Contacts of the helix formed by residues 910 - 923 (chain C) in PDB entry 5C0V
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 LEU 910 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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833A GLN* 3.9 9.2 - - - +
836A ASN* 3.6 31.4 - - + +
872A TYR* 3.6 53.0 - - + +
875A GLU* 5.1 1.0 + - - -
905C TYR* 3.8 20.4 - - + -
909C GLN* 1.3 76.5 + - - +
911C TYR* 1.3 65.8 + - - +
912C GLY 3.4 2.5 - - - -
913C LEU* 3.7 33.9 - - + -
914C GLU* 3.0 25.8 + - - +
941C PHE* 4.3 18.6 - - + -
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Residues in contact with TYR 911 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A TYR* 5.9 0.2 - - - -
875A GLU* 4.1 32.3 + - - +
879A ARG* 5.2 3.8 - - - -
911A TYR* 3.8 13.0 - + - -
1001A SO4 2.9 31.7 + - - -
871C ARG* 4.3 11.7 - - - +
875C GLU* 3.7 37.7 - - + -
878C PHE* 3.9 20.2 - + + -
879C ARG* 2.7 37.0 + - - +
904C ASP* 3.7 4.8 + - - +
909C GLN* 4.5 1.0 - - + +
910C LEU* 1.3 77.2 - - - +
912C GLY* 1.3 64.5 + - - +
914C GLU* 4.0 3.5 - - - +
915C LYS* 3.1 40.4 + - + +
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Residues in contact with GLY 912 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878C PHE* 3.6 32.0 - - - -
897C PHE* 4.4 0.9 - - - -
901C THR* 4.0 8.4 + - - -
904C ASP* 2.9 23.2 + - - -
911C TYR* 1.3 73.4 - - - +
913C LEU* 1.3 63.5 + - - +
915C LYS* 3.1 4.3 + - - +
916C PHE* 2.9 23.0 + - - +
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Residues in contact with LEU 913 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901C THR* 3.7 13.6 + - + +
904C ASP* 4.4 2.0 + - - +
905C TYR* 3.5 37.7 - - + +
909C GLN 5.4 0.4 + - - -
910C LEU* 3.4 25.5 + - + +
912C GLY* 1.3 74.1 - - - +
914C GLU* 1.3 57.3 + - - +
916C PHE* 3.1 3.6 + - - +
917C TRP* 2.8 27.4 + - - +
934C LEU* 3.7 24.9 - - + -
937C TYR* 3.7 24.9 - - + +
938C LEU* 3.7 24.2 - - + -
941C PHE* 3.9 18.8 - - + -
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Residues in contact with GLU 914 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840A ARG* 4.2 14.2 + - - -
872A TYR* 4.4 9.0 + - - -
879A ARG* 4.3 24.6 + - - -
910C LEU 3.0 17.1 + - - +
911C TYR* 4.0 4.2 - - - +
913C LEU* 1.3 76.2 - - - +
915C LYS* 1.3 63.9 + - - +
917C TRP* 3.3 11.4 + - + +
918C ALA* 2.7 36.1 + - + +
941C PHE* 3.7 35.2 - - + -
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Residues in contact with LYS 915 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001A SO4 2.5 34.5 + - - -
878C PHE* 4.1 18.6 - - + +
879C ARG* 4.0 6.3 - - + -
882C SER* 2.8 44.7 + - - +
883C TYR* 3.7 22.0 - - + -
897C PHE* 3.7 3.8 - - + -
911C TYR* 3.1 48.6 + - + +
912C GLY 3.1 9.9 + - - +
914C GLU* 1.3 85.3 - - - +
916C PHE* 1.3 58.1 + - - +
918C ALA* 3.8 6.5 - - + +
919C PHE* 3.0 14.2 + - - +
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Residues in contact with PHE 916 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894C PHE* 3.7 29.6 - + - -
897C PHE* 3.4 31.4 - + + -
898C GLN* 3.6 35.7 - - + -
901C THR* 3.7 19.7 - - + +
912C GLY 2.9 12.7 + - - +
913C LEU* 3.1 8.5 + - - +
915C LYS* 1.3 76.4 - - - +
917C TRP* 1.3 64.6 + - - +
919C PHE* 3.3 3.9 + + - +
920C LEU* 3.1 41.5 + - + +
930C ILE* 4.5 5.8 - - + -
934C LEU* 3.6 19.3 - - + -
938C LEU* 3.8 21.8 - - + -
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Residues in contact with TRP 917 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840A ARG* 5.4 12.1 - - - -
913C LEU 2.8 12.6 + - - +
914C GLU* 3.5 19.3 - - + +
916C PHE* 1.3 77.5 - - - +
918C ALA* 1.3 83.0 + - + +
920C LEU* 3.2 11.0 + - + +
921C LYS* 3.1 48.7 + - + +
922C TYR* 6.1 0.7 - + - -
938C LEU* 4.0 26.0 - - + +
941C PHE* 4.0 37.7 + + + -
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Residues in contact with ALA 918 (chain C).
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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882C SER* 4.4 5.2 - - - +
883C TYR* 6.2 2.5 - - + -
914C GLU* 2.7 24.1 + - + +
915C LYS* 3.8 11.9 - - + +
917C TRP* 1.3 88.0 - - + +
919C PHE* 1.3 64.2 + - - +
921C LYS* 3.1 11.9 + - - +
922C TYR* 2.9 37.2 - - + -
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Residues in contact with PHE 919 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882C SER* 3.6 28.1 + - - +
885C LEU* 3.5 36.1 - - + -
886C GLU* 3.6 6.7 - - + -
889C PHE* 4.0 22.4 - + - -
894C PHE* 3.5 27.4 - + - -
897C PHE* 3.9 15.0 - + + -
915C LYS 3.0 18.9 + - - +
916C PHE* 3.5 6.1 - + - +
917C TRP 3.2 0.2 - - - -
918C ALA* 1.3 76.6 - - - +
920C LEU* 1.3 63.4 + - + +
922C TYR* 3.1 4.8 + - - -
923C SER* 2.7 59.5 + - - -
928C LEU* 3.9 14.8 - - + -
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Residues in contact with LEU 920 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916C PHE* 3.1 22.5 + - + +
917C TRP* 3.2 11.4 + - + +
919C PHE* 1.3 86.2 - - + +
921C LYS* 1.3 63.0 + - - +
922C TYR 3.4 0.2 + - - -
923C SER* 3.8 13.0 + - - +
928C LEU* 3.6 30.5 - - + -
930C ILE* 3.7 27.8 - - + -
935C GLN* 5.8 0.2 - - - +
938C LEU* 3.8 23.3 - - + -
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Residues in contact with LYS 921 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917C TRP* 3.1 44.5 + - + +
918C ALA* 3.1 9.4 + - - +
920C LEU* 1.3 79.8 - - - +
922C TYR* 1.3 97.3 + - + +
923C SER 4.7 1.4 - - - +
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Residues in contact with TYR 922 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886C GLU* 3.6 40.0 - - + +
917C TRP* 6.1 0.6 - + - -
918C ALA* 2.9 37.6 + - + +
919C PHE* 3.1 4.2 + - - +
921C LYS* 1.3 112.9 - - + +
923C SER* 1.3 67.0 + - - +
924C LYS* 3.5 10.9 + - - +
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Residues in contact with SER 923 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885C LEU 5.0 2.3 + - - -
886C GLU* 4.8 9.4 - - - +
889C PHE* 5.1 0.3 - - - +
919C PHE* 2.7 52.1 + - - -
920C LEU* 3.8 11.5 + - - +
921C LYS 3.6 2.0 - - - +
922C TYR* 1.3 75.3 - - - +
924C LYS* 1.3 61.1 + - - +
925C ALA* 3.1 27.0 + - - +
928C LEU* 5.1 3.1 - - - -
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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