Contacts of the helix formed by residues 558 - 574 (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 LEU 558 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522A MET* 3.7 30.3 - - + -
526A PRO* 3.8 24.9 - - + +
553A PHE* 3.0 21.6 + - + +
554A MET* 5.7 0.2 - - - -
556A TYR* 3.4 33.9 - - + +
557A ASN* 1.3 76.0 - - - +
559A ILE* 1.3 54.5 + - - +
560A GLN 3.4 2.5 - - - -
561A GLN* 3.3 32.3 - - + +
562A CYS* 2.7 38.4 + - - +
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Residues in contact with ILE 559 (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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554A MET* 3.8 28.9 - - + -
557A ASN* 3.2 37.2 + - + +
558A LEU* 1.3 72.8 - - - +
560A GLN* 1.3 66.1 + - + +
562A CYS* 3.4 6.3 + - - +
563A THR* 2.7 43.4 + - - +
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Residues in contact with GLN 560 (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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557A ASN 4.0 8.3 + - - -
558A LEU* 5.6 0.2 - - - +
559A ILE* 1.3 94.2 - - + +
561A GLN* 1.3 84.4 + - - +
563A THR* 3.4 8.0 - - - -
564A ALA* 3.0 26.0 + - - +
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Residues in contact with GLN 561 (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* 5.2 10.5 - - - +
527A ASP* 6.3 0.4 - - - +
530A GLN* 3.6 24.1 - - + +
553A PHE* 4.3 7.6 - - + -
558A LEU* 3.3 46.0 - - + +
560A GLN* 1.3 111.0 + - - +
562A CYS* 1.3 56.2 + - - +
564A ALA* 3.6 7.3 - - - +
565A PHE* 2.8 34.8 + - - +
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Residues in contact with CYS 562 (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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550A VAL* 4.1 24.9 - - - -
553A PHE* 3.7 33.1 - - + -
554A MET* 4.8 13.9 - - - -
558A LEU 2.7 26.2 + - - +
559A ILE* 3.6 8.3 - - - +
561A GLN* 1.3 72.0 - - - +
563A THR* 1.3 64.8 + - - +
565A PHE* 3.2 7.0 + - - +
566A LEU* 3.1 35.3 + - - +
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Residues in contact with THR 563 (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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559A ILE* 2.7 27.9 + - - +
560A GLN* 3.4 8.4 - - - -
562A CYS* 1.3 77.7 - - - +
564A ALA* 1.3 61.7 + - - +
566A LEU* 3.3 9.6 + - - +
567A LEU* 3.0 41.6 + - + +
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Residues in contact with ALA 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A GLN* 3.9 15.0 - - - +
560A GLN 3.0 18.2 + - - +
561A GLN* 3.3 9.2 + - - +
563A THR* 1.3 75.8 - - - +
565A PHE* 1.3 57.2 + - - +
567A LEU* 3.4 9.6 + - - +
568A ASP* 2.9 37.4 + - - +
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Residues in contact with PHE 565 (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* 3.8 20.2 - - + +
533A ALA* 3.4 38.1 - - + -
534A GLN* 3.9 10.7 - - + +
537A VAL* 4.8 3.6 - - + -
546A ILE* 3.6 15.0 - - + -
549A ILE* 3.5 27.1 - - + -
550A VAL* 4.0 12.8 - - + -
553A PHE* 4.0 18.6 - + + -
561A GLN 2.8 21.3 + - - +
562A CYS 3.2 8.7 + - - +
564A ALA* 1.3 75.2 - - - +
566A LEU* 1.3 79.0 + - + +
568A ASP* 3.5 4.6 + - - +
569A ALA* 3.0 29.0 + - + +
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Residues in contact with LEU 566 (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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546A ILE* 4.2 15.0 - - + -
550A VAL* 4.1 13.5 - - + -
562A CYS* 3.1 32.7 + - - +
563A THR* 3.8 7.4 - - - +
565A PHE* 1.3 95.0 - - + +
567A LEU* 1.3 66.4 + - + +
569A ALA* 3.2 8.9 + - + +
570A LEU* 3.1 28.6 + - + +
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Residues in contact with LEU 567 (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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563A THR* 3.0 40.3 + - + +
564A ALA* 3.9 7.6 - - - +
566A LEU* 1.3 74.7 - - + +
568A ASP* 1.3 66.6 + - - +
570A LEU* 3.3 19.3 + - + +
571A LYS* 3.2 21.3 + - - +
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Residues in contact with ASP 568 (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* 5.1 8.2 + - - +
534A GLN* 4.7 19.2 - - + +
564A ALA* 2.9 22.4 + - - +
565A PHE* 3.6 7.4 - - + +
567A LEU* 1.3 78.0 - - - +
569A ALA* 1.3 63.0 + - - +
571A LYS* 3.2 8.1 + - - +
572A ASN* 3.1 25.3 + - - +
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Residues in contact with ALA 569 (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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534A GLN* 6.2 2.4 - - - +
537A VAL* 5.8 9.4 - - + +
546A ILE* 5.5 5.2 - - + -
565A PHE* 3.0 26.0 + - + +
566A LEU* 3.3 17.3 - - + +
568A ASP* 1.3 78.1 - - - +
570A LEU* 1.3 59.2 + - + +
572A ASN* 3.7 5.5 + - - +
573A ASN* 3.4 21.7 + - - +
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Residues in contact with LEU 570 (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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566A LEU* 3.1 18.4 + - + +
567A LEU* 3.6 22.9 - - + +
568A ASP 3.2 0.2 - - - -
569A ALA* 1.3 77.0 - - - +
571A LYS* 1.3 61.6 + - - +
573A ASN* 3.3 9.5 + - + +
574A ARG* 3.2 21.5 + - - +
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Residues in contact with LYS 571 (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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567A LEU 3.2 10.7 + - - +
568A ASP* 3.2 10.5 + - - +
570A LEU* 1.3 77.9 - - - +
572A ASN* 1.3 59.9 + - - +
574A ARG* 3.5 21.2 + - - +
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Residues in contact with ASN 572 (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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534A GLN* 5.1 9.9 + - + +
537A VAL 5.1 1.6 + - - -
538A GLN* 3.6 35.2 - - - +
568A ASP 3.1 15.0 + - - +
569A ALA* 4.1 7.0 - - - +
570A LEU 3.2 0.4 - - - -
571A LYS* 1.3 75.8 - - - +
573A ASN* 1.3 62.6 + - - +
574A ARG 3.2 3.4 + - - -
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Residues in contact with ASN 573 (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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569A ALA 3.4 15.3 + - - +
570A LEU* 3.3 10.9 + - + +
572A ASN* 1.3 79.2 - - - +
574A ARG* 1.3 58.0 + - - +
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Residues in contact with ARG 574 (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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570A LEU 3.2 14.5 + - - +
571A LYS* 3.5 16.8 + - - +
572A ASN 3.2 4.1 - - - -
573A ASN* 1.3 81.6 - - - +
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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