Contacts of the helix formed by residues 744 - 754 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A ARG* 2.8 44.3 + - - +
741A TRP 4.7 0.6 + - - -
743A VAL* 1.3 73.8 - - - +
745A PRO* 1.3 81.3 - - - +
746A LEU* 3.4 6.1 + - - +
747A ASP* 3.0 42.7 + - - +
748A ARG 3.0 9.0 + - - -
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Residues in contact with PRO 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PHE* 6.1 2.7 - - + -
211A LEU* 3.8 19.8 - - + +
668A THR* 6.0 4.0 - - + -
740A TYR* 3.5 35.9 - - + +
741A TRP* 4.9 13.0 - - + +
743A VAL 3.0 6.6 - - - +
744A ASP* 1.3 90.5 - - - +
746A LEU* 1.3 57.7 + - + +
748A ARG* 3.0 18.5 + - + +
749A ALA* 2.8 29.3 + - - +
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Residues in contact with LEU 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ARG* 3.4 59.7 - - + +
210A ARG* 4.0 23.6 - - + +
211A LEU* 3.9 33.6 - - + +
214A THR* 4.5 1.6 - - - +
744A ASP* 3.2 11.1 + - - +
745A PRO* 1.3 81.6 - - + +
747A ASP* 1.3 58.8 + - - +
749A ALA* 3.3 1.2 + - + +
750A LEU* 2.9 51.1 + - + +
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Residues in contact with ASP 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ARG* 3.5 15.5 + - - -
743A VAL* 4.7 7.4 - - + +
744A ASP* 3.0 31.2 + - + +
746A LEU* 1.3 78.8 - - - +
748A ARG* 1.3 64.7 + - - +
750A LEU* 3.4 14.9 + - - +
751A ALA* 2.9 24.1 + - - +
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Residues in contact with ARG 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739A SER 5.0 0.8 + - - -
740A TYR* 2.5 62.3 + - - +
743A VAL* 2.8 44.0 + - + +
744A ASP 3.0 8.3 + - - +
745A PRO* 3.0 18.1 + - - +
747A ASP* 1.3 76.7 - - - +
749A ALA* 1.3 64.6 + - - +
751A ALA* 3.0 21.7 + - + +
752A GLU* 3.6 14.1 + - + +
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Residues in contact with ALA 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LEU* 3.4 32.3 - - + -
214A THR* 4.3 17.3 - - + -
215A GLN* 6.6 0.2 - - + -
218A LYS* 4.7 8.7 - - - +
745A PRO 2.8 8.5 + - - +
746A LEU* 3.6 6.5 - - + +
748A ARG* 1.3 75.7 - - - +
750A LEU* 1.3 61.2 + - - +
752A GLU* 3.0 13.0 + - - +
753A LEU* 3.0 23.0 - - - +
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Residues in contact with LEU 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A THR* 4.2 15.0 - - + +
233A VAL* 3.9 36.6 - - + -
746A LEU* 2.9 42.6 + - + +
747A ASP* 3.6 15.9 - - - +
749A ALA* 1.3 76.1 - - - +
751A ALA* 1.3 58.3 + - - +
752A GLU 3.1 4.2 + - - -
753A LEU* 3.7 6.2 + - + +
754A ALA* 3.6 25.1 + - - +
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Residues in contact with ALA 751 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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747A ASP 2.9 12.9 + - - +
748A ARG* 3.0 15.1 + - - +
750A LEU* 1.3 75.7 - - - +
752A GLU* 1.3 58.5 + - + +
754A ALA 4.2 4.3 - - - +
755A ALA* 3.4 19.0 - - - +
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Residues in contact with GLU 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LYS* 3.6 26.2 + - - +
221A ARG* 4.2 9.1 + - - +
748A ARG* 3.9 16.1 - - + +
749A ALA* 3.0 10.8 + - - +
751A ALA* 1.3 80.8 - - + +
753A LEU* 1.3 70.2 + - - +
755A ALA* 3.4 15.2 - - - +
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Residues in contact with LEU 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A THR* 3.3 28.5 - - + +
218A LYS* 3.4 47.3 - - + +
221A ARG* 3.9 24.0 + - - +
230A GLN* 5.8 1.2 + - - -
231A VAL* 4.1 40.5 + - + +
233A VAL* 6.5 1.3 - - + -
749A ALA 3.0 22.0 - - - +
750A LEU* 3.7 5.8 + - + +
752A GLU* 1.3 76.0 - - - +
754A ALA* 1.3 59.5 + - + +
755A ALA* 2.9 8.8 + - - +
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Residues in contact with ALA 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLN* 5.5 7.0 - - - +
231A VAL 4.6 10.5 - - - +
232A SER* 5.9 2.2 - - - -
233A VAL* 6.3 3.6 - - + +
750A LEU 3.6 13.6 + - - +
751A ALA* 4.2 5.0 - - - +
752A GLU 3.5 0.9 - - - -
753A LEU* 1.3 75.3 - - + +
755A ALA* 1.3 60.5 + - - +
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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