Contacts of the helix formed by residues 946 - 958 (chain B) in PDB entry 1M8X
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 PRO 946 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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911B LEU* 4.0 31.0 - - + -
915B LEU* 5.0 0.7 - - + -
944B PHE 4.4 2.2 - - - +
945B ILE* 1.3 97.8 - - + +
947B SER* 1.3 59.8 + - - +
948B ASP* 3.4 2.9 - - + +
949B GLN* 3.1 33.9 + - + +
950B GLN* 2.9 23.0 + - - +
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Residues in contact with SER 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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946B PRO* 1.3 72.5 - - - +
948B ASP* 1.3 55.5 + - - +
950B GLN* 3.0 19.7 + - - +
951B ASN* 2.7 41.1 + - - -
982B GLN* 4.1 32.1 + - - +
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Residues in contact with ASP 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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946B PRO* 3.4 2.2 - - + +
947B SER* 1.3 79.0 - - - +
949B GLN* 1.3 75.9 + - - +
951B ASN* 3.5 13.1 + - - +
952B GLU* 3.1 31.4 + - - +
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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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915B LEU* 3.7 30.0 - - + +
918B ALA* 4.9 10.1 - - + -
945B ILE* 3.6 21.6 - - + +
946B PRO* 3.1 43.4 + - + +
947B SER 3.1 0.2 - - - -
948B ASP* 1.3 82.0 + - - +
950B GLN* 1.3 66.3 + - - +
952B GLU* 3.3 27.4 + - - +
953B MET* 3.3 25.3 + - - +
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Residues in contact with GLN 950 (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 LEU* 2.4 46.5 + - + +
943B GLU* 4.7 2.2 + - - +
945B ILE* 3.4 24.6 + - + +
946B PRO 2.9 18.3 + - - +
947B SER* 3.0 20.3 + - - +
949B GLN* 1.3 74.1 - - - +
951B ASN* 1.3 69.3 + - - +
953B MET* 3.1 12.2 + - - +
954B VAL* 3.2 19.9 + - - +
980B CYS* 3.5 29.1 + - - +
981B VAL* 3.8 14.3 - - + -
982B GLN* 4.6 1.7 + - - +
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Residues in contact with ASN 951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947B SER* 2.7 26.8 + - - +
948B ASP* 3.8 12.4 - - - +
950B GLN* 1.3 74.1 + - - +
952B GLU* 1.3 62.2 + - - +
954B VAL* 3.6 9.5 - - - +
955B ARG* 3.2 25.5 + - - +
981B VAL* 3.5 25.1 - - - +
982B GLN* 3.3 25.1 + - - +
985B SER* 3.6 16.4 + - - +
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Residues in contact with GLU 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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922B ARG* 2.7 53.6 + - - +
948B ASP* 3.1 22.3 + - - +
949B GLN* 3.4 32.4 - - - +
950B GLN 3.1 0.4 - - - -
951B ASN* 1.3 81.0 - - + +
953B MET* 1.3 63.2 + - + +
955B ARG* 3.6 25.3 + - - +
956B GLU* 3.9 10.6 + - - +
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Residues in contact with MET 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B PHE* 5.1 0.2 - - + -
918B ALA* 4.3 19.7 - - + +
921B ILE* 4.0 27.1 - - + -
922B ARG* 5.6 4.7 - - - +
925B VAL* 3.6 29.1 - - + +
938B ILE* 4.6 11.2 - - + -
941B ALA* 3.7 22.7 - - + -
942B LEU* 4.2 19.7 - - + -
945B ILE* 3.5 29.2 - - + -
949B GLN 3.3 7.6 + - - +
950B GLN 3.1 8.8 + - - +
952B GLU* 1.3 78.1 - - + +
954B VAL* 1.3 65.4 + - - +
956B GLU* 3.1 22.0 + - - +
957B LEU* 3.7 2.4 - - - +
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Residues in contact with VAL 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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942B LEU* 4.3 5.4 - - + -
950B GLN 3.2 14.2 + - - +
951B ASN* 3.6 14.8 - - - +
953B MET* 1.3 69.5 - - - +
955B ARG* 1.3 63.4 + - + +
956B GLU 2.9 2.5 - - - -
957B LEU* 2.6 44.1 + - + +
977B CYS* 4.0 18.8 - - + -
981B VAL* 3.4 29.4 - - + -
985B SER* 4.4 17.7 - - - +
986B LEU* 5.2 2.9 - - + -
988B PHE* 3.6 25.9 - - + -
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Residues in contact with ARG 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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922B ARG* 3.7 24.5 - - - +
951B ASN 3.2 14.5 + - - +
952B GLU* 3.6 14.7 + - - +
953B MET 3.2 0.4 - - - -
954B VAL* 1.3 84.5 - - - +
956B GLU* 1.3 62.1 + - + +
958B ASP* 3.3 23.8 + - + +
988B PHE* 5.2 2.9 - - - -
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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
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922B ARG* 3.8 13.2 + - - +
923B GLY* 2.9 33.9 + - - -
925B VAL* 2.9 49.6 + - + +
926B LEU* 4.4 5.7 + - + +
952B GLU 4.3 9.8 - - - +
953B MET* 3.1 11.2 + - - +
954B VAL 2.9 0.8 - - - -
955B ARG* 1.3 79.9 - - - +
957B LEU* 1.3 63.5 + - - +
958B ASP 3.3 7.3 + - - +
960B HIS* 3.5 12.1 + - - -
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Residues in contact with LEU 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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925B VAL* 3.8 22.4 - - + -
926B LEU* 4.3 18.8 - - + -
929B ALA* 4.6 6.5 - - + -
938B ILE* 6.1 0.4 - - + -
953B MET 3.7 6.7 - - - +
954B VAL* 2.6 43.1 + - + +
956B GLU* 1.3 70.0 - - - +
958B ASP* 1.3 66.5 + - - -
960B HIS* 2.8 22.7 + - - +
961B VAL* 3.4 8.0 + - - +
964B CYS* 4.1 25.4 - - + -
973B VAL* 4.7 10.5 - - + -
974B VAL* 6.0 3.4 - - + -
977B CYS* 4.7 14.1 - - - -
988B PHE* 3.8 11.7 - - + -
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Residues in contact with ASP 958 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955B ARG* 3.3 20.7 + - + +
956B GLU 3.1 2.8 - - - +
957B LEU* 1.3 81.8 - - - +
959B GLY* 1.3 76.5 + - - +
960B HIS* 3.1 15.8 + - - -
961B VAL* 5.4 0.2 - - - +
988B PHE* 3.3 40.2 - - + +
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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