Contacts of the helix formed by residues 959 - 975 (chain E) in PDB entry 3U5P
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 SER 959 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957E GLY 4.0 1.6 + - - -
958E LEU* 1.3 77.2 - - - +
960E PRO* 1.3 69.9 - - - +
961E VAL* 3.4 17.8 + - - +
962E ASP* 3.3 28.8 + - - -
963E GLN* 2.8 36.4 + - - +
1019E GLN 5.2 1.2 + - - -
1020E ILE* 6.4 0.7 - - - -
3N THR* 4.3 12.7 + - - +
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Residues in contact with PRO 960 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958E LEU 3.6 2.6 - - - +
959E SER* 1.3 90.7 - - - +
961E VAL* 1.3 65.6 + - + +
963E GLN* 3.6 6.8 - - + +
964E ARG* 3.1 38.1 + - - +
1012E LYS* 5.5 2.2 - - - +
898F ASP* 3.8 22.7 - - + +
3N THR* 4.6 10.8 - - - +
4N LYS* 5.9 1.6 - - - -
5N GLN* 3.5 33.9 - - + +
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Residues in contact with VAL 961 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934E ILE* 3.9 17.7 - - + +
935E GLY* 5.5 3.6 - - - -
959E SER* 3.3 10.7 - - - +
960E PRO* 1.3 75.6 - - + +
962E ASP* 1.3 68.7 + - - +
963E GLN 3.0 1.1 - - - -
964E ARG* 2.8 25.0 + - - +
965E LYS* 3.1 38.3 + - - +
898F ASP* 4.7 7.9 - - - +
921F PHE* 3.7 40.2 - - + -
3N THR* 6.1 1.3 - - + -
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Residues in contact with ASP 962 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958E LEU* 3.8 8.5 - - + -
959E SER* 3.3 25.7 + - - -
961E VAL* 1.3 81.8 - - - +
963E GLN* 1.3 61.7 + - - +
965E LYS* 3.1 19.6 + - - +
966E CYS* 3.0 28.9 + - - -
1020E ILE* 4.7 5.7 - - - +
1021E PRO* 3.3 35.6 - - + +
1081E TYR* 3.4 17.0 + - - -
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Residues in contact with GLN 963 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945E ASN* 3.1 21.9 - - - +
958E LEU* 3.0 32.8 - - - +
959E SER 2.8 23.6 + - - +
960E PRO* 3.6 11.2 - - + +
961E VAL 2.9 0.2 + - - -
962E ASP* 1.3 73.8 - - - +
964E ARG* 1.3 59.4 + - + +
966E CYS* 4.1 2.3 - - - +
967E GLU* 3.1 54.3 + - - +
1010E LEU* 2.9 34.9 + - - +
1012E LYS* 4.2 7.1 + - - +
1017E HIS* 4.5 0.9 - - - -
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Residues in contact with ARG 964 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929E THR* 5.3 1.0 - - - +
932E ARG* 3.4 37.9 - - - +
933E ASP 4.5 3.8 - - - -
934E ILE* 2.5 51.7 + - + +
935E GLY* 3.9 4.8 + - - -
937E PRO* 3.2 32.3 - - - +
960E PRO* 3.1 31.7 + - - +
961E VAL* 2.8 13.3 + - - +
963E GLN* 1.3 79.6 - - + +
965E LYS* 1.3 63.6 + - - +
966E CYS 3.3 0.2 - - - -
967E GLU* 3.8 9.7 - - - +
968E ARG* 3.3 24.8 + - - +
898F ASP* 4.1 14.5 + - - -
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Residues in contact with LYS 965 (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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934E ILE* 3.8 18.4 - - + -
961E VAL* 3.4 36.2 - - - +
962E ASP* 3.1 20.5 + - - +
964E ARG* 1.3 78.2 - - - +
966E CYS* 1.3 58.2 + - - +
968E ARG* 4.0 4.1 - - - +
969E LEU* 3.1 30.0 + - - +
1080E ILE* 3.8 31.4 - - + +
1081E TYR* 3.6 40.7 - - + +
1083E ASP* 5.8 2.6 + - - -
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Residues in contact with CYS 966 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958E LEU* 5.3 4.7 - - - -
962E ASP* 3.0 19.7 + - - +
963E GLN* 4.1 3.8 - - - +
965E LYS* 1.3 78.3 - - - +
967E GLU* 1.3 60.6 + - - +
969E LEU* 3.1 3.0 + - - -
970E LEU* 2.8 27.0 + - - +
1010E LEU* 4.1 13.0 - - + -
1021E PRO* 4.6 11.2 - - - -
1024E PHE* 3.3 59.3 - - + -
1025E VAL* 6.0 0.4 - - - -
1081E TYR* 4.4 11.2 - - - -
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Residues in contact with GLU 967 (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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915E VAL* 3.7 28.3 - - + +
916E PRO* 3.6 32.3 - - + +
929E THR* 4.1 7.9 + - + -
932E ARG* 4.3 12.3 + - - -
943E CYS* 5.0 5.2 - - - -
963E GLN* 3.1 48.5 + - - +
964E ARG* 3.8 11.8 - - - +
965E LYS 3.5 0.2 - - - -
966E CYS* 1.3 75.8 - - - +
968E ARG* 1.3 53.0 + - - +
970E LEU* 3.0 4.7 + - - +
971E LEU* 2.7 35.7 + - - +
1010E LEU* 4.6 11.1 - - + +
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Residues in contact with ARG 968 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929E THR* 2.6 44.1 + - + +
930E PHE* 3.3 33.3 + - - -
932E ARG 3.7 14.1 + - - -
933E ASP* 5.6 0.2 - - - +
934E ILE* 3.6 32.8 - - + +
964E ARG 3.3 18.1 + - - +
965E LYS* 4.0 5.4 - - - +
967E GLU* 1.3 76.2 - - - +
969E LEU* 1.3 59.0 + - - +
971E LEU* 3.9 1.3 - - - -
972E TYR* 3.0 59.0 + - + -
1080E ILE* 3.9 28.3 - - + +
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Residues in contact with LEU 969 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965E LYS 3.1 21.2 + - - +
966E CYS* 3.1 10.1 + - - +
968E ARG* 1.3 76.8 - - - +
970E LEU* 1.3 65.5 + - - +
972E TYR* 3.0 17.2 + - + +
973E LEU* 3.1 19.2 + - - +
1024E PHE* 3.5 28.9 - - + -
1025E VAL* 5.0 0.2 - - + -
1073E PHE* 4.2 14.8 - - + -
1076E LYS* 4.0 37.2 - - + +
1077E LEU* 3.6 25.8 - - + -
1080E ILE* 4.1 13.0 - - + -
1081E TYR* 4.5 11.2 - - + -
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Residues in contact with LEU 970 (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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915E VAL* 4.1 11.2 - - + -
966E CYS 2.8 15.8 + - - +
967E GLU 3.6 5.8 - - - +
969E LEU* 1.3 71.7 - - - +
971E LEU* 1.3 63.2 + - - +
973E LEU* 3.1 9.3 + - + +
974E TYR* 3.0 37.1 + - + -
1003E LEU* 3.8 26.9 - - + -
1006E VAL* 3.5 19.7 - - + -
1007E LYS* 3.4 46.4 - - + +
1010E LEU* 3.7 17.9 - - + -
1024E PHE* 4.0 4.8 - - + -
1028E VAL* 5.7 0.7 - - + -
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Residues in contact with LEU 971 (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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892E VAL* 4.2 10.8 - - + -
909E PHE* 3.6 15.7 - - + -
913E CYS 4.0 9.4 - - - +
914E HIS* 4.1 0.9 - - + -
915E VAL* 3.4 44.8 - - + +
929E THR* 4.2 12.6 - - + -
930E PHE* 3.2 45.1 - - + +
967E GLU 2.7 20.8 + - - +
968E ARG 4.2 0.7 - - - +
970E LEU* 1.3 69.0 - - - +
972E TYR* 1.3 68.5 + - - +
973E LEU 3.0 0.3 + - - -
974E TYR* 3.3 4.8 + - + +
975E CYS* 2.9 41.9 + - - +
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Residues in contact with TYR 972 (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 PHE* 3.6 28.1 - + - -
968E ARG* 3.0 48.8 + - + -
969E LEU* 3.0 14.3 + - + +
971E LEU* 1.3 77.2 - - - +
973E LEU* 1.3 69.0 + - + +
975E CYS* 3.5 3.4 + - + +
976E HIS* 3.2 17.7 + - - +
1072E TYR* 3.3 30.3 + - + +
1076E LYS* 3.2 50.4 + - + -
1079E GLU* 4.7 5.2 + - - -
1080E ILE* 4.5 8.5 - - + +
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Residues in contact with LEU 973 (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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969E LEU 3.4 13.9 - - - +
970E LEU* 3.1 9.3 + - + +
971E LEU 3.0 0.8 - - - -
972E TYR* 1.3 79.4 - - + +
974E TYR* 1.3 57.0 + - - +
976E HIS* 2.8 29.8 + - - +
979E SER* 3.1 15.7 + - - -
1003E LEU* 4.2 27.6 - - + -
1028E VAL* 3.8 32.3 - - + -
1032E PHE* 4.5 9.4 - - + -
1069E VAL* 4.6 9.9 - - + -
1072E TYR* 4.2 17.3 - - + -
1073E PHE* 3.8 33.7 - - + -
1076E LYS* 6.1 0.2 - - + -
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Residues in contact with TYR 974 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892E VAL* 3.7 37.5 - - + +
913E CYS 5.2 2.9 - - - -
915E VAL* 4.0 15.0 - - + -
970E LEU* 3.0 41.3 + - + +
971E LEU* 3.6 11.4 - - + +
973E LEU* 1.3 76.7 - - - +
975E CYS* 1.3 59.1 + - - +
976E HIS 3.3 2.6 + - - +
979E SER* 3.3 12.4 + - - -
983E GLN* 3.5 46.5 + - + +
984E GLU* 5.0 2.7 + - - -
1003E LEU* 3.7 22.6 - - + +
1004E SER* 3.1 34.0 + - - -
1007E LYS* 4.2 12.7 - - + +
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Residues in contact with CYS 975 (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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891E ALA* 3.6 38.4 - - - +
892E VAL* 3.9 12.8 - - - +
907E LYS* 4.7 3.8 - - - -
930E PHE* 3.7 15.7 - - + -
971E LEU* 2.9 45.3 + - - +
972E TYR* 3.9 4.7 - - + +
974E TYR* 1.3 71.9 - - - +
976E HIS* 1.3 59.9 + - - +
977E GLU* 3.1 15.4 - - - +
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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