Contacts of the helix formed by residues 872 - 893 (chain C) in PDB entry 5NC5
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 GLN 872 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459C PHE* 3.8 28.0 - - + -
460C GLY* 4.0 17.5 + - - +
463C THR* 3.4 35.2 - - - +
464C GLY 4.4 1.0 - - - +
467C TYR* 3.9 15.2 - - - +
868C LEU* 3.2 24.2 + - - +
869C SER* 3.6 7.4 - - - +
871C ASN* 1.3 80.0 - - - +
873C ALA* 1.3 70.1 + - - +
874C PRO* 3.1 0.7 - - - -
875C SER* 2.9 20.9 + - - -
876C LEU* 3.4 9.3 + - + +
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Residues in contact with ALA 873 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C TYR* 5.2 1.8 - - - -
869C SER 3.8 11.2 + - - +
870C GLY* 3.1 10.1 + - - +
872C GLN* 1.3 81.7 - - - +
874C PRO* 1.4 69.5 - - + +
876C LEU* 3.0 17.3 + - - +
877C TYR* 3.2 36.6 + - + +
923C ASN* 5.9 0.4 - - - +
928C GLN* 3.9 21.1 - - - +
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Residues in contact with PRO 874 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870C GLY 3.4 8.7 - - - +
871C ASN* 3.0 19.7 - - - +
872C GLN 3.1 1.8 - - - +
873C ALA* 1.4 91.6 - - + +
875C SER* 1.3 63.0 - - - +
876C LEU 3.1 0.2 + - - -
877C TYR* 3.3 11.7 + - + +
878C ALA* 3.1 24.9 + - - +
1117C D10 4.1 51.0 - - + +
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Residues in contact with SER 875 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C PHE* 4.4 10.0 - - - -
871C ASN 4.6 3.3 + - - -
872C GLN* 2.9 14.4 + - - -
874C PRO* 1.3 79.7 - - - +
876C LEU* 1.3 56.8 + - - +
877C TYR 3.4 0.2 - - - -
878C ALA* 3.8 6.5 - - - +
879C ILE* 3.2 29.5 + - - +
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Residues in contact with LEU 876 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C PRO* 4.2 2.7 - - + -
456C MET* 3.6 32.5 - - + +
459C PHE* 3.6 33.0 - - + -
467C TYR* 4.0 31.9 - - + +
872C GLN* 3.4 3.3 + - + +
873C ALA* 3.0 10.9 + - - +
875C SER* 1.3 77.3 - - - +
877C TYR* 1.3 70.7 + - + +
878C ALA 3.3 0.2 - - - -
879C ILE* 4.1 1.6 - - - -
880C SER* 3.0 33.0 + - - +
928C GLN* 5.1 2.2 - - + +
932C LEU* 3.5 27.2 - - + +
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Residues in contact with TYR 877 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C PHE* 4.3 18.5 - + - -
873C ALA* 3.2 30.3 - - + +
874C PRO* 3.7 9.0 - - + +
876C LEU* 1.3 83.4 - - + +
878C ALA* 1.3 59.5 + - - +
880C SER* 3.4 3.5 + - - -
881C LEU* 2.9 39.4 + - + +
923C ASN* 4.4 4.3 + - - -
928C GLN* 3.3 35.1 - - + +
931C LEU* 3.4 39.7 - - + +
932C LEU* 3.3 28.3 - - + -
935C ILE* 4.7 6.2 - - + +
1117C D10 4.5 14.8 - - + -
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Residues in contact with ALA 878 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874C PRO 3.1 16.7 + - - +
875C SER* 3.7 6.9 + - - +
877C TYR* 1.3 78.9 - - - +
879C ILE* 1.3 62.9 + - - +
881C LEU* 3.2 2.9 + - - +
882C ILE* 3.0 31.2 + - + +
1115C D10 4.5 24.8 - - + +
1117C D10 3.9 23.6 - - + -
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Residues in contact with ILE 879 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.6 10.3 - - + -
1107B DD9 3.5 51.4 - - + -
455C PRO* 4.0 16.6 - - + -
459C PHE* 4.7 10.1 - - + -
875C SER 3.2 17.9 + - - +
876C LEU* 4.1 8.7 - - - +
878C ALA* 1.3 79.5 - - - +
880C SER* 1.3 65.9 + - - +
882C ILE* 4.4 13.2 - - + -
883C VAL* 3.0 33.8 + - + +
1107C D12 4.3 19.3 - - + -
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Residues in contact with SER 880 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C ALA 4.7 0.5 - - - +
452C VAL* 3.1 32.4 + - - -
455C PRO* 3.6 19.8 - - - +
876C LEU* 3.0 27.4 + - - +
877C TYR 3.8 2.9 - - - -
878C ALA 3.3 0.2 - - - -
879C ILE* 1.3 82.8 - - - +
881C LEU* 1.3 62.7 + - - +
883C VAL* 3.5 1.4 + - - +
884C VAL* 3.0 30.2 + - - +
932C LEU* 4.1 13.1 - - - +
935C ILE* 4.9 1.6 - - - -
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Residues in contact with LEU 881 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877C TYR* 2.9 21.6 + - + +
878C ALA* 3.6 3.4 - - - +
880C SER* 1.3 73.2 - - - +
882C ILE* 1.3 67.6 + - - +
884C VAL* 3.3 1.8 + - - -
885C PHE* 2.9 24.1 + - - +
902C MET* 3.5 27.4 - - + +
905C VAL* 4.0 17.0 - - + -
935C ILE* 3.6 31.8 - - + +
1115C D10 4.4 19.3 - - + -
1116C D10 5.5 11.0 - - + -
1117C D10 3.2 35.9 - - + -
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Residues in contact with ILE 882 (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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17B ILE* 6.0 0.4 - - + -
21B LEU* 4.3 18.2 - - + -
878C ALA* 3.0 23.1 + - + +
879C ILE* 3.8 17.0 - - + +
881C LEU* 1.3 75.9 - - - +
883C VAL* 1.3 59.0 + - + +
885C PHE* 3.1 8.2 + - + +
886C LEU* 2.8 50.7 + - + +
1115C D10 4.0 33.0 - - + -
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Residues in contact with VAL 883 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107B DD9 4.4 13.7 - - + -
451C ALA* 3.7 26.9 - - + +
455C PRO* 3.9 18.6 - - + -
879C ILE* 3.0 22.1 + - + +
880C SER 3.8 3.6 - - - +
882C ILE* 1.3 74.4 - - + +
884C VAL* 1.3 67.1 + - - +
886C LEU* 4.2 6.6 - - + +
887C CYS* 3.0 25.6 + - - +
1107C D12 4.1 37.5 - - + -
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Residues in contact with VAL 884 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C VAL* 3.9 33.2 - - + +
451C ALA* 4.2 6.5 - - + -
452C VAL* 3.6 39.0 - - + +
880C SER 3.0 20.4 + - - +
881C LEU 3.8 3.6 - - - +
883C VAL* 1.3 76.6 - - - +
885C PHE* 1.3 58.3 + - - +
887C CYS* 3.4 2.5 + - - +
888C LEU* 2.9 30.6 + - + +
902C MET* 4.0 21.8 - - + -
935C ILE* 4.4 8.5 - - + -
936C GLY* 6.1 0.4 - - - -
939C ALA* 4.8 5.8 - - + -
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Residues in contact with PHE 885 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881C LEU 2.9 14.4 + - - +
882C ILE* 3.4 8.1 - - + +
884C VAL* 1.3 76.8 - - - +
886C LEU* 1.4 72.5 + - + +
888C LEU* 3.1 5.8 + - - +
889C ALA* 3.0 25.5 + - + +
895C TRP* 4.0 38.1 - + - -
898C PRO* 3.2 30.7 - - + -
899C PHE* 3.8 21.8 - + + -
902C MET* 3.7 27.8 - - + +
1103C D12 4.6 12.8 - - + -
1115C D10 3.7 27.4 - - + -
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Residues in contact with LEU 886 (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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14B VAL* 3.3 29.3 - - + +
17B ILE* 3.7 46.2 - - + -
18B ILE* 4.1 24.2 - - + +
21B LEU* 4.7 5.6 - - + -
1107B DD9 6.0 1.3 - - + -
1121B D12 5.3 0.4 - - + -
882C ILE* 2.8 39.5 + - + +
883C VAL* 4.2 5.6 - - + +
885C PHE* 1.4 92.3 - - + +
887C CYS* 1.3 62.5 + - - +
889C ALA* 3.5 1.5 + - - +
890C ALA* 3.2 18.9 + - - +
895C TRP* 5.0 1.8 - - + -
1103C D12 5.9 2.5 - - + -
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Residues in contact with CYS 887 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121B D12 3.9 26.8 - - - +
447C MET* 3.5 35.9 - - + +
448C VAL* 6.2 0.7 - - + -
451C ALA* 4.1 17.0 - - + -
883C VAL* 3.0 30.1 + - - +
884C VAL* 3.7 5.4 - - - +
886C LEU* 1.3 75.6 - - - +
888C LEU* 1.3 64.3 + - - +
890C ALA* 3.4 3.0 + - - +
891C LEU 3.1 17.7 + - - -
1107C D12 4.8 9.9 - - - -
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Residues in contact with LEU 888 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C GLY* 4.9 6.1 - - - +
447C MET* 5.1 2.7 - - - -
448C VAL* 3.8 22.0 - - + -
884C VAL* 2.9 26.1 + - + +
885C PHE 3.1 5.8 + - - +
887C CYS* 1.3 78.0 - - - +
889C ALA* 1.3 64.5 + - - +
891C LEU* 3.3 4.1 + - + +
892C TYR* 3.1 58.4 + - + +
897C ILE* 6.0 0.2 - - + -
898C PRO* 3.9 15.8 - - + +
901C VAL* 3.8 34.3 - - + -
902C MET* 4.6 6.3 - - - -
939C ALA* 5.0 0.2 - - + -
943C ILE* 3.7 17.7 - - + -
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Residues in contact with ALA 889 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 3.7 9.4 - - + +
14B VAL* 4.1 3.6 - - + -
885C PHE* 3.0 16.0 + - + +
886C LEU* 3.8 5.4 - - - +
888C LEU* 1.3 76.6 - - - +
890C ALA* 1.3 57.4 + - - +
893C GLU* 2.8 31.0 + - - -
894C SER 3.2 23.7 + - - +
895C TRP* 3.9 27.8 - - + -
898C PRO* 3.5 7.1 - - + +
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Residues in contact with ALA 890 (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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11B PHE* 3.9 36.8 - - + +
14B VAL* 4.1 12.7 - - + +
1121B D12 3.5 36.6 - - + +
886C LEU 3.2 14.3 + - - +
887C CYS 3.8 4.0 - - - +
889C ALA* 1.3 82.0 - - - +
891C LEU* 1.3 62.1 + - - +
892C TYR 3.5 0.2 + - - -
893C GLU* 3.6 7.5 + - - +
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Residues in contact with LEU 891 (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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1121B D12 3.6 42.3 - - + +
440C GLY* 3.9 6.7 - - - +
443C VAL* 3.8 22.0 - - + +
444C GLY* 3.4 39.3 - - - +
447C MET* 4.3 10.8 - - - -
887C CYS 3.1 17.2 + - - +
888C LEU* 3.3 4.7 + - + +
890C ALA* 1.3 78.2 - - - +
892C TYR* 1.3 85.9 + - + +
893C GLU 3.3 0.4 + - - -
1112C D10 4.8 8.7 - - + -
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Residues in contact with TYR 892 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C GLY* 2.8 27.7 + - - -
444C GLY* 3.7 4.7 - - - -
888C LEU* 3.1 42.1 + - + +
891C LEU* 1.3 96.4 - - + +
893C GLU* 1.3 72.9 + - - +
894C SER* 3.1 7.7 + - - +
897C ILE* 3.5 42.6 - - + +
898C PRO* 5.3 0.9 - - + -
943C ILE* 3.6 28.1 - - + +
947C GLU* 2.5 32.0 + - + -
950C LYS* 4.1 24.1 + - - +
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Residues in contact with GLU 893 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASP 4.3 7.2 - - - +
8B ARG* 2.8 45.4 - - + +
9B PRO* 3.3 5.5 - - + +
10B ILE* 2.8 46.2 + - + +
11B PHE* 3.6 10.9 + - - +
1121B D12 4.8 8.9 - - + +
889C ALA 2.8 12.9 + - - -
890C ALA 3.6 6.0 + - - +
891C LEU 3.3 2.4 - - - -
892C TYR* 1.3 80.7 - - - +
894C SER* 1.3 58.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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