Contacts of the helix formed by residues 471 - 482 (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 ASP 471 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445B LYS* 5.6 3.5 - - - +
467B VAL* 2.8 21.5 + - + +
468B LYS 3.6 0.2 - - - -
470B VAL* 1.3 85.7 - - + +
472B PRO* 1.3 64.2 - - - +
473B THR* 2.7 27.9 + - - -
474B LEU* 2.8 37.4 + - + +
475B ALA 3.5 9.9 + - - -
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Residues in contact with PRO 472 (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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468B LYS* 3.4 31.2 - - + +
469B SER 5.1 1.6 - - - +
470B VAL 4.2 3.1 - - - -
471B ASP* 1.3 85.3 - - - +
473B THR* 1.3 70.3 + - + +
475B ALA* 3.2 21.3 + - + +
476B LEU* 3.3 6.2 + - - +
491B CYS* 3.9 15.3 - - - -
494B GLU* 5.8 2.5 - - - +
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Residues in contact with THR 473 (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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471B ASP* 2.7 24.4 + - - -
472B PRO* 1.3 85.5 - - + +
474B LEU* 1.3 65.1 + - - +
476B LEU* 3.6 19.6 + - - +
477B SER* 4.2 2.9 + - - -
495B THR* 5.5 11.4 - - + -
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Residues in contact with LEU 474 (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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445B LYS* 3.9 30.7 - - + -
448B LEU* 4.6 19.3 - - + -
449B GLU* 5.0 12.8 - - + +
452B LEU* 5.5 8.1 - - + -
467B VAL* 4.8 6.7 - - + -
471B ASP* 2.8 34.7 + - + +
473B THR* 1.3 80.5 + - - +
475B ALA* 1.3 65.4 + - - +
477B SER* 3.1 28.5 + - - -
478B VAL* 3.5 11.6 + - + +
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Residues in contact with ALA 475 (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 3.5 21.8 - - - +
467B VAL* 3.6 15.2 - - + +
468B LYS* 3.6 24.9 - - + +
471B ASP 3.5 2.6 + - - +
472B PRO* 3.2 11.9 + - + +
474B LEU* 1.3 78.5 - - - +
476B LEU* 1.3 56.7 + - - +
478B VAL* 3.1 4.5 + - - +
479B TYR* 2.8 40.0 + - + -
491B CYS* 5.1 0.9 - - - -
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Residues in contact with LEU 476 (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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472B PRO 3.3 4.3 + - - +
473B THR* 3.7 14.4 - - - +
474B LEU 3.2 0.6 - - - -
475B ALA* 1.3 77.9 - - - +
477B SER* 1.3 58.9 + - - +
479B TYR* 3.4 5.1 + - - +
480B LEU* 2.8 44.9 + - + +
488B VAL* 3.9 8.3 - - + +
491B CYS* 3.8 35.4 - - + -
492B PHE* 3.6 42.0 - - + -
495B THR* 5.7 0.9 - - - +
497B GLN* 4.9 7.2 - - - +
500B LYS* 6.2 0.9 - - - +
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Residues in contact with SER 477 (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 LEU* 3.9 24.1 - - - +
473B THR 4.2 2.1 + - - -
474B LEU* 3.1 20.2 + - - -
476B LEU* 1.3 80.8 - - - +
478B VAL* 1.3 61.9 + - - +
480B LEU* 3.5 8.6 + - - +
481B ARG* 3.4 28.6 + - - +
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Residues in contact with VAL 478 (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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448B LEU* 6.5 0.9 - - + -
452B LEU* 4.9 17.3 - - + -
459B CYS* 3.7 17.1 - - + +
460B SER 4.5 2.5 - - - +
463B LEU* 3.8 29.2 - - + -
464B GLY* 3.7 27.1 - - - +
467B VAL* 4.0 18.2 - - + -
474B LEU* 3.9 13.9 - - + +
475B ALA 3.1 7.3 + - - +
477B SER* 1.3 76.3 - - - +
479B TYR* 1.3 63.0 + - - +
480B LEU 3.3 0.3 + - - -
481B ARG* 3.3 2.4 + - - -
482B ALA* 3.0 20.4 + - - +
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Residues in contact with TYR 479 (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 5.6 0.2 - - - -
461B GLU* 3.8 15.0 + - + -
464B GLY* 3.4 28.3 - - - -
465B ASP* 2.9 29.3 + - - +
468B LYS* 4.8 10.8 - - + +
475B ALA* 2.8 35.6 + - + +
476B LEU* 3.7 8.1 - - - +
478B VAL* 1.3 73.7 - - + +
480B LEU* 1.3 63.7 + - - +
482B ALA* 3.3 10.9 + - + -
483B ASN* 3.4 8.1 + - - -
484B VAL* 3.6 26.8 + - + +
487B LYS* 3.6 50.9 - - + +
488B VAL* 3.6 20.7 - - + +
491B CYS* 4.8 5.2 - - - -
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Residues in contact with LEU 480 (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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476B LEU* 2.8 41.9 + - + +
477B SER* 3.5 8.7 - - - +
478B VAL 3.2 0.4 - - - -
479B TYR* 1.3 78.3 - - - +
481B ARG* 1.3 63.7 + - + +
483B ASN* 3.4 10.7 + - - -
488B VAL* 3.8 22.2 - - + +
492B PHE* 4.6 7.9 - - + -
504B TYR* 3.8 29.8 + - + -
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Residues in contact with ARG 481 (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 LEU* 3.1 52.1 + - - +
453B LYS* 4.6 7.7 + - - +
455B ASP* 4.4 25.2 + - - +
457B LEU 5.9 2.2 - - - +
459B CYS* 4.1 17.9 + - - +
477B SER* 3.4 9.1 + - - +
478B VAL 3.3 7.2 + - - +
480B LEU* 1.3 74.1 - - + +
482B ALA* 1.3 61.6 + - - +
483B ASN* 3.1 8.1 + - - +
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Residues in contact with ALA 482 (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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459B CYS* 3.6 32.6 - - + +
460B SER* 4.1 13.3 - - - +
461B GLU* 4.6 0.9 - - - +
478B VAL 3.0 17.1 + - - +
479B TYR* 3.7 8.7 - - + +
480B LEU 3.3 0.6 - - - -
481B ARG* 1.3 74.4 - - - +
483B ASN* 1.3 64.0 + - - +
484B VAL* 3.2 24.1 + - + +
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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