Contacts of the helix formed by residues 472 - 481 (chain B) in PDB entry 3DGR
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 472 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B TYR 3.5 10.8 - - - -
232B GLY 3.6 10.3 - - - -
471B TYR* 1.3 76.2 - - - +
473B PHE* 1.3 64.6 + - - +
474B ASP* 3.4 11.8 + - - +
475B GLU* 3.1 37.3 + - - +
476B ILE* 3.2 19.8 + - - +
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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
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60B TYR* 3.7 22.0 - + - -
209B SER 3.3 19.5 - - - -
212B LEU 3.4 5.6 - - - -
213B VAL* 3.6 28.0 - - + -
227B ILE* 3.6 36.6 - - + -
231B TYR* 3.8 21.5 - + + +
232B GLY 2.7 20.1 + - - +
233B THR* 3.4 19.7 - - + -
238B PRO* 4.5 0.7 - - + -
472B SER* 1.3 71.9 - - - +
474B ASP* 1.3 55.1 + - - -
476B ILE* 3.3 8.3 + - + +
477B ARG* 2.9 66.8 + - + +
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Residues in contact with ASP 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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232B GLY 4.4 0.7 - - - +
233B THR* 3.4 21.4 - - - +
234B LYS* 2.9 35.4 + - - +
235B ASP* 4.7 5.5 - - - +
472B SER* 3.1 9.5 + - - +
473B PHE* 1.3 75.1 - - - +
475B GLU* 1.3 64.8 + - + +
477B ARG* 3.5 13.6 + - - +
478B LYS* 3.1 23.4 + - - +
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Residues in contact with GLU 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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469B LYS* 5.8 0.7 - - - -
470B SER 4.3 3.1 - - - +
471B TYR* 3.6 30.9 - - + -
472B SER* 3.1 38.6 + - - +
474B ASP* 1.3 75.0 - - + +
476B ILE* 1.3 57.8 + - - +
478B LYS* 3.2 12.0 + - + +
479B ASN* 2.8 39.6 + - - +
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Residues in contact with ILE 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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60B TYR* 4.1 10.1 - - + -
121B GLU* 3.5 34.5 - - + +
122B GLY* 3.6 15.3 - - - +
213B VAL* 3.9 28.3 - - + -
231B TYR* 3.2 43.7 - - + -
471B TYR* 4.1 9.6 - - + -
472B SER 3.2 11.7 + - - +
473B PHE* 3.5 13.0 - - + +
474B ASP 3.2 0.2 - - - -
475B GLU* 1.3 77.3 - - - +
477B ARG* 1.3 61.6 + - - +
479B ASN* 3.2 4.3 + - - +
480B ALA* 3.0 22.2 + - - +
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Residues in contact with ARG 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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212B LEU* 2.7 29.9 + - - +
213B VAL* 3.7 22.5 + - - +
214B ASN 6.0 0.4 - - - -
215B PHE 3.4 12.0 + - - -
216B LYS* 3.2 27.8 - - - +
233B THR* 5.1 4.2 - - - +
235B ASP* 5.3 5.7 + - - -
238B PRO* 3.0 43.8 + - - +
473B PHE* 2.9 43.5 + - + +
474B ASP* 3.8 13.1 + - - +
476B ILE* 1.3 71.2 - - - +
478B LYS* 1.3 63.0 + - - +
480B ALA* 3.1 12.1 + - - +
481B GLN* 3.2 15.9 + - - +
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Residues in contact with LYS 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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474B ASP 3.1 15.0 + - - +
475B GLU* 3.2 13.2 + - + +
477B ARG* 1.3 77.2 - - - +
479B ASN* 1.3 68.5 + - - +
480B ALA 3.3 0.7 + - - -
481B GLN* 3.1 41.2 + - - +
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Residues in contact with ASN 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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120B PRO* 4.5 4.3 - - - +
121B GLU 3.0 17.2 - - - +
122B GLY* 3.2 27.4 - - - +
123B PHE* 3.7 28.9 - - + +
124B VAL* 3.9 10.9 + - - +
471B TYR* 5.2 3.1 - - - -
475B GLU* 2.8 27.8 + - - +
476B ILE 3.2 2.2 + - - +
478B LYS* 1.3 80.9 - - - +
480B ALA* 1.3 58.7 + - - +
481B GLN* 3.4 2.6 + - - +
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Residues in contact with ALA 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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58B VAL* 4.3 8.7 - - + -
122B GLY 3.4 11.2 - - - +
124B VAL* 4.1 4.9 - - - -
166B ARG* 2.7 32.0 + - - +
169B LYS* 5.7 1.4 + - - -
213B VAL* 3.5 29.4 - - + +
214B ASN* 4.4 6.1 - - - +
476B ILE 3.0 14.9 + - - +
477B ARG* 3.1 5.9 + - - +
479B ASN* 1.3 76.0 - - - +
481B GLN* 1.3 60.8 + - - +
482B LEU* 3.6 0.9 + - - +
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Residues in contact with GLN 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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124B VAL* 5.0 0.2 - - - +
166B ARG* 3.0 13.0 + - - -
169B LYS* 5.4 7.6 - - - +
477B ARG 3.2 10.5 + - - +
478B LYS* 3.1 36.8 + - - +
479B ASN 3.4 3.9 - - - +
480B ALA* 1.3 81.9 - - - +
482B LEU* 1.3 69.3 + - - +
483B ASN* 5.2 0.7 - - - +
484B ILE* 3.4 21.1 - - + +
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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