Contacts of the helix formed by residues 935 - 956 (chain B) in PDB entry 2O8C
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 935 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928B THR* 5.8 2.2 - - - -
932B GLY* 3.6 4.6 - - - -
933B PHE* 3.4 32.9 - - - +
936B ASP* 1.3 66.4 + - - +
937B TYR* 3.2 30.3 + - - -
938B ASP* 3.2 23.5 + - - +
939B GLN* 3.3 8.3 + - - +
1028B SER* 3.5 24.2 + - - -
1031B ASP* 3.8 26.0 + - - +
1032B CYS* 5.6 1.3 - - - -
1035B ARG* 5.4 7.3 - - - +
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Residues in contact with ASP 936 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928B THR* 4.8 5.3 - - + +
929B PRO 3.9 12.0 - - - +
930B LYS* 3.4 9.9 - - - +
931B ALA* 3.0 41.0 + - - -
932B GLY* 3.5 9.0 - - - +
935B SER* 1.3 73.8 - - - +
937B TYR* 1.3 57.0 + - - +
938B ASP 2.9 6.0 + - - -
939B GLN* 2.8 21.2 + - - +
940B ALA* 2.5 68.1 + - - +
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Residues in contact with TYR 937 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931B ALA 4.0 14.1 + - - +
932B GLY* 5.7 0.7 - - - -
935B SER* 4.0 27.2 + - - -
936B ASP* 1.3 76.9 - - - +
938B ASP* 1.3 80.1 + - - +
940B ALA* 4.8 2.5 - - - -
941B LEU* 4.3 17.2 - - - +
1035B ARG* 5.9 1.6 + - - -
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Residues in contact with ASP 938 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935B SER* 3.2 14.2 + - - +
936B ASP 2.9 0.4 - - - -
937B TYR* 1.3 101.3 - - - +
939B GLN* 1.3 61.0 + - - +
941B LEU* 4.2 4.4 + - - +
942B ALA* 3.4 20.6 + - - +
1024B ARG* 4.6 10.3 - - + +
1028B SER* 3.4 17.4 + - - +
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Residues in contact with GLN 939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927B ILE* 4.8 7.1 - - - +
928B THR* 3.4 40.8 + - - +
935B SER 3.3 2.1 + - - -
936B ASP* 2.8 19.7 + - - +
938B ASP* 1.3 77.0 - - - +
940B ALA* 1.3 54.4 + - - +
941B LEU 3.2 1.8 - - - -
942B ALA* 2.8 6.8 + - - +
943B ASP* 2.6 47.0 + - + +
1025B ARG* 4.8 12.7 - - + +
1028B SER* 3.6 27.0 + - - -
1029B LEU* 4.1 24.4 - - - +
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Residues in contact with ALA 940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930B LYS* 6.3 1.6 - - + -
936B ASP* 2.5 44.6 + - - +
937B TYR* 5.2 1.6 - - - -
939B GLN* 1.3 70.1 - - - +
941B LEU* 1.3 55.5 + - - +
943B ASP* 4.0 6.0 - - - +
944B ILE* 3.1 42.7 + - + +
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Residues in contact with LEU 941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936B ASP 4.2 1.6 + - - -
937B TYR 4.3 16.5 + - - +
938B ASP* 4.2 3.8 + - - +
939B GLN 3.2 0.6 - - - -
940B ALA* 1.3 78.3 - - - +
942B ALA* 1.3 61.6 + - - +
944B ILE* 4.3 6.3 - - + +
945B ARG* 3.4 49.9 + - + +
1024B ARG* 5.1 10.3 - - - +
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Residues in contact with ALA 942 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938B ASP 3.4 18.3 + - - +
939B GLN* 2.8 6.3 + - - +
941B LEU* 1.3 78.3 - - - +
943B ASP* 1.3 63.3 + - - +
945B ARG* 3.5 1.7 + - - -
946B GLU* 3.3 28.9 + - - +
1021B ALA* 3.6 29.5 - - - +
1024B ARG* 3.8 22.4 - - + +
1025B ARG* 4.1 9.0 - - + +
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Residues in contact with ASP 943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939B GLN* 2.6 33.8 + - + +
940B ALA* 4.0 6.3 - - - +
942B ALA* 1.3 70.8 - - - +
944B ILE* 1.3 61.6 + - + +
946B GLU* 3.2 14.3 + - - +
947B ASN* 3.0 50.9 + - - +
1025B ARG* 5.5 2.0 - - + +
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Residues in contact with ILE 944 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940B ALA* 3.1 25.0 + - + +
941B LEU* 4.3 7.0 - - + +
943B ASP* 1.3 79.2 - - + +
945B ARG* 1.3 59.4 + - + +
947B ASN* 3.4 9.9 + - + +
948B GLU* 2.9 35.7 + - + +
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Residues in contact with ARG 945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941B LEU* 3.4 35.4 + - + +
942B ALA* 3.9 5.2 - - - +
943B ASP 3.3 0.8 - - - -
944B ILE* 1.3 78.6 - - + +
946B GLU* 1.3 60.9 + - - +
948B GLU* 3.9 17.0 + - - +
949B GLN* 3.5 36.7 + - - +
1017B ASN 5.9 0.2 - - - +
1018B LEU* 4.8 0.2 - - - +
1021B ALA* 4.2 12.7 - - + +
1024B ARG* 4.1 31.2 - - - +
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Residues in contact with GLU 946 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942B ALA 3.3 14.5 + - - +
943B ASP* 3.2 14.2 + - - +
944B ILE 3.2 0.6 - - - -
945B ARG* 1.3 75.2 - - - +
947B ASN* 1.3 58.0 + - - +
948B GLU 3.0 3.6 - - - -
949B GLN* 3.0 3.3 + - - +
950B SER* 2.7 42.3 + - - +
1018B LEU* 3.9 19.5 - - + -
1021B ALA* 2.9 36.1 - - + +
1022B GLU* 3.4 13.3 - - + +
1025B ARG* 3.3 40.4 + - - +
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Residues in contact with ASN 947 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943B ASP* 3.0 42.2 + - - +
944B ILE* 3.8 10.0 - - + +
946B GLU* 1.3 77.1 - - - +
948B GLU* 1.3 59.8 + - - +
950B SER* 4.3 6.1 - - - -
951B LEU* 3.5 24.9 + - - +
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Residues in contact with GLU 948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944B ILE* 2.9 21.1 + - + +
945B ARG* 3.9 20.9 + - - +
947B ASN* 1.3 79.4 - - - +
949B GLN* 1.3 62.6 + - + +
951B LEU* 3.3 3.7 + - - +
952B LEU* 2.7 48.1 + - + +
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Residues in contact with GLN 949 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945B ARG* 3.5 22.3 + - - +
946B GLU 3.0 3.7 + - - +
948B GLU* 1.3 81.1 + - + +
950B SER* 1.3 57.8 + - - +
951B LEU 3.2 5.2 - - - -
952B LEU* 3.9 22.8 - - + +
953B GLU* 3.5 35.5 + - + +
977B TYR* 4.5 0.7 + - - -
1014B LYS* 3.1 31.6 + - + +
1017B ASN* 3.6 25.1 - - - +
1018B LEU* 3.2 29.3 + - + +
1021B ALA* 5.8 0.2 - - - +
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Residues in contact with SER 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946B GLU* 2.7 30.3 + - - +
947B ASN* 3.9 6.7 + - - -
948B GLU 3.3 0.2 - - - -
949B GLN* 1.3 73.3 - - - +
951B LEU* 1.3 58.8 + - - +
953B GLU 4.8 0.2 - - - -
954B TYR* 3.3 26.5 - - - -
977B TYR* 4.1 16.6 + - - -
1018B LEU* 4.2 10.7 - - - +
1022B GLU* 5.5 0.2 + - - -
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Residues in contact with LEU 951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947B ASN 3.5 17.5 - - - +
948B GLU* 3.3 3.3 + - - +
950B SER* 1.3 82.3 - - - +
952B LEU* 1.3 58.1 + - - +
953B GLU 3.3 1.6 - - - -
954B TYR* 3.3 15.3 + - + +
955B LEU* 3.0 46.5 + - + +
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Residues in contact with LEU 952 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948B GLU* 2.7 32.2 + - + +
949B GLN* 3.9 20.2 - - + +
951B LEU* 1.3 78.0 - - - +
953B GLU* 1.3 59.0 + - + +
955B LEU* 3.3 17.9 + - + +
956B GLU* 3.0 39.4 + - + +
1014B LYS* 3.4 42.4 - - + +
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Residues in contact with GLU 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949B GLN* 3.5 22.8 + - + +
951B LEU 3.3 0.2 - - - -
952B LEU* 1.3 79.8 - - + +
954B TYR* 1.3 61.9 + - + +
956B GLU* 3.4 7.9 - - + +
957B LYS* 3.0 25.6 + - - +
969B TYR* 3.3 20.4 + - - +
977B TYR* 3.3 48.3 - - + -
1010B THR* 6.1 2.5 - - + -
1011B ILE* 4.1 22.6 - - + +
1014B LYS* 3.9 30.5 - - + +
1015B LEU* 4.5 3.5 + - - +
1018B LEU* 4.7 2.6 - - - +
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Residues in contact with TYR 954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950B SER* 3.3 25.4 - - - -
951B LEU* 3.3 16.7 + - + +
952B LEU 3.3 0.6 - - - -
953B GLU* 1.3 77.2 - - - +
955B LEU* 1.3 63.9 + - - +
957B LYS* 3.4 32.2 + - + +
958B GLN* 3.7 5.5 + - - +
961B ARG* 3.6 15.4 + - - +
969B TYR* 4.4 20.8 - + - +
977B TYR* 4.4 22.1 - + - -
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Residues in contact with LEU 955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951B LEU* 3.0 31.0 + - + +
952B LEU* 3.5 20.9 - - + +
954B TYR* 1.3 78.7 - - - +
956B GLU* 1.3 59.1 + - + +
957B LYS 3.2 1.6 - - - -
958B GLN* 3.5 26.1 - - + +
959B ARG* 4.1 5.7 + - - +
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Residues in contact with GLU 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952B LEU* 3.0 28.7 + - + +
953B GLU* 3.4 9.6 + - + +
954B TYR 3.3 0.2 - - - -
955B LEU* 1.3 76.3 - - + +
957B LYS* 1.3 60.8 + - - +
958B GLN 3.3 0.9 - - - -
959B ARG* 3.6 54.5 + - - +
960B ASN* 4.1 2.1 - - - +
1007B TRP* 3.5 32.7 - - + -
1010B THR* 3.5 27.8 + - - +
1014B LYS* 3.8 17.1 + - - -
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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
------------------------------------------------------------
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