Contacts of the helix formed by residues 946 - 955 (chain A) in PDB entry 4UHW
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 946 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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945A LEU* 1.3 75.5 - - - +
947A PRO* 1.3 74.2 - - - +
948A GLU* 3.0 15.8 + - - +
949A LYS* 3.1 49.6 + - - +
950A VAL* 3.4 9.9 + - - +
986A TYR* 4.8 5.2 + - - -
990A LYS* 5.7 10.1 - - - -
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Residues in contact with PRO 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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936A ILE* 4.1 2.0 - - + +
937A THR* 3.6 30.5 - - + +
940A ALA* 3.6 21.3 - - + -
945A LEU 4.0 4.0 - - - +
946A SER* 1.3 82.2 - - - +
948A GLU* 1.3 67.1 + - - +
950A VAL* 3.2 4.5 + - + +
951A ARG* 2.8 54.1 + - - +
1285A ASP* 5.6 5.4 - - - +
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Residues in contact with GLU 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 SER* 3.0 9.1 + - - +
947A PRO* 1.3 86.4 - - - +
949A LYS* 1.3 60.3 + - - +
951A ARG* 3.2 19.9 + - - +
952A ILE* 3.2 28.1 + - - +
977A TRP* 3.9 14.0 - - + -
981A MET* 5.7 2.2 - - - -
986A TYR* 3.0 38.8 + - + +
990A LYS* 5.8 0.7 + - - -
1007A LEU 4.3 1.7 - - - +
1008A ALA* 3.2 11.1 - - - +
1009A MET* 2.8 44.5 + - + +
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Residues in contact with LYS 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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862A ASP 5.9 0.4 - - - -
945A LEU* 3.7 34.5 - - + +
946A SER* 3.1 35.3 + - - +
948A GLU* 1.3 75.9 - - - +
950A VAL* 1.3 63.9 + - - +
952A ILE* 3.3 21.7 - - + +
953A ILE* 3.3 17.2 + - + +
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Residues in contact with VAL 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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862A ASP 5.1 0.7 - - - +
863A GLY* 3.4 35.0 - - - +
865A ILE* 4.8 1.1 - - + -
936A ILE* 3.7 28.3 - - + +
939A VAL* 4.5 6.5 - - + +
940A ALA* 3.7 29.8 - - + +
945A LEU* 4.2 13.0 - - + -
946A SER 3.4 4.5 + - - +
947A PRO 3.2 7.9 + - - +
949A LYS* 1.3 73.5 - - - +
951A ARG* 1.3 64.6 + - - +
953A ILE* 3.7 7.0 + - - +
954A ASN* 3.2 30.7 + - - +
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Residues in contact with ARG 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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898A TYR* 3.4 31.8 + - + +
933A GLU* 2.7 36.1 + - - +
936A ILE* 3.9 10.2 - - + +
937A THR* 3.4 23.2 - - - +
947A PRO* 2.8 35.4 + - - +
948A GLU* 3.2 23.5 + - - +
949A LYS 3.4 0.2 - - - -
950A VAL* 1.3 77.2 - - - +
952A ILE* 1.3 62.3 + - - +
954A ASN 3.2 2.8 + - - -
955A MET* 3.1 28.4 + - + +
977A TRP* 4.1 13.2 - - + -
1008A ALA* 5.1 3.0 - - - +
1009A MET 3.0 30.0 + - - +
1010A VAL* 4.0 11.2 - - - +
1011A PRO* 4.0 6.7 - - + -
1281A PHE* 4.2 6.9 - - - +
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Residues in contact with ILE 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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948A GLU 3.2 16.6 + - - +
949A LYS* 3.3 20.6 - - - +
951A ARG* 1.3 80.5 - - - +
953A ILE* 1.3 66.1 + - + +
954A ASN 3.8 0.2 + - - -
955A MET* 3.8 23.2 + - + +
957A LYS* 5.8 2.1 + - - -
977A TRP* 3.4 35.0 - - + +
978A ARG* 4.0 22.4 - - - +
981A MET* 5.9 4.7 - - + -
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Residues in contact with ILE 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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862A ASP* 3.6 20.2 - - - +
863A GLY 3.8 2.7 - - - +
864A ARG* 3.4 53.8 - - + +
949A LYS* 3.3 19.3 + - + +
950A VAL* 3.8 6.1 - - - +
952A ILE* 1.3 83.7 - - + +
954A ASN* 1.3 62.0 + - - +
955A MET 3.5 2.7 - - - +
957A LYS* 5.7 5.0 + - - +
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Residues in contact with ASN 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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863A GLY 3.0 25.2 + - - -
864A ARG* 3.5 13.6 - - - +
865A ILE* 3.1 45.8 + - - +
898A TYR* 3.1 18.6 - - + -
899A LYS* 2.8 41.4 + - - +
900A PHE* 5.3 3.3 - - + -
936A ILE* 5.4 2.3 - - + +
950A VAL* 3.2 23.1 + - - +
951A ARG 3.2 2.9 + - - +
953A ILE* 1.3 74.5 - - - +
955A MET* 1.3 56.7 + - - +
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Residues in contact with MET 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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897A ALA* 3.4 22.0 - - + +
898A TYR* 4.1 4.3 - - + +
899A LYS* 4.2 5.0 - - - +
951A ARG 3.1 19.2 + - - +
952A ILE* 3.8 18.9 + - + +
953A ILE 3.5 3.8 - - - +
954A ASN* 1.3 82.0 - - - +
956A TYR* 1.3 64.8 + - - +
957A LYS* 3.7 10.2 + - - +
973A LEU* 3.7 32.1 - - + +
974A ILE* 3.4 35.0 - - + -
977A TRP* 4.4 31.0 - - + -
1011A PRO* 4.8 5.4 - - - -
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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