Contacts of the helix formed by residues 908 - 917 (chain G) in PDB entry 5O9Z
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 HIS 908 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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874G LEU* 5.8 0.2 - - - +
904G ALA* 4.5 10.7 + - + -
905G GLU 3.0 14.7 + - - +
906G PRO* 2.9 3.0 - - + +
907G ARG* 1.3 74.2 - - - +
909G GLY* 1.3 59.2 + - - +
910G GLU 3.4 0.2 - - - -
911G LEU* 3.0 17.2 - - + +
912G TRP* 2.9 28.8 + - - +
39H THR* 5.0 17.0 - - - -
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Residues in contact with GLY 909 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906G PRO 3.3 8.8 + - - -
907G ARG 3.0 2.8 + - - -
908G HIS* 1.3 78.6 - - - +
910G GLU* 1.3 57.9 + - - +
912G TRP* 3.3 5.5 + - - +
913G CYS* 2.9 26.2 + - - +
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Residues in contact with GLU 910 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873G ASP 4.2 12.8 - - - +
874G LEU* 4.5 3.2 - - + +
907G ARG 3.4 9.7 + - - +
909G GLY* 1.3 70.7 - - - +
911G LEU* 1.3 59.5 + - - +
913G CYS* 3.5 10.2 - - - +
914G ALA* 2.9 32.4 + - - +
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Residues in contact with LEU 911 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874G LEU* 3.8 11.1 - - - +
875G GLY* 3.1 35.8 + - - +
876G ASP 5.3 0.5 + - - -
907G ARG 3.9 1.8 + - - -
908G HIS* 3.0 27.2 + - + +
910G GLU* 1.3 78.5 - - - +
912G TRP* 1.3 59.6 + - - +
914G ALA* 4.1 0.7 - - - +
915G VAL* 2.9 34.5 + - - +
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Residues in contact with TRP 912 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908G HIS 2.9 17.8 + - - +
909G GLY* 3.9 4.9 - - - +
911G LEU* 1.3 72.8 - - - +
913G CYS* 1.3 51.9 + - - +
915G VAL* 4.7 3.4 - - - -
916G SER* 2.6 43.1 + - - +
936G ARG* 5.5 10.7 - - + +
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Residues in contact with CYS 913 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909G GLY 2.9 13.9 + - - +
910G GLU* 3.5 14.1 - - - +
911G LEU 3.1 0.2 - - - -
912G TRP* 1.3 77.8 - - - +
914G ALA* 1.3 58.3 + - - +
916G SER* 3.7 2.7 - - - -
917G LYS* 2.9 30.4 + - - +
936G ARG* 5.8 6.3 - - + +
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Residues in contact with ALA 914 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874G LEU* 5.2 5.2 - - + -
876G ASP* 5.1 11.7 - - + -
910G GLU 2.9 19.1 + - - +
911G LEU* 4.1 2.2 - - - +
913G CYS* 1.3 70.7 - - - +
915G VAL* 1.3 61.7 + - - +
917G LYS* 3.0 7.6 + - - +
918G ASP* 2.9 32.0 + - - +
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Residues in contact with VAL 915 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875G GLY 5.4 2.9 - - - -
876G ASP* 5.2 17.8 - - + +
911G LEU 2.9 17.6 + - - +
912G TRP* 4.6 2.5 - - - +
914G ALA* 1.3 77.2 - - - +
916G SER* 1.3 58.9 + - - +
918G ASP* 4.4 5.2 - - - +
919G ILE* 3.0 14.1 + - + +
920G ALA* 2.9 33.5 + - + +
42H ASP* 6.6 0.2 - - + -
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Residues in contact with SER 916 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912G TRP* 2.6 24.7 + - - -
913G CYS* 3.8 3.6 - - - -
915G VAL* 1.3 77.3 - - - +
917G LYS* 1.3 57.9 + - - +
920G ALA* 3.0 25.1 - - - +
921G ASN* 4.2 14.4 - - - -
936G ARG* 5.5 6.3 - - - -
940G THR* 4.5 22.9 - - - -
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Residues in contact with LYS 917 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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913G CYS 2.9 17.3 + - - +
914G ALA* 3.0 8.9 + - - +
916G SER* 1.3 77.2 - - - +
918G ASP* 1.3 56.0 + - - +
940G THR* 5.5 5.2 - - - -
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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