Contacts of the helix formed by residues 471 - 486 (chain B) in PDB entry 1DGB
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 GLN 471 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A PHE* 3.8 12.3 - - - -
180B ASP* 2.7 26.0 + - - +
470B ALA* 1.3 76.7 - - - +
472B ILE* 1.3 62.3 + - - +
473B PHE* 3.5 25.8 - - + -
474B ILE* 3.1 7.2 + - + +
475B GLN* 2.9 24.1 + - - +
5D ARG* 3.0 29.4 - - - +
10D ASP* 5.6 0.4 - - - -
13D GLN* 2.9 41.9 + - - +
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Residues in contact with ILE 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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470B ALA 5.3 0.4 - - - +
471B GLN* 1.3 69.8 - - - +
473B PHE* 1.3 67.8 + - - +
475B GLN* 2.9 30.8 + - - +
476B LYS* 2.7 45.9 + - + +
501B ASN* 3.7 18.2 - - + +
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Residues in contact with PHE 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A SER* 3.8 27.6 - - - -
409A PHE* 3.8 20.0 - + - -
184B ASP* 4.3 0.7 - - - -
471B GLN* 3.5 35.7 - - + -
472B ILE* 1.3 78.6 - - - +
474B ILE* 1.3 90.4 + - + +
476B LYS* 3.1 8.3 + - - +
477B LYS* 2.9 32.2 + - + +
13D GLN* 4.3 5.6 - - - -
16D LYS* 4.6 12.3 - - - -
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Residues in contact with ILE 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PHE* 4.3 3.4 - - + -
180B ASP* 3.7 46.4 - - + +
183B TRP* 3.5 40.8 - - + +
184B ASP* 3.9 12.6 - - + +
187B SER* 4.4 2.9 - - - +
467B LEU* 4.5 1.3 - - + -
470B ALA* 4.0 5.8 - - + -
471B GLN* 3.1 10.2 + - + +
473B PHE* 1.3 110.1 - - + +
475B GLN* 1.3 64.9 + - - +
477B LYS* 3.3 5.8 + - - +
478B ALA* 2.8 22.9 + - - +
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Residues in contact with GLN 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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467B LEU* 3.9 26.2 - - + +
468B LYS* 3.0 29.8 - - - +
470B ALA 3.1 10.1 - - - +
471B GLN 2.9 17.6 + - - +
472B ILE* 3.2 23.4 - - - +
474B ILE* 1.3 76.6 - - - +
476B LYS* 1.3 55.7 + - + +
478B ALA* 3.2 1.6 + - - +
479B VAL* 2.7 41.3 + - - +
494B GLN* 5.1 4.0 - - - +
497B LEU* 3.9 26.0 - - + +
501B ASN* 3.2 29.6 + - - -
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Residues in contact with LYS 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ILE* 2.7 37.5 + - + +
473B PHE* 3.4 10.1 - - - +
475B GLN* 1.3 74.7 - - + +
477B LYS* 1.3 64.2 + - - +
479B VAL* 3.0 6.0 + - + +
480B LYS* 2.8 24.8 + - - +
494B GLN* 3.9 30.7 - - - +
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Residues in contact with LYS 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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187B SER* 3.3 38.9 + - - +
188B LEU* 4.9 17.2 + - + +
190B PRO* 5.5 2.6 - - - +
473B PHE* 2.9 21.9 + - + +
474B ILE* 3.6 6.1 - - - +
476B LYS* 1.3 71.2 - - - +
478B ALA* 1.3 63.6 + - - +
480B LYS* 3.2 38.5 + - + +
481B ASN* 3.2 30.0 + - - +
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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
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183B TRP* 4.2 19.3 - - + +
187B SER* 3.9 16.8 - - - -
467B LEU* 4.1 19.7 - - + -
474B ILE 2.8 18.3 + - - +
475B GLN 3.6 3.1 - - - +
477B LYS* 1.3 76.3 - - - +
479B VAL* 1.3 62.4 + - - +
481B ASN* 3.2 15.5 + - - +
482B PHE* 3.1 24.0 + - + -
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Residues in contact with VAL 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B LEU* 4.8 2.2 - - + -
475B GLN 2.7 25.0 + - - +
476B LYS* 3.5 5.4 - - + +
478B ALA* 1.3 70.0 - - - +
480B LYS* 1.3 66.2 + - - +
482B PHE* 3.3 7.3 + - - +
483B THR* 2.8 35.7 + - - +
490B GLY 3.6 22.0 - - - +
493B ILE* 4.3 11.7 - - + -
494B GLN* 3.6 30.5 - - + +
497B LEU* 3.8 22.7 - - + -
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Residues in contact with LYS 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 LYS 2.8 11.1 + - - +
477B LYS* 3.2 35.6 + - + +
479B VAL* 1.3 79.6 - - - +
481B ASN* 1.3 74.4 + - - +
483B THR* 3.4 8.2 + - - -
484B GLU* 3.1 32.7 + - - +
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Residues in contact with ASN 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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186B TRP 4.2 1.8 + - - -
187B SER* 2.9 39.4 + - - +
190B PRO* 4.1 20.5 - - - +
193B LEU* 4.0 23.9 - - + +
477B LYS* 3.2 23.9 + - - +
478B ALA* 3.2 8.7 + - - +
479B VAL 3.2 0.6 - - - -
480B LYS* 1.3 83.6 + - - +
482B PHE* 1.3 63.6 + - - +
484B GLU* 2.9 28.5 + - - +
485B VAL* 3.2 9.7 + - - +
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Residues in contact with PHE 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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183B TRP* 4.1 27.1 - + - -
193B LEU* 3.8 22.2 - - + -
196B VAL* 4.3 9.9 - - + -
197B SER* 4.5 4.0 - - - -
463B ILE* 3.6 21.3 - - + -
467B LEU* 5.2 1.8 - - + -
478B ALA* 3.1 30.3 + - + -
479B VAL* 3.3 7.6 + - + +
481B ASN* 1.3 76.8 - - - +
483B THR* 1.3 59.6 + - - +
485B VAL* 2.8 25.5 + - - +
486B HIS 2.9 11.6 + - - +
489B TYR* 3.4 44.6 - + + +
490B GLY* 3.9 17.3 - - - +
493B ILE* 3.7 19.7 - - + -
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Residues in contact with THR 483 (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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479B VAL* 2.8 28.4 + - - +
480B LYS* 3.4 9.7 - - - -
482B PHE* 1.3 75.7 - - - +
484B GLU* 1.3 63.7 + - - +
486B HIS* 3.0 26.7 - - - -
487B PRO* 3.2 21.6 - - + +
490B GLY* 3.3 16.0 - - - -
491B SER 4.4 0.6 + - - +
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Residues in contact with GLU 484 (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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440B VAL* 4.3 25.1 - - + +
444B ARG* 3.0 16.5 + - - -
480B LYS* 3.1 22.7 + - - +
481B ASN* 2.9 19.9 + - - +
483B THR* 1.3 76.9 - - - +
485B VAL* 1.3 63.4 + - - +
486B HIS* 4.3 0.3 - - - -
487B PRO* 5.5 0.2 - - - +
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Residues in contact with VAL 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.9 24.5 - - + -
440B VAL* 4.3 11.4 - - + +
443B VAL* 3.6 32.3 - - + +
444B ARG* 2.8 54.5 + - - +
447B TYR* 4.8 2.2 - - + -
481B ASN 3.6 9.4 - - - +
482B PHE* 2.8 18.0 + - - +
484B GLU* 1.3 75.1 - - - +
486B HIS* 1.3 60.9 + - + +
489B TYR* 3.8 17.9 - - + -
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Residues in contact with HIS 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ARG* 4.6 8.9 - - - +
447B TYR* 4.1 15.5 - + + -
448B VAL* 3.7 27.2 - - + +
482B PHE 2.9 3.3 + - - +
483B THR 3.0 7.5 + - - +
485B VAL* 1.3 82.8 + - + +
487B PRO* 1.3 84.7 - - + +
488B ASP* 2.9 45.8 - - + +
489B TYR* 3.0 22.9 + - + +
490B GLY 3.1 10.6 + - - -
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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