Contacts of the helix formed by residues 946 - 956 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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911A LEU* 5.1 9.2 - - + -
914A LYS* 6.4 0.7 - - + -
915A LEU* 4.1 17.3 - - + -
944A PHE 4.4 2.0 - - - +
945A ILE* 1.3 91.5 - - + +
947A SER* 1.3 67.8 + - - +
948A ASP* 3.2 2.7 - - + +
949A GLN* 3.0 32.8 + - - +
950A GLN* 3.0 18.5 + - - +
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Residues in contact with SER 947 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946A PRO* 1.3 73.5 - - - +
948A ASP* 1.3 59.0 + - - +
950A GLN* 3.3 18.4 + - - +
951A ASN* 2.9 38.0 + - - -
982A GLN* 4.1 29.5 + - - -
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Residues in contact with ASP 948 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946A PRO* 3.2 2.3 - - + +
947A SER* 1.3 83.5 + - - +
949A GLN* 1.3 76.1 + - - +
951A ASN* 3.6 7.5 + - - +
952A GLU* 3.2 29.3 + - - +
955A ARG* 5.1 7.2 + - - -
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Residues in contact with GLN 949 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915A LEU* 3.9 25.1 - - + +
918A ALA* 4.4 15.3 - - + -
945A ILE* 3.6 22.8 - - + +
946A PRO* 3.0 38.4 + - + +
948A ASP* 1.3 89.6 - - - +
950A GLN* 1.3 65.2 + - - +
952A GLU* 3.4 11.0 + - - +
953A MET* 3.1 25.9 + - + +
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Residues in contact with GLN 950 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942A LEU* 2.6 30.3 + - + +
943A GLU 4.9 2.0 + - - -
945A ILE* 3.7 30.2 + - + -
946A PRO 3.0 13.5 + - - +
947A SER* 3.2 23.1 + - - +
949A GLN* 1.3 77.4 - - - +
951A ASN* 1.3 61.2 + - - +
953A MET* 3.1 5.9 + - - +
954A VAL* 2.8 33.7 + - - +
980A CYS* 3.5 27.8 + - - +
981A VAL* 4.0 19.4 - - + +
982A GLN* 5.2 2.3 + - - +
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Residues in contact with ASN 951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947A SER* 2.9 24.0 + - - +
948A ASP* 3.9 7.9 - - - +
950A GLN* 1.3 75.7 + - - +
952A GLU* 1.3 63.0 + - - +
954A VAL* 3.9 5.1 - - - +
955A ARG* 3.0 59.6 + - - +
981A VAL* 3.5 14.5 - - - +
982A GLN* 3.4 19.6 + - - +
985A SER* 3.0 31.8 + - - +
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Residues in contact with GLU 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918A ALA 5.3 1.9 - - - +
922A ARG* 3.2 39.7 + - - +
948A ASP* 3.2 22.8 + - - +
949A GLN* 3.7 11.0 - - - +
950A GLN 3.2 0.2 - - - -
951A ASN* 1.3 79.8 - - - +
953A MET* 1.3 64.5 + - + +
955A ARG* 3.5 21.2 + - - +
956A GLU* 3.5 22.1 + - + +
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Residues in contact with MET 953 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918A ALA* 4.4 15.0 - - + +
921A ILE* 3.9 27.8 - - + -
925A VAL* 3.6 36.1 - - + +
938A ILE* 4.5 11.9 - - + -
941A ALA* 3.9 22.0 - - + -
942A LEU* 4.3 18.6 - - + -
945A ILE* 3.5 30.1 - - + -
949A GLN* 3.1 10.2 + - + +
950A GLN 3.1 8.9 + - - +
952A GLU* 1.3 75.0 - - - +
954A VAL* 1.3 67.3 + - - +
956A GLU* 3.0 20.3 + - - +
957A LEU* 4.0 0.8 + - - +
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Residues in contact with VAL 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942A LEU* 4.5 3.3 - - + +
950A GLN 2.8 23.9 + - - +
951A ASN* 3.9 6.5 - - - +
953A MET* 1.3 71.1 - - - +
955A ARG* 1.3 59.4 + - + +
957A LEU* 2.9 36.2 + - + +
977A CYS* 3.9 19.3 - - + -
981A VAL* 3.5 32.5 - - + -
985A SER* 3.8 11.4 - - - +
986A LEU* 4.3 8.3 - - + -
988A PHE* 3.2 37.1 - - + -
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Residues in contact with ARG 955 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948A ASP* 5.1 7.3 + - - -
951A ASN* 3.0 54.5 + - - +
952A GLU* 3.7 15.6 - - - +
953A MET 3.2 0.4 - - - -
954A VAL* 1.3 73.0 - - + +
956A GLU* 1.3 56.3 + - - +
957A LEU 3.0 6.5 - - - -
958A ASP* 3.1 29.2 - - + +
985A SER* 5.0 6.1 + - - +
988A PHE* 5.2 2.7 - - + -
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Residues in contact with GLU 956 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922A ARG* 3.7 9.5 - - - +
923A GLY* 2.9 32.4 + - - -
924A HIS 3.4 2.1 + - - -
925A VAL* 3.0 44.8 + - + +
926A LEU* 4.3 9.3 + - + +
952A GLU* 3.5 20.7 - - + +
953A MET* 3.0 12.2 + - - +
955A ARG* 1.3 77.1 - - - +
957A LEU* 1.3 61.2 + - - +
958A ASP 3.3 3.1 + - - +
960A HIS* 3.8 14.6 - - - -
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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