Contacts of the helix formed by residues 945 - 960 (chain B) in PDB entry 3CQC
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 945 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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939B HIS* 4.1 9.6 - - - -
940B GLU* 2.8 29.4 + - + +
943B SER* 3.0 30.1 + - - +
944B GLN* 1.3 74.4 - - - +
946B LEU* 1.3 56.9 + - - +
947B GLU* 3.5 7.2 - - - -
948B LYS* 3.3 41.0 + - + +
949B ALA* 3.0 22.0 + - - +
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Residues in contact with LEU 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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898A ARG* 3.5 36.8 - - + +
901A LEU* 4.2 16.4 - - + -
941B ILE* 4.0 35.0 - - + +
944B GLN* 3.1 17.5 + - - +
945B GLU* 1.3 72.7 - - - +
947B GLU* 1.3 70.1 + - - +
949B ALA* 4.3 1.1 - - + -
950B HIS* 3.0 23.7 + - - +
977B ALA* 3.6 12.9 - - + +
980B ALA* 3.7 22.9 - - + +
981B SER* 3.5 17.5 - - - -
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Residues in contact with GLU 947 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944B GLN 5.1 1.4 - - - +
945B GLU* 4.5 3.8 - - - -
946B LEU* 1.3 83.1 + - - +
948B LYS* 1.3 66.5 + - - +
950B HIS* 3.3 8.0 + - - +
951B ALA* 3.1 21.1 + - - +
981B SER* 3.2 12.9 - - - +
982B ASP* 3.0 36.7 + - - +
983B PHE* 3.8 40.5 - - + +
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Residues in contact with LYS 948 (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 GLU* 3.4 20.4 - - + +
945B GLU* 3.3 46.1 + - + +
946B LEU 3.2 0.4 - - - -
947B GLU* 1.3 81.1 + - - +
949B ALA* 1.3 56.3 + - - +
951B ALA* 3.1 9.0 + - + +
952B THR* 2.7 33.8 + - + +
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Residues in contact with ALA 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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937B TRP* 4.3 7.4 - - + +
940B GLU* 3.0 23.9 + - + +
941B ILE* 4.1 23.8 - - + +
945B GLU 3.0 14.0 + - - +
946B LEU* 3.4 10.5 + - - +
948B LYS* 1.3 74.0 - - - +
950B HIS* 1.3 57.8 + - - +
952B THR* 3.8 0.7 - - - +
953B LEU* 2.9 39.4 + - + +
977B ALA* 4.4 6.3 - - + -
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Residues in contact with HIS 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946B LEU 3.0 14.8 + - - +
947B GLU* 3.4 9.9 - - - +
949B ALA* 1.3 77.4 - - - +
951B ALA* 1.3 63.5 + - + +
954B LEU* 2.8 45.0 + - + +
974B SER* 2.8 45.7 + - - +
977B ALA* 3.8 16.8 - - + +
978B ALA* 3.8 15.8 - - + +
983B PHE* 4.1 20.9 - + - -
991B LYS* 3.9 25.7 + - + +
994B GLU* 6.2 0.2 - - - -
995B MET* 3.4 23.6 - - + -
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Residues in contact with ALA 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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932B SER* 4.8 0.2 + - - -
947B GLU 3.1 9.6 + - - +
948B LYS* 3.1 12.7 + - + +
950B HIS* 1.3 87.3 - - + +
952B THR* 1.3 57.4 + - + +
954B LEU* 3.4 5.7 + - - +
955B GLY* 2.9 24.6 + - - -
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Residues in contact with THR 952 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932B SER* 3.7 17.7 + - - -
933B HIS 4.4 5.5 + - - -
936B SER* 4.2 9.0 - - - -
937B TRP* 3.8 19.7 + - - +
940B GLU* 2.6 40.8 - - - +
948B LYS* 2.7 12.7 + - + +
949B ALA 3.8 3.1 - - - +
951B ALA* 1.3 71.9 - - + +
953B LEU* 1.3 60.0 + - - +
955B GLY* 3.4 0.5 + - - -
956B LEU* 2.8 34.1 + - - +
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Residues in contact with LEU 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A LEU* 5.9 0.4 - - + -
937B TRP* 3.7 48.0 - - + -
941B ILE* 5.0 2.9 - - + -
949B ALA* 2.9 31.1 + - + +
952B THR* 1.3 72.7 - - - +
954B LEU* 1.3 65.8 + - - +
956B LEU* 3.4 4.5 + - + +
957B ALA* 3.0 23.9 + - - +
970B LEU* 3.8 25.8 - - + +
973B LEU* 3.8 40.2 - - + +
974B SER* 3.5 19.1 - - - +
977B ALA* 4.5 4.0 - - + -
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Residues in contact with LEU 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 HIS* 2.8 41.0 + - + +
951B ALA* 3.6 6.1 - - - +
953B LEU* 1.3 75.4 - - - +
955B GLY* 1.3 57.5 + - - +
957B ALA* 3.1 2.1 + - - +
958B ASN* 2.9 48.5 + - - +
971B LEU* 3.8 26.9 - - + -
974B SER* 3.5 9.3 + - - +
994B GLU* 3.4 29.8 - - + +
995B MET* 4.6 7.9 - - + -
998B GLN* 4.3 6.1 - - + +
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Residues in contact with GLY 955 (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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932B SER* 4.1 11.7 - - - -
951B ALA 2.9 14.5 + - - -
952B THR 3.6 3.8 - - - -
953B LEU 3.2 0.2 - - - -
954B LEU* 1.3 76.0 - - - +
956B LEU* 1.3 62.5 + - - +
958B ASN* 3.2 8.2 + - - +
959B MET* 3.1 28.7 + - - +
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Residues in contact with LEU 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932B SER* 3.5 30.5 - - - +
933B HIS 4.3 2.0 - - - +
934B MET* 4.1 24.0 - - + -
937B TRP* 3.7 33.9 - - + +
952B THR* 2.8 25.4 + - - +
953B LEU* 3.4 5.4 + - - +
955B GLY* 1.3 71.0 - - - +
957B ALA* 1.3 62.4 + - - +
959B MET* 3.2 17.6 + - + +
960B GLU* 3.2 23.4 + - - +
970B LEU* 4.0 25.3 - - + +
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Residues in contact with ALA 957 (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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953B LEU 3.0 17.1 + - - +
954B LEU* 3.1 5.4 + - + +
956B LEU* 1.3 77.0 - - - +
958B ASN* 1.3 62.9 + - - +
960B GLU* 3.2 8.5 + - - -
967B LYS* 2.9 31.6 + - + +
970B LEU* 3.8 23.3 - - + -
971B LEU* 3.9 32.3 - - + +
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Residues in contact with ASN 958 (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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954B LEU* 2.9 34.0 + - - +
955B GLY* 3.2 6.8 + - - +
957B ALA* 1.3 80.3 - - - +
959B MET* 1.3 59.5 + - + +
960B GLU 3.5 1.4 + - - +
961B THR* 5.3 1.9 - - - +
967B LYS* 4.1 8.8 + - - +
998B GLN* 3.1 38.3 + - - +
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Residues in contact with MET 959 (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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932B SER* 4.2 34.8 - - - +
955B GLY 3.1 18.5 + - - +
956B LEU* 3.2 16.8 + - + +
958B ASN* 1.3 76.7 - - + +
960B GLU* 1.3 63.7 + - - +
961B THR* 3.6 11.9 + - - +
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Residues in contact with GLU 960 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956B LEU 3.2 11.9 + - - +
957B ALA* 3.2 13.7 + - - +
958B ASN 4.3 0.3 - - - +
959B MET* 1.3 79.1 - - - +
961B THR* 1.3 69.9 + - - +
962B ARG* 3.7 10.8 + - - +
963B TYR* 3.2 40.8 + - - +
966B LYS* 3.5 38.1 + - + +
967B LYS* 3.4 36.8 + - + +
970B LEU* 4.6 2.9 - - + +
1025B VAL* 3.8 5.7 - - - +
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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
------------------------------------------------------------
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