Contacts of the helix formed by residues 909 - 917 (chain X) in PDB entry 2OO8
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 ASN 909 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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907X HIS 4.3 0.3 - - - +
908X GLY* 1.3 75.8 - - - -
910X LEU* 1.3 63.3 + - - +
911X LEU* 3.1 13.0 + - - +
912X ASP* 3.0 44.3 + - - +
913X PHE* 3.1 18.0 + - - +
968X ARG* 3.6 24.1 + - - +
970X ILE 3.1 11.9 - - - +
971X LEU* 3.9 5.0 - - + +
972X VAL* 4.3 0.4 - - - -
983X PHE* 4.4 10.7 - - + -
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Residues in contact with LEU 910 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908X GLY 3.9 0.4 + - - -
909X ASN* 1.3 70.3 - - - +
911X LEU* 1.3 60.7 + - - +
913X PHE* 4.1 2.5 - - + -
914X LEU* 2.8 51.3 + - + +
944X PHE* 3.9 35.2 - - + -
948X VAL* 5.2 1.8 - - + -
967X ALA* 3.5 19.9 + - + +
970X ILE* 2.7 41.3 + - + +
972X VAL* 3.8 22.9 - - + +
1027X LEU* 4.5 3.1 - - + -
1031X ILE* 4.1 28.7 - - + -
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Residues in contact with LEU 911 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909X ASN* 3.1 9.4 + - - +
910X LEU* 1.3 79.7 - - - +
912X ASP* 1.3 68.1 + - - +
914X LEU* 3.4 4.2 + - - +
915X ARG* 3.2 59.3 + - - +
967X ALA* 3.3 10.5 + - + -
968X ARG* 3.8 30.3 - - + +
1004X TRP* 6.3 1.3 - - + -
1030X GLU* 3.6 20.9 - - - +
1035X GLY* 3.7 27.8 - - - +
1036X GLY 5.1 0.7 - - - +
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Residues in contact with ASP 912 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908X GLY* 6.4 0.2 - - - -
909X ASN* 3.0 36.0 + - - +
911X LEU* 1.3 81.7 - - - +
913X PHE* 1.3 60.9 + - - +
915X ARG* 3.3 13.6 + - - +
916X LYS* 2.9 31.3 + - - +
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Residues in contact with PHE 913 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907X HIS* 3.7 36.3 + + + +
909X ASN 3.1 17.1 + - - +
910X LEU* 3.6 5.6 - - + +
912X ASP* 1.3 74.6 - - - +
914X LEU* 1.3 66.5 + - - +
916X LYS* 3.4 8.5 + - + +
917X SER* 3.2 20.2 + - - -
936X LEU* 3.8 24.5 - - + -
944X PHE* 3.7 35.2 - + - -
972X VAL* 3.8 15.0 - - + -
976X TYR* 3.7 25.4 - + - -
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Residues in contact with LEU 914 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910X LEU* 2.8 49.0 + - + +
911X LEU* 3.7 4.7 - - - +
913X PHE* 1.3 72.8 - - - +
915X ARG* 1.3 61.1 + - - +
917X SER* 2.8 24.1 + - - -
918X ARG 3.8 2.1 + - - -
936X LEU* 4.2 8.7 - - + -
941X LEU* 3.7 29.2 - - + -
944X PHE* 5.0 1.3 - - + -
967X ALA* 4.3 10.3 - - + -
1030X GLU 3.7 22.0 - - - +
1031X ILE* 3.8 24.2 - - + +
1034X LEU* 3.6 25.7 - - + +
1035X GLY* 4.0 6.1 - - - +
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Residues in contact with ARG 915 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911X LEU* 3.2 46.6 + - - +
912X ASP* 3.7 13.9 + - - +
913X PHE 3.2 0.4 - - - -
914X LEU* 1.3 76.3 - - - +
916X LYS* 1.3 64.4 + - - +
917X SER 3.1 2.0 - - - -
918X ARG* 3.1 25.0 + - - +
922X THR* 4.5 3.1 + - - -
1034X LEU 3.7 15.9 - - - +
1035X GLY* 2.6 25.7 + - - +
1036X GLY 4.3 0.8 - - - -
1037X THR* 3.8 15.4 + - - +
1116X ILE* 3.5 45.1 - - + +
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Residues in contact with LYS 916 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912X ASP 2.9 17.6 + - - +
913X PHE* 3.4 10.1 + - + +
915X ARG* 1.3 75.8 - - - +
917X SER* 1.3 59.8 + - - +
918X ARG 3.2 1.3 + - - -
919X VAL* 5.1 0.7 - - - +
922X THR* 3.6 26.3 + - + +
935X THR* 4.9 0.3 + - - -
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Residues in contact with SER 917 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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913X PHE* 3.2 7.9 + - - -
914X LEU 2.8 17.2 + - - -
915X ARG 3.1 1.0 - - - -
916X LYS* 1.3 74.4 - - - +
918X ARG* 1.3 54.1 + - - +
919X VAL* 2.7 18.0 + - - +
934X SER* 2.8 39.5 + - - -
935X THR* 3.2 23.9 + - - -
936X LEU* 3.7 24.3 - - - +
1034X LEU* 4.1 5.7 - - - +
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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