Contacts of the helix formed by residues 460 - 469 (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 460 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B LYS* 4.2 19.2 + - - +
433B LEU* 4.2 15.4 - - - +
458B GLU 3.9 1.8 + - - -
459B CYS* 1.3 76.2 - - - +
461B GLU* 1.3 66.5 + - - +
462B GLU* 3.0 22.0 + - - -
463B LEU* 3.4 19.4 + - - +
464B GLY 3.7 2.6 + - - -
478B VAL* 4.5 1.4 - - - +
479B TYR* 5.6 0.2 - - - -
482B ALA* 4.1 10.6 - - - +
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Residues in contact with GLU 461 (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 SER* 1.3 73.5 - - - +
462B GLU* 1.3 71.3 + - - +
463B LEU 3.0 0.2 - - - -
464B GLY* 2.7 23.7 + - - -
465B ASP* 2.9 37.1 + - - +
479B TYR* 3.8 9.3 - - + -
482B ALA* 4.6 1.4 - - - +
484B VAL* 4.8 12.7 - - + +
487B LYS* 3.3 47.8 - - + +
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Residues in contact with GLU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU* 3.8 24.4 - - + +
460B SER* 3.0 19.9 + - - +
461B GLU* 1.3 86.5 + - - +
463B LEU* 1.3 60.2 + - - +
465B ASP* 2.9 27.8 - - - +
466B LEU* 3.1 14.2 - - - +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LYS 5.7 0.2 - - - +
432B SER* 4.2 3.8 - - - +
433B LEU* 3.8 30.6 - - + +
436B CYS* 4.1 28.7 - - + -
457B LEU* 3.8 27.6 - - + -
458B GLU 4.0 7.2 - - - +
459B CYS* 4.0 11.7 - - - -
460B SER* 3.4 14.5 + - - +
461B GLU 3.0 0.2 - - - -
462B GLU* 1.3 81.0 - - - +
464B GLY* 1.3 62.2 + - - +
466B LEU* 3.5 4.6 + - + +
467B VAL* 3.1 31.5 + - + +
478B VAL* 3.8 23.8 - - + -
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Residues in contact with GLY 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B SER 3.7 0.4 + - - -
461B GLU 2.7 10.6 + - - -
463B LEU* 1.3 79.9 - - - +
465B ASP* 1.3 55.9 + - - -
467B VAL* 3.1 11.3 - - - +
468B LYS* 2.9 27.2 + - - +
475B ALA* 3.5 4.2 - - - +
478B VAL* 3.7 16.2 - - - +
479B TYR* 3.3 23.1 - - - -
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Residues in contact with ASP 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B GLU* 2.9 37.8 + - - +
462B GLU* 2.9 22.3 - - - +
464B GLY* 1.3 72.0 - - - +
466B LEU* 1.3 82.9 + - - +
468B LYS* 3.4 18.4 - - + +
469B SER* 3.3 14.6 + - - -
479B TYR* 2.9 16.8 + - - +
487B LYS* 5.8 0.2 - - + -
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Residues in contact with LEU 466 (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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433B LEU* 4.5 14.4 - - + +
436B CYS* 4.3 27.6 - - + +
437B ARG* 4.2 37.2 - - + +
462B GLU 3.1 16.7 + - - +
463B LEU* 3.7 7.4 - - + +
464B GLY 3.2 0.2 - - - -
465B ASP* 1.3 86.9 + - - +
467B VAL* 1.3 59.8 + - + +
469B SER* 3.3 18.7 + - - -
470B VAL* 5.0 2.4 + - - +
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Residues in contact with VAL 467 (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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436B CYS* 5.5 9.6 - - + -
448B LEU* 5.5 13.2 - - + -
463B LEU* 3.1 21.3 - - + +
464B GLY* 3.1 21.8 - - - +
466B LEU* 1.3 78.9 - - + +
468B LYS* 1.3 63.1 + - - +
469B SER 3.3 0.2 - - - -
470B VAL* 3.8 4.6 + - - +
471B ASP* 2.8 30.6 + - - +
474B LEU* 5.3 5.2 - - + -
475B ALA* 3.6 23.1 - - + +
478B VAL* 4.0 14.6 - - + -
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Residues in contact with LYS 468 (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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464B GLY 2.9 18.9 + - - +
465B ASP* 3.4 15.7 - - + +
466B LEU 3.3 0.2 - - - -
467B VAL* 1.3 76.5 - - - +
469B SER* 1.3 66.2 + - - +
471B ASP 4.1 0.9 - - - -
472B PRO* 3.3 35.9 - - + +
475B ALA* 3.6 14.1 - - + -
479B TYR* 4.8 9.4 - - + +
491B CYS* 5.9 3.8 - - - -
494B GLU* 3.8 27.4 + - - -
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Residues in contact with SER 469 (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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465B ASP 3.3 9.6 + - - -
466B LEU* 3.3 16.5 + - - -
467B VAL 3.3 0.4 - - - -
468B LYS* 1.3 80.0 - - - +
470B VAL* 1.3 70.0 + - - +
472B PRO* 5.1 1.7 - - - +
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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