Contacts of the helix formed by residues 744 - 754 (chain B) in PDB entry 1D0N
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 744 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207B ARG* 3.0 40.0 + - - +
741B TRP 4.8 0.9 + - - -
742B SER 4.3 0.6 + - - -
743B VAL* 1.3 78.9 - - - +
745B PRO* 1.3 72.7 - - - +
746B LEU* 3.0 21.5 + - - +
747B ASP* 3.1 21.8 + - - +
748B ARG* 2.9 23.6 + - - +
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Residues in contact with PRO 745 (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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208B PHE* 6.3 0.4 - - + -
211B LEU* 4.0 22.1 - - + +
668B THR* 6.2 4.7 - - + -
740B TYR* 3.5 36.1 - - + +
741B TRP* 5.2 11.0 - - + -
743B VAL 3.2 6.4 - - - +
744B ASP* 1.3 94.5 - - - +
746B LEU* 1.3 53.2 + - + +
748B ARG* 3.0 13.7 + - + +
749B ALA* 2.7 37.4 + - - +
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Residues in contact with LEU 746 (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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207B ARG* 3.7 42.8 - - + +
210B ARG* 3.8 36.6 - - + +
211B LEU* 3.7 37.4 - - + +
214B THR* 4.3 2.2 - - - +
744B ASP* 3.0 12.8 + - - +
745B PRO* 1.3 80.8 - - + +
747B ASP* 1.3 57.0 + - - +
749B ALA* 5.4 0.4 - - + -
750B LEU* 2.8 59.9 + - + +
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Residues in contact with ASP 747 (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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207B ARG* 3.1 19.9 + - - -
743B VAL* 4.8 8.3 - - + -
744B ASP* 3.1 30.3 + - + +
746B LEU* 1.3 75.6 - - - +
748B ARG* 1.3 66.7 + - - +
750B LEU* 4.0 12.6 - - - +
751B ALA* 3.4 17.7 + - - +
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Residues in contact with ARG 748 (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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737B ASP* 5.1 3.3 + - - -
739B SER 4.5 1.0 + - - -
740B TYR* 2.7 57.9 + - - +
743B VAL* 3.5 33.2 + - + +
744B ASP 2.9 11.9 + - - +
745B PRO* 3.0 14.3 + - - +
747B ASP* 1.3 78.1 - - - +
749B ALA* 1.3 59.4 + - - +
751B ALA* 2.8 28.4 + - - +
752B GLU* 3.5 8.0 + - + +
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Residues in contact with ALA 749 (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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211B LEU* 3.6 23.3 - - + -
214B THR* 4.4 15.9 - - + -
215B GLN* 5.8 4.3 - - - +
745B PRO 2.7 18.8 + - - +
746B LEU* 3.9 3.6 - - + +
748B ARG* 1.3 73.0 - - - +
750B LEU* 1.3 54.9 + - - +
751B ALA 2.8 5.6 - - - -
752B GLU* 2.7 30.8 + - - +
753B LEU* 3.3 14.7 + - + +
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Residues in contact with LEU 750 (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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214B THR* 4.1 18.6 - - + +
233B VAL* 3.7 42.2 - - + -
746B LEU* 2.8 44.7 + - + +
747B ASP* 4.0 14.1 - - - +
749B ALA* 1.3 73.0 - - - +
751B ALA* 1.3 56.6 + - - +
752B GLU 3.4 0.2 - - - -
753B LEU* 4.1 3.1 - - + +
754B ALA* 3.1 36.5 + - + +
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Residues in contact with ALA 751 (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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747B ASP 3.4 11.0 + - - +
748B ARG* 2.8 17.3 - - + +
749B ALA 2.8 0.4 - - - -
750B LEU* 1.3 82.0 - - - +
752B GLU* 1.3 57.7 + - + +
753B LEU 3.5 0.2 - - - -
754B ALA* 5.2 0.9 - - - -
755B ALA* 2.8 27.8 - - - +
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Residues in contact with GLU 752 (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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218B LYS* 2.5 34.6 + - - -
221B ARG* 3.9 12.1 + - - -
748B ARG* 4.6 8.3 - - + +
749B ALA* 2.7 14.0 + - - +
751B ALA* 1.3 82.1 - - + +
753B LEU* 1.3 68.3 + - + +
755B ALA* 3.8 14.4 - - - +
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Residues in contact with LEU 753 (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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214B THR* 3.8 28.3 - - + +
217B SER* 5.2 0.2 - - - -
218B LYS* 3.7 51.8 - - + +
221B ARG* 3.8 11.0 + - - +
230B GLN* 4.4 5.2 + - - -
231B VAL* 3.3 60.4 - - + +
233B VAL* 5.2 7.0 - - + -
749B ALA* 3.3 10.3 + - + +
750B LEU* 4.7 3.6 - - - +
752B GLU* 1.3 83.7 - - + +
754B ALA* 1.3 59.3 + - - +
755B ALA* 2.9 14.3 + - - +
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Residues in contact with ALA 754 (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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230B GLN* 5.3 4.5 - - - +
231B VAL 4.6 7.4 - - - +
232B SER* 6.3 0.4 - - - -
233B VAL* 6.0 7.4 - - + +
750B LEU* 3.1 23.6 + - + +
751B ALA* 4.4 0.4 - - - -
753B LEU* 1.3 77.1 - - - +
755B ALA* 1.3 60.1 - - - +
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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