Contacts of the helix formed by residues 928 - 952 (chain U) in PDB entry 5MQF
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 THR 928 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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927U TYR* 3.8 29.8 - - - +
929U CYS* 3.8 28.7 - - - +
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Residues in contact with CYS 929 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928U THR* 3.8 28.9 - - - +
930U GLU* 3.8 24.5 - - - +
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Residues in contact with GLU 930 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929U CYS* 3.8 29.2 - - - +
931U THR* 3.8 26.9 - - - +
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Residues in contact with THR 931 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930U GLU* 3.8 25.6 - - - +
932U ALA* 3.8 29.4 - - - +
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Residues in contact with ALA 932 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931U THR* 3.8 25.1 - - - +
933U GLY* 3.8 28.9 - - - +
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Residues in contact with GLY 933 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932U ALA* 3.8 29.2 - - - +
934U TYR* 3.8 25.6 - - - +
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Residues in contact with TYR 934 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933U GLY* 3.8 26.2 - - - +
935U PHE* 3.8 29.2 - - - +
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Residues in contact with PHE 935 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934U TYR* 3.8 29.2 - - - +
936U PHE* 3.8 26.0 - - - +
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Residues in contact with PHE 936 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935U PHE* 3.8 28.7 - - - +
937U LEU* 3.8 27.1 - - - +
940U VAL* 4.7 19.1 - - - +
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Residues in contact with LEU 937 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936U PHE* 3.8 26.9 - - - +
938U TYR* 3.8 28.7 - - - +
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Residues in contact with TYR 938 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937U LEU* 3.8 28.7 - - - +
939U GLN* 3.8 28.0 - - - +
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Residues in contact with GLN 939 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938U TYR* 3.8 29.4 - - - +
940U VAL* 3.8 28.7 - - - +
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Residues in contact with VAL 940 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936U PHE* 4.7 16.6 - - - +
939U GLN* 3.8 28.7 - - - +
941U MSE 3.8 29.4 - - - +
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Residues in contact with MSE 941 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940U VAL* 3.8 26.0 - - - +
942U SER* 3.8 29.2 - - - +
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Residues in contact with SER 942 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941U MSE 3.8 29.2 - - - +
943U ARG* 3.8 26.5 - - - +
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Residues in contact with ARG 943 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942U SER* 3.8 25.6 - - - +
944U TRP* 3.8 28.9 - - - +
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Residues in contact with TRP 944 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943U ARG* 3.8 28.5 - - - +
945U GLU* 3.8 27.6 - - - +
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Residues in contact with GLU 945 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944U TRP* 3.8 26.0 - - - +
946U GLU* 3.8 28.9 - - - +
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Residues in contact with GLU 946 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945U GLU* 3.8 25.8 - - - +
947U TYR* 3.8 28.5 - - - +
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Residues in contact with TYR 947 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946U GLU* 3.8 28.9 - - - +
948U ILE* 3.8 27.1 - - - +
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Residues in contact with ILE 948 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947U TYR* 3.8 24.7 - - - +
949U SER* 3.8 29.2 - - - +
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Residues in contact with SER 949 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948U ILE* 3.8 28.9 - - - +
950U LYS* 3.8 25.1 - - - +
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Residues in contact with LYS 950 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949U SER* 3.8 28.5 - - - +
951U VAL* 3.8 29.4 - - - +
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Residues in contact with VAL 951 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950U LYS* 3.8 28.9 - - - +
952U LYS* 3.8 28.7 - - - +
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Residues in contact with LYS 952 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951U VAL* 3.8 28.0 - - - +
953U ASN* 3.8 28.5 - - - +
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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