Contacts of the helix formed by residues 466 - 478 (chain B) in PDB entry 3DDN
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 GLY 466 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B ARG 3.2 0.6 + - - -
465B PRO* 1.3 71.7 - - - +
467B ALA* 1.3 62.9 + - - +
468B LEU 3.5 1.6 - - - -
469B GLY* 3.1 8.6 + - - -
470B LYS* 2.9 39.8 + - - +
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Residues in contact with ALA 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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461B TYR* 3.6 29.2 - - + -
462B VAL 4.2 2.2 - - - +
463B ASP* 4.6 2.5 - - - +
464B ARG* 3.2 31.9 + - + +
465B PRO 3.2 2.0 + - - -
466B GLY* 1.3 76.3 - - - +
468B LEU* 1.3 63.5 + - - +
470B LYS* 3.1 16.4 + - - +
471B ILE* 3.2 17.9 + - - +
518B VAL* 3.7 13.8 - - + +
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Residues in contact with LEU 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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461B TYR* 4.4 11.3 + - - +
466B GLY 3.5 0.4 - - - -
467B ALA* 1.3 78.5 - - - +
469B GLY* 1.3 62.3 + - - +
471B ILE* 3.4 18.0 + - + +
472B GLY* 3.0 22.8 + - - +
487B LEU* 4.2 18.4 - - + -
498B ILE* 3.5 31.0 - - + -
500B LEU* 5.6 1.3 - - + -
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Residues in contact with GLY 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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466B GLY* 3.1 10.7 + - - -
467B ALA 3.1 1.2 - - - -
468B LEU* 1.3 79.5 - - - +
470B LYS* 1.3 53.7 + - - +
472B GLY* 3.5 0.7 + - - -
473B THR* 2.7 39.8 + - - -
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Residues in contact with LYS 470 (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 ARG* 6.2 0.7 - - - +
465B PRO 5.2 1.5 + - - -
466B GLY* 2.9 29.3 + - - +
467B ALA* 3.1 9.8 + - - +
469B GLY* 1.3 76.1 - - - +
471B ILE* 1.3 64.5 + - - +
473B THR* 3.1 5.3 + - - -
474B LEU* 3.0 33.5 + - + +
517B ALA* 3.7 41.1 - - + +
518B VAL* 4.5 1.6 - - + -
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Residues in contact with ILE 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ILE* 4.1 19.3 - - + -
461B TYR* 3.8 38.1 - - + +
467B ALA 3.2 13.9 + - - +
468B LEU* 3.6 15.5 - - + +
470B LYS* 1.3 76.0 - - - +
472B GLY* 1.3 64.9 + - - +
474B LEU* 3.9 3.4 - - - +
475B LEU* 3.1 42.3 + - + +
498B ILE* 4.3 10.1 - - + -
500B LEU* 4.4 13.2 - - + -
514B ILE* 4.4 20.2 - - + +
517B ALA* 5.8 0.2 - - - +
518B VAL* 3.9 16.1 - - + +
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Residues in contact with GLY 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B LEU* 3.0 16.3 + - - +
469B GLY* 3.8 3.1 - - - -
471B ILE* 1.3 77.9 - - - +
473B THR* 1.3 62.2 + - - +
475B LEU* 3.4 4.9 + - - +
476B GLY* 2.9 22.5 + - - -
482B ILE* 4.8 14.2 - - - +
500B LEU* 6.2 0.2 - - - -
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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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469B GLY* 2.7 29.0 + - - -
470B LYS* 3.1 7.1 + - - -
472B GLY* 1.3 73.6 - - - +
474B LEU* 1.3 55.5 + - + +
476B GLY* 3.7 1.0 - - - -
477B THR* 2.7 50.4 + - - +
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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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470B LYS* 3.0 21.6 + - + +
471B ILE* 3.9 3.1 - - - +
473B THR* 1.3 78.7 - - + +
475B LEU* 1.3 66.9 + - - +
477B THR* 3.5 9.7 + - + +
478B ALA* 3.0 24.6 + - - +
510B VAL* 4.4 8.6 - - + +
513B ALA* 3.9 17.0 - - + +
514B ILE* 3.8 39.7 - - + +
517B ALA* 3.9 19.1 - - + -
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Residues in contact with LEU 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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457B LEU* 3.9 17.0 - - + -
471B ILE* 3.1 38.9 + - + +
472B GLY* 3.8 4.5 - - - +
474B LEU* 1.3 77.7 - - - +
476B GLY* 1.3 59.7 + - - +
478B ALA* 3.2 7.7 + - - +
479B GLY 3.3 0.2 + - - -
480B VAL* 3.0 50.9 + - + +
482B ILE* 4.5 12.8 - - + -
500B LEU* 4.2 13.9 - - + -
502B LEU* 4.7 5.4 - - + -
506B VAL* 4.1 28.3 - - + -
510B VAL* 4.8 1.3 - - + -
514B ILE* 3.6 22.7 - - + -
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Residues in contact with GLY 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 GLY 2.9 17.2 + - - -
473B THR* 3.8 0.7 - - - -
475B LEU* 1.3 72.3 - - - +
477B THR* 1.3 58.6 + - - +
479B GLY* 2.8 25.2 + - - -
480B VAL 4.2 6.9 + - - -
482B ILE* 6.0 0.6 - - - +
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Residues in contact with THR 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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473B THR* 2.7 39.1 + - - +
474B LEU* 3.7 12.7 - - + +
475B LEU 3.4 0.2 - - - -
476B GLY* 1.3 71.4 - - - +
478B ALA* 1.3 59.3 + - + +
479B GLY 3.4 0.9 + - - -
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Residues in contact with ALA 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B LEU 3.0 17.6 + - - +
475B LEU 3.5 5.2 - - - +
476B GLY 3.0 1.2 - - - -
477B THR* 1.3 76.8 - - - +
479B GLY* 1.3 60.1 + - - +
480B VAL* 3.3 16.3 + - + +
504B GLN* 4.9 3.5 - - - +
507B PRO* 5.5 3.8 - - + +
510B VAL* 4.2 26.5 - - + -
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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