Contacts of the helix formed by residues 525 - 537 (chain B) in PDB entry 5ODS
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 525 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521B VAL* 2.9 20.0 + - - +
522B MET* 3.9 3.2 - - - -
523B ARG 3.4 1.6 - - - -
524B ILE* 1.3 91.7 + - - +
526B PRO* 1.3 70.5 - - - +
527B ASP* 3.3 3.8 + - - -
528B GLN* 3.6 28.4 + - - +
529B GLY* 3.1 17.5 + - - -
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Residues in contact with PRO 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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522B MET* 4.3 19.9 - - + +
523B ARG 4.9 1.6 - - - +
524B ILE 4.3 3.1 - - - +
525B SER* 1.3 82.7 - - - +
527B ASP* 1.3 65.0 + - + +
529B GLY* 3.1 11.6 + - - +
530B GLN* 3.2 14.4 + - - +
553B PHE* 5.5 1.0 - - - -
558B LEU* 4.4 33.7 - - + -
561B GLN* 5.7 5.3 - - + +
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Residues in contact with ASP 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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525B SER* 3.3 4.2 - - - -
526B PRO* 1.3 81.1 - - + +
528B GLN* 1.3 64.1 + - + +
530B GLN* 3.7 9.9 + - - +
531B GLN* 3.5 16.1 + - - +
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Residues in contact with GLN 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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496B GLY* 2.5 42.2 + - - +
497B GLN* 3.8 4.9 - - - +
498B VAL* 4.1 20.0 - - + +
521B VAL* 4.1 5.7 - - + +
524B ILE* 5.4 0.2 - - - +
525B SER* 3.6 26.5 + - - +
527B ASP* 1.3 79.5 - - + +
529B GLY* 1.3 55.9 + - - +
530B GLN 3.2 2.5 - - - -
531B GLN* 2.9 9.9 + - + +
532B PHE* 2.4 38.5 + - - +
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Residues in contact with GLY 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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518B LEU* 4.7 3.3 - - - +
521B VAL* 3.8 13.8 - - - +
522B MET* 3.6 28.6 - - - +
525B SER 3.1 13.1 + - - -
526B PRO 3.1 5.9 + - - -
528B GLN* 1.3 75.8 - - - +
530B GLN* 1.3 56.2 + - - +
532B PHE* 3.5 2.5 + - - +
533B ALA* 2.9 30.1 + - - +
553B PHE* 4.2 1.1 - - - -
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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 PRO 3.2 10.6 + - - +
527B ASP* 3.9 10.8 - - - +
528B GLN 3.2 0.2 - - - -
529B GLY* 1.3 75.3 - - - +
531B GLN* 1.3 61.6 - - - +
533B ALA* 3.4 2.9 + - - +
534B GLN* 3.1 21.7 + - - +
553B PHE* 3.8 16.6 - - + -
561B GLN* 3.1 40.2 + - + +
564B ALA* 3.4 20.6 - - - +
565B PHE* 3.8 21.4 - - + +
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Residues in contact with GLN 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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498B VAL* 3.9 17.2 - - + +
499B GLN* 5.2 10.2 + - - +
527B ASP 3.5 5.9 + - - +
528B GLN* 2.9 21.6 + - + +
530B GLN* 1.3 76.2 + - - +
532B PHE* 1.3 66.6 + - - +
534B GLN* 3.2 36.6 + - - +
535B MET* 3.5 18.6 - - - +
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Residues in contact with PHE 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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498B VAL* 3.8 21.7 - - + +
501B ILE* 4.3 10.3 - - + -
502B VAL* 3.9 13.5 - - + -
514B TRP* 3.2 41.3 - + - -
517B LEU* 4.0 7.2 - - + -
518B LEU* 3.6 45.1 - - + -
521B VAL* 4.1 16.2 - - + -
528B GLN 2.4 20.2 + - - +
529B GLY 3.8 2.7 - - - +
531B GLN* 1.3 71.9 - - - +
533B ALA* 1.3 56.3 + - - +
535B MET* 2.9 43.2 + - + +
536B LEU* 3.1 26.5 - - + +
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Residues in contact with ALA 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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518B LEU* 4.1 13.5 - - + -
529B GLY 2.9 19.5 + - - +
530B GLN 3.5 5.8 - - - +
532B PHE* 1.3 76.7 - - - +
534B GLN* 1.3 62.1 + - - +
536B LEU* 3.3 22.1 + - - +
537B VAL* 3.6 7.6 + - - +
549B ILE* 4.7 3.6 - - + +
553B PHE* 3.9 24.7 - - + -
565B PHE* 3.7 21.9 - - + -
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Residues in contact with GLN 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 3.1 12.9 + - - +
531B GLN* 3.3 28.6 + - - +
532B PHE 3.0 1.0 + - - -
533B ALA* 1.3 77.9 - - - +
535B MET* 1.3 63.4 + - - +
537B VAL* 2.9 16.1 + - - +
538B GLN* 2.8 38.6 + - - +
565B PHE* 4.5 10.7 - - + -
568B ASP* 4.6 19.5 - - + +
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Residues in contact with MET 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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498B VAL* 3.4 38.6 - - + +
499B GLN* 3.7 18.2 - - + +
502B VAL* 3.7 33.9 - - + +
531B GLN* 3.5 28.6 + - - +
532B PHE* 2.9 26.4 + - + +
534B GLN* 1.3 79.6 - - - +
536B LEU* 1.3 65.2 + - - +
537B VAL 3.1 2.8 + - - -
538B GLN* 3.3 21.2 - - + +
543B LEU* 3.2 18.3 - - - +
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Residues in contact with LEU 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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502B VAL* 5.5 1.1 - - + -
514B TRP* 4.1 25.8 - - + +
515B ILE* 5.2 0.2 - - + -
518B LEU* 3.9 20.0 - - + -
532B PHE* 3.1 55.4 - - + +
533B ALA* 3.3 12.7 + - - +
535B MET* 1.3 79.1 - - + +
537B VAL* 1.3 62.0 + - - +
542B PRO 3.8 0.2 - - - -
543B LEU* 2.8 60.4 + - + +
544B ALA* 3.8 17.0 - - + -
549B ILE* 4.3 14.1 - - + -
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Residues in contact with VAL 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ALA 3.6 5.1 + - - +
534B GLN* 2.9 21.2 + - - +
535B MET 3.1 0.2 - - - -
536B LEU* 1.3 82.1 - - - +
538B GLN* 1.3 73.6 + - - +
542B PRO* 5.2 8.5 - - + -
543B LEU 4.9 2.2 - - - +
544B ALA 5.3 2.5 - - - +
546B ILE* 4.2 26.0 - - + -
549B ILE* 4.1 23.8 - - + -
565B PHE* 4.6 7.2 - - + -
569B ALA* 4.7 21.9 - - + +
572B ASN* 5.7 5.9 - - + +
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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