Contacts of the helix formed by residues 906 - 912 (chain A) in PDB entry 3U44
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 PRO 906 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A GLU* 6.3 3.6 - - + -
897A SER* 3.6 24.7 - - - +
900A GLN* 3.3 31.9 - - + +
905A LEU* 1.3 91.5 - - + -
907A GLU* 1.3 66.6 + - - +
908A PHE* 3.1 3.5 + - + +
909A ASP* 3.2 39.6 + - + +
910A ARG* 3.3 13.3 + - - +
926A ARG* 5.3 0.2 - - - +
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Residues in contact with GLU 907 (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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228A MET* 4.7 19.2 - - + +
498A GLY* 3.8 17.7 - - - -
499A LYS* 3.5 46.5 + - + +
500A ILE* 5.0 3.4 - - + +
904A LEU* 5.8 0.9 - - - +
905A LEU 3.2 3.6 + - - -
906A PRO* 1.3 71.0 - - - +
908A PHE* 1.3 60.4 + - - +
910A ARG* 3.5 29.4 + - - +
911A TYR* 3.4 18.7 + - - +
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Residues in contact with PHE 908 (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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228A MET* 3.5 41.2 - - + +
229A VAL* 4.2 19.7 - - + -
232A GLY* 4.3 20.9 - - - -
236A LYS* 4.9 12.1 - - + -
315A LEU* 3.5 37.7 - - + -
906A PRO* 3.1 1.9 - - + -
907A GLU* 1.3 79.0 - - - +
909A ASP* 1.3 72.6 + - - +
910A ARG 3.2 0.2 - - - -
911A TYR* 3.0 24.9 - + - +
912A GLN* 3.0 50.3 + - + +
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Residues in contact with ASP 909 (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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236A LYS* 5.3 9.2 + - - -
897A SER* 4.4 26.7 - - - -
905A LEU* 6.1 0.4 - - + -
906A PRO* 3.2 33.7 + - + +
908A PHE* 1.3 85.6 - - - +
910A ARG* 1.3 64.5 + - + +
912A GLN* 3.3 17.3 + - - +
913A ALA* 3.4 9.5 + - - +
918A ASP* 5.5 1.9 - - - +
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Residues in contact with ARG 910 (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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494A GLN 3.8 4.2 + - - -
495A LEU* 3.2 32.0 + - + +
497A GLY 3.5 8.2 + - - -
500A ILE* 3.0 43.9 - - + +
860A LEU* 3.5 7.1 - - - +
904A LEU* 3.2 32.5 - - - +
905A LEU* 3.2 40.3 + - + -
906A PRO 3.3 8.2 + - - +
907A GLU* 3.5 31.1 + - - +
908A PHE 3.2 0.4 - - - -
909A ASP* 1.3 75.7 - - - +
911A TYR* 1.3 64.2 + - - +
913A ALA* 2.9 22.1 - - - +
918A ASP 5.7 1.8 - - - -
919A PHE* 3.6 16.7 - - + -
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Residues in contact with TYR 911 (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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225A ASP* 4.5 6.6 + - - -
228A MET* 3.4 31.6 - - + -
229A VAL* 6.1 1.3 - - + -
500A ILE* 4.0 9.3 - - + +
853A LYS* 4.2 36.0 + - + +
856A ARG* 3.4 42.4 + - + -
857A ARG* 4.2 29.4 - - + -
860A LEU* 3.2 21.0 - - + +
907A GLU 3.4 13.8 + - - +
908A PHE* 3.0 14.3 + + - +
910A ARG* 1.3 79.7 - - - +
912A GLN* 1.3 81.3 + - - +
913A ALA 3.0 7.1 + - - +
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Residues in contact with GLN 912 (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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236A LYS* 6.2 0.7 - - - +
315A LEU* 4.8 8.0 - - - +
856A ARG* 4.3 6.9 + - - +
908A PHE* 3.0 60.0 + - + +
909A ASP* 3.3 11.8 + - - +
911A TYR* 1.3 89.3 - - - +
913A ALA* 1.3 64.8 + - - +
914A ARG* 3.4 15.6 - - - +
918A ASP* 4.6 1.6 - - - +
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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