Contacts of the helix formed by residues 525 - 537 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A VAL 2.8 20.2 + - - +
522A MET 3.9 0.2 - - - -
523A ARG 3.5 0.6 - - - -
524A ILE* 1.3 89.2 + - - +
526A PRO* 1.3 68.4 - - - +
527A ASP* 2.5 27.1 + - - -
528A GLN* 3.3 22.2 + - - +
529A GLY 3.2 10.9 + - - -
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Residues in contact with PRO 526 (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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522A MET* 3.5 26.4 - - - +
523A ARG 5.0 0.9 - - - +
524A ILE 4.4 2.2 - - - +
525A SER* 1.3 82.6 - - - +
527A ASP* 1.3 66.0 + - + +
528A GLN 3.2 2.2 - - - -
529A GLY* 2.8 16.5 + - - +
530A GLN* 2.9 15.6 + - - +
553A PHE* 5.5 0.5 - - - -
558A LEU* 3.8 30.9 - - + +
561A GLN* 5.2 10.6 - - + +
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Residues in contact with ASP 527 (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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525A SER* 2.5 33.4 + - - -
526A PRO* 1.3 76.8 - - + +
528A GLN* 1.3 70.8 + - - +
530A GLN* 3.6 12.8 + - - +
531A GLN* 3.6 10.4 + - - +
561A GLN* 6.3 0.9 - - - +
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Residues in contact with GLN 528 (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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496A GLY* 3.3 29.6 + - - +
498A VAL* 4.2 10.7 + - + +
521A VAL* 3.7 11.4 - - + -
524A ILE* 6.2 0.8 - - - +
525A SER* 3.3 20.7 + - - +
526A PRO 3.2 0.4 - - - -
527A ASP* 1.3 86.8 - - - +
529A GLY* 1.3 58.3 + - - +
531A GLN* 3.2 18.9 + - - +
532A PHE* 2.9 29.6 + - - +
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Residues in contact with GLY 529 (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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518A LEU* 3.8 9.1 - - - +
521A VAL* 3.4 19.0 - - - +
522A MET* 4.2 15.7 - - - -
525A SER 3.2 7.4 + - - -
526A PRO* 2.8 11.6 + - - -
528A GLN* 1.3 78.1 - - - +
530A GLN* 1.3 55.7 + - - -
532A PHE* 3.3 4.5 + - - +
533A ALA* 2.9 27.9 + - - +
553A PHE* 4.8 0.4 - - - -
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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 PRO 2.9 10.5 + - - +
527A ASP* 4.0 9.9 - - - +
528A GLN 3.3 0.2 - - - -
529A GLY* 1.3 72.7 - - - +
531A GLN* 1.3 66.4 + - - +
533A ALA* 3.3 3.6 + - - +
534A GLN* 3.1 19.6 + - - +
553A PHE* 3.9 18.5 - - + -
561A GLN* 3.6 27.8 - - + +
564A ALA* 3.9 12.2 + - - +
565A PHE* 3.8 37.8 - - + +
568A ASP* 5.1 8.5 + - - +
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Residues in contact with GLN 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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498A VAL* 5.4 6.1 - - - +
499A GLN* 3.4 30.5 - - - +
527A ASP 3.6 9.3 + - - +
528A GLN* 3.2 20.2 + - - +
530A GLN* 1.3 78.6 - - - +
532A PHE* 1.3 63.7 + - - +
534A GLN* 3.1 29.3 + - - +
535A MET* 3.3 22.6 + - + +
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Residues in contact with PHE 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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498A VAL* 3.2 34.5 - - + +
501A ILE* 5.0 6.7 - - + -
502A VAL* 4.1 16.2 - - + -
514A TRP* 4.0 21.3 - + - -
517A LEU* 3.7 15.7 - - + -
518A LEU* 3.5 48.0 - - + -
521A VAL* 3.9 15.5 - - + -
528A GLN 2.9 17.9 + - - +
529A GLY* 3.5 4.9 - - - +
530A GLN 3.3 0.2 - - - -
531A GLN* 1.3 74.8 - - - +
533A ALA* 1.3 64.1 + - - +
535A MET* 3.2 12.4 + - - +
536A LEU* 3.2 36.5 + - + +
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Residues in contact with ALA 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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518A LEU* 4.8 15.0 - - + +
529A GLY 2.9 14.6 + - - +
530A GLN 3.4 9.9 - - - +
531A GLN 3.3 0.2 - - - -
532A PHE* 1.3 75.5 - - - +
534A GLN* 1.3 62.3 + - - +
536A LEU* 3.4 16.5 + - - +
537A VAL* 3.6 8.8 + - - +
549A ILE* 4.4 3.2 - - + +
553A PHE* 3.7 23.3 - - + -
565A PHE* 3.4 28.5 - - + -
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Residues in contact with GLN 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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530A GLN 3.1 10.9 + - - +
531A GLN* 3.1 21.5 + - - +
533A ALA* 1.3 76.9 - - - +
535A MET* 1.3 68.1 + - - +
537A VAL* 3.3 22.6 + - - +
538A GLN* 3.6 27.2 + - - +
565A PHE* 3.9 12.5 - - + +
568A ASP* 4.7 19.6 - - + +
569A ALA* 6.2 1.8 - - - +
572A ASN* 5.1 8.3 - - + +
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Residues in contact with MET 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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498A VAL* 4.2 12.8 - - - -
499A GLN* 3.7 38.8 - - + +
502A VAL* 3.7 44.2 - - + +
503A LEU* 5.4 5.2 - - + -
506A LYS* 5.0 3.3 + - - -
531A GLN* 3.6 25.1 - - + +
532A PHE 3.2 6.7 + - - +
534A GLN* 1.3 83.9 - - - +
536A LEU* 1.3 66.2 + - + +
537A VAL 3.3 2.8 + - - -
538A GLN* 4.1 20.4 + - - +
543A LEU* 4.0 11.7 - - - +
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Residues in contact with LEU 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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502A VAL* 4.9 1.1 - - + -
514A TRP* 3.9 32.8 - - + +
515A ILE 5.1 0.2 - - - +
518A LEU* 4.6 10.3 - - + -
532A PHE* 3.2 43.2 + - + +
533A ALA* 3.7 11.0 - - - +
534A GLN 3.3 0.4 - - - -
535A MET* 1.3 81.8 - - - +
537A VAL* 1.3 62.1 + - + +
538A GLN 3.9 0.6 + - - -
542A PRO* 3.7 1.0 - - - +
543A LEU* 2.9 43.8 + - + -
544A ALA* 3.4 34.6 + - + -
549A ILE* 4.2 15.3 - - + -
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Residues in contact with VAL 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 ALA 3.6 5.5 + - - +
534A GLN 3.3 9.8 + - - +
535A MET 3.2 0.8 - - - -
536A LEU* 1.3 81.0 - - - +
538A GLN* 1.3 71.7 + - - +
542A PRO* 4.6 10.3 - - + -
544A ALA 4.2 12.1 - - - +
546A ILE* 3.8 23.8 - - + -
549A ILE* 3.6 31.2 - - + -
565A PHE* 4.8 2.7 - - + -
569A ALA* 5.8 9.4 - - + +
572A ASN* 5.1 1.6 + - - -
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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