILE* 3.6 29.6 - - + -
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Residues in contact with LYS 527 (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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523B LEU* 2.9 11.9 + - - +
524B GLU* 3.6 10.3 - - - +
526B LEU* 1.3 74.3 - - - +
528B ALA* 1.3 65.4 + - - +
530B GLN* 3.0 17.4 + - + +
531B ARG* 2.9 71.7 + - + +
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Residues in contact with ALA 528 (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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524B GLU* 2.8 14.2 + - + +
525B GLN* 3.5 18.2 - - - +
527B LYS* 1.3 78.9 - - - +
529B LYS* 1.3 62.4 + - - +
531B ARG* 3.1 6.4 + - - +
532B LYS* 2.9 25.9 + - - +
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Residues in contact with LYS 529 (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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451B PHE* 3.6 31.4 + - - +
452B PHE* 3.8 29.2 - - + -
525B GLN 3.1 12.2 + - - +
526B LEU 3.1 2.0 + - - -
528B ALA* 1.3 79.1 - - - +
530B GLN* 1.3 61.1 + - - +
532B LYS* 4.5 9.4 - - - -
533B ASP* 3.2 51.2 + - - +
536B PHE* 3.4 30.9 - - + -
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Residues in contact with GLN 530 (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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526B LEU* 2.7 26.4 + - - +
527B LYS* 3.0 26.7 + - + +
529B LYS* 1.3 73.6 - - - +
531B ARG* 1.3 62.3 + - + +
533B ASP 3.6 6.6 + - - +
534B PRO* 5.0 0.2 - - - +
536B PHE* 3.4 19.7 - - + -
537B CYS* 3.4 38.9 - - + +
540B VAL* 3.5 32.5 - - + +
544B GLU* 5.3 0.8 + - - -
554B LEU* 5.0 4.4 - - - +
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Residues in contact with ARG 531 (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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527B LYS* 2.9 65.4 + - + +
528B ALA* 3.9 4.5 - - - +
530B GLN* 1.3 76.8 - - + +
532B LYS* 1.3 64.0 + - - +
533B ASP 3.6 0.3 + - - -
534B PRO* 5.8 0.2 - - - +
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Residues in contact with LYS 532 (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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528B ALA 2.9 18.7 + - - +
529B LYS* 4.3 8.7 - - - +
531B ARG* 1.3 78.6 - - - +
533B ASP* 1.3 60.0 + - + +
534B PRO* 4.0 6.0 - - - +
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Residues in contact with ASP 533 (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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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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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