Contacts of the helix formed by residues 930 - 945 (chain E) in PDB entry 1NYE
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 ASP 930 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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928E GLY 4.3 0.2 + - - -
929E ILE* 1.3 74.6 - - - +
931E ALA* 1.3 68.3 + - - +
932E SER* 2.8 16.9 + - - +
933E THR* 2.7 46.7 + - - +
934E PHE* 3.1 17.1 + - - +
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Residues in contact with ALA 931 (chain E).
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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929E ILE 3.7 2.6 + - - -
930E ASP* 1.3 71.1 - - - +
932E SER* 1.3 57.6 + - - +
934E PHE* 3.5 9.9 - - - +
935E ASP* 3.2 26.3 + - - +
959E TYR* 4.6 1.9 + - - -
961E LEU* 4.7 15.3 - - + +
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Residues in contact with SER 932 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930E ASP* 2.8 17.1 + - - +
931E ALA* 1.3 73.1 - - - +
933E THR* 1.3 66.7 + - - +
934E PHE 3.0 1.7 + - - -
935E ASP* 3.2 16.1 + - - +
936E GLY* 3.3 8.7 + - - -
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Residues in contact with THR 933 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893E PHE* 5.1 5.1 - - - -
929E ILE* 3.1 19.6 - - - +
930E ASP* 2.7 32.3 + - - +
932E SER* 1.3 78.0 - - - +
934E PHE* 1.3 62.2 + - - +
936E GLY* 3.4 7.9 + - - +
937E ILE* 3.4 19.3 + - - +
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Residues in contact with PHE 934 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884E LEU* 4.5 7.6 - - + -
888E LEU* 4.1 12.6 - - + -
924E VAL* 4.1 19.7 - - + -
926E VAL* 4.3 11.7 - - + -
929E ILE* 3.8 27.1 - - + -
930E ASP 3.1 11.7 + - - +
931E ALA* 3.5 12.6 - - - +
933E THR* 1.3 80.0 + - - +
935E ASP* 1.3 59.4 + - - +
937E ILE* 2.8 22.9 + - + +
938E ILE* 3.1 39.7 + - + +
959E TYR* 3.5 35.7 - + - -
961E LEU* 3.6 37.7 - - + -
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Residues in contact with ASP 935 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931E ALA 3.2 10.1 + - - +
932E SER* 3.2 10.7 + - - +
934E PHE* 1.3 80.5 - - - +
936E GLY* 1.3 62.2 + - - +
937E ILE 3.1 0.2 + - - -
938E ILE* 3.0 16.2 - - - +
939E GLN* 3.0 50.2 + - - +
959E TYR* 2.7 23.9 + - - +
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Residues in contact with GLY 936 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932E SER 3.3 9.1 + - - -
933E THR* 3.4 5.3 + - - -
934E PHE 3.2 0.8 - - - -
935E ASP* 1.3 82.9 + - - +
937E ILE* 1.3 59.3 + - - +
939E GLN* 4.3 4.2 - - - +
940E LYS* 3.1 30.2 + - - +
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Residues in contact with ILE 937 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884E LEU* 4.0 11.7 - - + -
887E MET* 3.5 42.7 - - + +
888E LEU* 3.9 16.2 - - + +
891E ALA* 4.4 18.6 - - + -
893E PHE* 6.0 1.6 - - + -
929E ILE* 6.2 0.9 - - + -
933E THR* 3.4 16.4 - - - +
934E PHE* 2.8 11.3 + - - +
936E GLY* 1.3 76.7 - - - +
938E ILE* 1.3 60.5 + - - +
939E GLN 3.2 1.3 - - - -
940E LYS* 3.0 12.7 + - + +
941E ALA* 2.8 24.9 + - - +
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Residues in contact with ILE 938 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880E PHE* 3.7 23.7 - - + -
884E LEU* 3.6 32.9 - - + +
922E SER* 5.7 1.1 - - - +
924E VAL* 5.4 1.8 - - + -
934E PHE* 3.1 31.4 + - + +
935E ASP* 3.0 41.5 - - - +
937E ILE* 1.3 73.9 - - - +
939E GLN* 1.3 56.5 + - - +
941E ALA* 3.0 2.6 + - - +
942E LYS* 2.5 39.4 + - - +
957E LEU* 4.1 8.5 - - + -
959E TYR* 3.2 32.8 - - + +
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Residues in contact with GLN 939 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935E ASP* 3.0 47.6 + - - +
936E GLY* 4.3 4.3 - - - +
938E ILE* 1.3 83.1 - - + +
940E LYS* 1.3 65.9 + - - +
942E LYS* 3.5 27.4 - - - +
943E ALA* 3.3 21.5 + - - +
957E LEU* 4.2 15.1 - - - +
959E TYR* 4.2 3.6 - - - -
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Residues in contact with LYS 940 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887E MET* 3.2 25.7 - - + +
936E GLY 3.1 19.8 + - - +
937E ILE* 3.0 17.4 + - + +
939E GLN* 1.3 79.5 - - - +
941E ALA* 1.3 57.4 + - - +
943E ALA* 3.9 0.3 - - - +
944E GLY* 2.8 29.1 + - - -
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Residues in contact with ALA 941 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880E PHE* 4.0 11.4 - - + -
883E ALA* 4.1 6.1 - - + -
884E LEU* 3.9 23.1 - - + +
887E MET* 3.8 21.9 - - + +
937E ILE 2.8 12.2 + - - +
938E ILE* 3.5 8.7 - - - +
940E LYS* 1.3 78.5 - - - +
942E LYS* 1.3 65.3 + - - +
943E ALA 3.0 1.4 + - - -
944E GLY* 3.0 9.3 + - - +
945E CYS* 3.1 21.7 + - - +
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Residues in contact with LYS 942 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880E PHE* 3.4 15.8 - - + -
920E LEU* 4.5 3.3 - - + +
938E ILE 2.5 21.0 + - - +
939E GLN* 3.5 26.0 - - - +
941E ALA* 1.3 71.7 - - - +
943E ALA* 1.3 67.0 + - - +
948E SER* 2.8 24.1 + - - -
955E ILE* 3.1 50.9 + - + +
956E THR* 5.2 0.9 - - - +
957E LEU* 3.8 33.4 - - + +
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Residues in contact with ALA 943 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939E GLN 3.3 10.4 + - - +
940E LYS 4.7 0.2 - - - +
941E ALA 3.1 0.4 - - - -
942E LYS* 1.3 90.0 - - - +
944E GLY* 1.3 60.7 + - - +
945E CYS 3.7 0.7 - - - -
948E SER* 4.1 8.1 - - - -
949E GLN* 3.2 27.9 - - - +
955E ILE* 6.0 0.4 - - - -
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Residues in contact with GLY 944 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887E MET* 5.8 2.5 - - - -
940E LYS 2.8 18.8 + - - -
941E ALA* 3.0 0.9 + - - -
943E ALA* 1.3 77.2 - - - +
945E CYS* 1.3 67.8 + - - +
946E PRO* 3.6 2.1 - - - +
949E GLN* 3.6 15.4 + - - +
1113F PHE 4.8 4.5 - - - +
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Residues in contact with CYS 945 (chain E).
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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876E HIS* 4.4 2.2 - - - -
879E CYS* 3.4 24.9 - - - -
880E PHE* 3.8 19.1 - - - -
883E ALA* 3.5 28.4 - - + +
941E ALA* 3.1 11.5 + - - +
944E GLY* 1.3 77.4 - - - +
946E PRO* 1.3 71.5 - - + +
948E SER* 2.9 40.3 + - - -
949E GLN* 3.1 16.8 + - - +
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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