Contacts of the helix formed by residues 958 - 980 (chain N) in PDB entry 5D4D
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 GLU 958 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956N ILE 3.8 1.9 + - - +
957N PRO* 1.3 74.2 - - - +
959N GLU* 1.3 73.8 + - - +
960N LYS 3.0 1.8 + - - -
961N LYS* 3.3 17.7 + - - +
962N GLN* 3.4 20.9 + - - +
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Residues in contact with GLU 959 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957N PRO* 3.1 18.1 - - - +
958N GLU* 1.3 90.9 + - - +
960N LYS* 1.3 58.9 + - - +
962N GLN* 3.4 24.4 + - - +
963N TYR* 2.9 61.2 + - + +
1006N ALA* 4.0 15.6 - - + +
1009N LYS* 6.3 3.4 - - - -
1010N ASN* 5.2 2.6 - - - +
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Residues in contact with LYS 960 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956N ILE* 3.9 18.2 - - + +
957N PRO* 3.3 21.4 + - + +
958N GLU 3.0 0.6 + - - -
959N GLU* 1.3 77.7 - - - +
961N LYS* 1.3 60.3 + - - +
963N TYR* 3.0 10.5 + - - +
964N LEU* 2.8 47.9 + - + +
1003N VAL* 4.2 21.0 - - + +
1006N ALA* 5.4 0.6 - - - +
1039N CYS 4.6 0.9 - - - +
1040N GLY 2.9 34.6 + - - +
1041N LEU* 4.0 4.9 - - - -
1058N ARG 3.2 17.5 + - - -
1060N SER* 4.4 0.2 - - - -
1063N GLU* 3.1 35.6 + - - +
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Residues in contact with LYS 961 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957N PRO 4.6 0.4 + - - -
958N GLU 3.3 10.1 + - - +
960N LYS* 1.3 79.6 - - - +
962N GLN* 1.3 59.1 + - + +
964N LEU* 3.2 10.6 + - + +
965N GLU* 2.9 54.1 + - + +
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Residues in contact with GLN 962 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958N GLU* 3.4 27.3 + - - +
959N GLU* 3.5 31.3 + - - +
960N LYS 3.3 0.4 - - - -
961N LYS* 1.3 77.3 - - + +
963N TYR* 1.3 64.4 + - + +
965N GLU* 3.2 13.1 + - - +
966N GLU* 2.9 43.2 + - - +
969N ARG* 5.5 0.3 + - - -
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Residues in contact with TYR 963 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959N GLU* 2.9 47.3 + - + +
960N LYS* 3.5 5.4 - - - +
962N GLN* 1.3 82.7 - - + +
964N LEU* 1.3 57.2 + - - +
966N GLU* 3.6 21.3 - - - +
967N ALA* 3.1 27.0 + - - +
999N THR* 4.0 17.7 + - + +
1002N LYS* 3.5 69.9 + - + -
1003N VAL* 4.1 9.6 - - + -
1006N ALA* 4.0 6.0 - - + +
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Residues in contact with LEU 964 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960N LYS* 2.8 41.5 + - + +
961N LYS* 3.5 11.4 - - + +
963N TYR* 1.3 74.3 - - - +
965N GLU* 1.3 61.0 + - + +
967N ALA* 3.2 4.3 + - - +
968N ASP* 2.9 33.6 + - - +
996N TRP* 3.8 23.3 - - + -
999N THR* 4.6 2.2 - - + -
1003N VAL* 5.8 0.4 - - + -
1041N LEU* 3.6 26.7 - - + -
1058N ARG* 4.0 31.0 + - + +
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Residues in contact with GLU 965 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961N LYS* 2.9 40.5 + - + +
962N GLN* 3.2 10.9 + - - +
964N LEU* 1.3 75.4 - - + +
966N GLU* 1.3 58.7 + - - +
968N ASP* 2.9 26.0 + - - +
969N ARG* 3.0 27.4 + - - +
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Residues in contact with GLU 966 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962N GLN* 2.9 30.6 + - - +
963N TYR* 3.6 28.5 - - - +
965N GLU* 1.3 75.1 - - - +
967N ALA* 1.3 64.3 + - - +
969N ARG* 3.2 38.9 + - + +
970N LYS* 3.0 24.9 + - - +
995N LEU* 5.1 0.4 - - - +
1002N LYS* 4.5 10.8 + - - -
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Residues in contact with ALA 967 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963N TYR 3.1 22.2 + - - +
964N LEU 3.2 7.9 - - - +
966N GLU* 1.3 79.6 - - - +
968N ASP* 1.3 56.5 + - - +
970N LYS 3.5 0.2 + - - -
971N LEU* 3.0 29.1 + - - +
995N LEU* 3.3 20.2 - - + +
996N TRP* 3.9 23.3 - - + -
999N THR* 3.7 18.8 - - - +
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Residues in contact with ASP 968 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964N LEU 2.9 13.5 + - - +
965N GLU* 2.9 12.6 + - - +
967N ALA* 1.3 77.7 - - - +
969N ARG* 1.3 56.3 + - - +
971N LEU* 3.1 15.5 + - - +
972N LEU* 2.9 31.6 + - - +
996N TRP* 4.4 0.7 - - - -
1058N ARG* 2.7 40.1 + - - -
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Residues in contact with ARG 969 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962N GLN 5.5 0.2 + - - -
965N GLU* 3.0 22.4 + - - +
966N GLU* 3.2 50.6 + - + +
968N ASP* 1.3 77.2 - - - +
970N LYS* 1.3 65.1 + - + +
972N LEU* 3.1 15.4 + - + +
973N GLN* 3.0 37.6 + - - +
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Residues in contact with LYS 970 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966N GLU 3.0 17.5 + - - +
969N ARG* 1.3 79.3 - - + +
971N LEU* 1.3 56.6 + - - +
973N GLN* 3.2 22.2 + - + +
974N ILE* 3.0 56.4 + - + +
991N GLN* 4.4 7.1 + - - +
995N LEU* 3.7 33.9 - - + +
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Residues in contact with LEU 971 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967N ALA 3.0 12.8 + - - +
968N ASP* 3.2 20.0 - - - +
970N LYS* 1.3 73.5 - - - +
972N LEU* 1.3 61.6 + - - +
974N ILE* 4.0 3.5 - - + +
975N GLU* 3.1 40.9 + - + +
992N ILE* 3.8 36.1 - - + -
995N LEU* 3.8 15.6 - - + +
996N TRP* 4.0 33.2 - - + +
1058N ARG* 5.2 2.0 - - - +
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Residues in contact with LEU 972 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968N ASP* 2.9 16.9 + - + +
969N ARG* 3.3 13.9 - - + +
971N LEU* 1.3 75.2 - - - +
973N GLN* 1.3 67.3 + - + +
975N GLU* 3.1 10.1 + - + +
976N GLN* 2.9 25.2 + - - +
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Residues in contact with GLN 973 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969N ARG* 3.0 30.7 + - - +
970N LYS* 3.2 25.6 + - + +
972N LEU* 1.3 78.0 - - + +
974N ILE* 1.3 57.1 + - + +
976N GLN* 3.3 13.7 + - - +
977N ALA* 2.9 28.1 + - - +
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Residues in contact with ILE 974 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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970N LYS* 3.0 46.8 + - + +
971N LEU* 4.0 7.2 - - - +
973N GLN* 1.3 77.6 - - + +
975N GLU* 1.3 63.9 + - + +
977N ALA* 3.0 10.3 + - - +
978N TYR* 3.0 20.1 + - - +
983N LEU* 3.8 10.6 - - + +
988N ARG* 3.9 30.5 - - + +
991N GLN* 3.5 42.8 - - + +
992N ILE* 4.0 12.6 - - + +
995N LEU* 5.0 3.4 - - + -
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Residues in contact with GLU 975 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971N LEU* 3.1 26.9 + - + +
972N LEU* 3.1 13.8 + - + +
974N ILE* 1.3 78.4 - - + +
976N GLN* 1.3 62.4 - - - +
978N TYR* 3.1 16.5 + - - +
979N GLU* 3.0 31.4 + - - +
988N ARG* 2.9 37.9 + - - -
992N ILE* 4.1 8.1 - - - +
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Residues in contact with GLN 976 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972N LEU 2.9 12.6 + - - +
973N GLN* 3.4 16.2 - - - +
975N GLU* 1.3 76.9 - - - +
977N ALA* 1.3 62.3 + - - +
979N GLU* 3.0 9.7 + - + +
980N MET* 3.0 57.2 + - + +
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Residues in contact with ALA 977 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973N GLN 2.9 13.8 + - - +
974N ILE* 3.4 10.3 - - - +
976N GLN* 1.3 74.6 - - - +
978N TYR* 1.3 58.6 + - - +
980N MET* 4.0 2.0 + - - -
981N GLY 3.5 1.7 + - - -
982N PHE* 2.9 46.1 + - + +
983N LEU* 3.1 27.7 + - + -
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Residues in contact with TYR 978 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974N ILE 3.0 11.3 + - - +
975N GLU* 3.3 15.5 - - - +
976N GLN 3.1 0.4 - - - -
977N ALA* 1.3 77.1 - - - +
979N GLU* 1.3 82.0 + - - +
981N GLY* 3.1 13.5 + - - -
983N LEU* 3.3 23.9 - - + +
985N ASP* 3.7 42.4 + - + +
988N ARG* 3.7 35.4 - - + -
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Residues in contact with GLU 979 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975N GLU* 3.0 22.7 + - - +
976N GLN* 3.5 11.4 - - + +
978N TYR* 1.3 88.1 - - - +
980N MET* 1.3 60.4 + - + +
981N GLY* 3.0 10.4 + - - -
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Residues in contact with MET 980 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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976N GLN* 3.0 52.2 + - + +
977N ALA* 5.3 0.7 - - - -
979N GLU* 1.3 76.3 - - + +
981N GLY* 1.3 60.1 + - - +
982N PHE* 3.4 41.0 + - + -
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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