Contacts of the helix formed by residues 932 - 944 (chain B) in PDB entry 3H44
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 932 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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882B PHE* 3.5 10.2 - - - -
930B THR 3.5 15.3 - - - +
931B LEU* 1.3 71.7 - - - +
933B LYS* 1.3 66.4 + - - +
934B GLU* 3.0 27.4 - - - +
935B ASP* 2.8 34.3 + - - +
936B ILE* 3.3 5.7 + - - +
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Residues in contact with LYS 933 (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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874B ILE* 2.6 44.0 + - + +
875B GLU* 2.9 20.1 + - - +
876B ASP 4.0 0.4 - - - -
877B MET* 2.9 31.7 + - + +
878B THR 4.9 0.4 - - - +
879B GLU* 5.4 7.9 - - - +
882B PHE* 3.2 40.6 - - + -
932B THR* 1.3 71.8 - - - +
934B GLU* 1.3 62.0 + - - +
935B ASP 3.3 0.2 + - - -
936B ILE* 3.3 3.5 + - + +
937B ILE* 3.1 32.7 + - + +
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Residues in contact with GLU 934 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932B THR* 3.0 16.6 - - - +
933B LYS* 1.3 77.2 - - - +
935B ASP* 1.3 66.4 - - - +
937B ILE* 3.1 11.3 + - - +
938B LYS* 3.0 22.6 + - - +
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Residues in contact with ASP 935 (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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807B PHE* 3.6 27.1 - - + -
930B THR 4.3 3.3 - - - +
931B LEU* 3.8 14.1 - - + +
932B THR* 2.8 43.4 + - - +
934B GLU* 1.3 76.0 - - - +
936B ILE* 1.3 66.5 + - - +
938B LYS* 3.0 8.4 + - - +
939B PHE* 2.9 24.3 + - - +
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Residues in contact with ILE 936 (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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807B PHE* 4.1 27.6 - - + +
810B LEU* 3.7 43.3 - - + -
811B PHE* 4.1 24.7 - - + +
814B ILE* 4.5 14.1 - - + -
874B ILE* 4.8 14.1 - - + -
882B PHE* 4.0 9.6 - - + -
931B LEU* 4.3 5.6 - - + -
932B THR 3.3 10.4 + - - +
933B LYS 3.7 7.2 - - - +
935B ASP* 1.3 76.6 - - + +
937B ILE* 1.3 57.8 + - - +
939B PHE* 3.5 6.9 - - + +
940B TYR* 2.8 28.3 + - + +
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Residues in contact with ILE 937 (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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871B GLU* 5.0 4.7 - - + +
874B ILE* 3.8 35.0 - - + +
875B GLU* 4.2 32.8 - - - +
933B LYS* 3.1 24.1 + - + +
934B GLU* 3.5 10.1 - - - +
936B ILE* 1.3 74.1 - - + +
938B LYS* 1.3 67.9 + - - +
940B TYR* 3.1 9.6 + - + +
941B LYS* 2.8 51.9 + - + +
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Residues in contact with LYS 938 (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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934B GLU 3.0 12.3 + - - +
935B ASP* 3.0 9.4 + - - +
937B ILE* 1.3 72.8 - - - +
939B PHE* 1.3 55.1 + - - +
941B LYS* 3.0 8.1 + - + +
942B GLU* 2.7 55.2 + - + +
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Residues in contact with PHE 939 (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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797B THR* 4.0 24.0 - - + -
804B GLU* 4.4 14.4 - - - -
807B PHE* 3.6 51.8 - + + -
808B LEU* 4.0 19.5 - - + -
811B PHE* 4.4 13.0 - + + -
935B ASP 2.9 16.4 + - - +
936B ILE* 3.5 9.4 - - + +
938B LYS* 1.3 77.7 - - - +
940B TYR* 1.3 60.4 + - - +
942B GLU* 4.5 4.5 - - - -
943B MET* 2.9 55.2 + - + +
944B LEU* 3.8 22.0 - - + -
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Residues in contact with TYR 940 (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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811B PHE* 3.8 33.2 - + + -
867B LEU* 3.5 39.4 + - + +
868B ILE* 4.3 4.2 + - - +
871B GLU* 3.7 40.7 + - + -
874B ILE* 6.2 2.0 - - + -
936B ILE* 2.8 20.3 + - + +
937B ILE* 3.5 8.5 - - + +
939B PHE* 1.3 78.1 - - - +
941B LYS* 1.3 70.6 + - + +
944B LEU* 3.0 28.2 + - + +
945B ALA* 2.8 62.5 + - + +
946B VAL* 4.7 2.1 + - - +
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Residues in contact with LYS 941 (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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871B GLU* 2.8 31.0 - - - +
875B GLU* 5.3 3.9 + - - -
937B ILE* 2.8 39.4 + - + +
938B LYS* 3.4 7.2 - - + +
940B TYR* 1.3 82.9 - - + +
942B GLU* 1.3 58.3 + - + +
945B ALA* 4.0 10.2 - - + +
947B ASP* 4.7 2.2 - - - +
948B ALA* 3.1 26.3 - - - +
949B PRO* 3.8 4.0 - - - +
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Residues in contact with GLU 942 (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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938B LYS* 2.7 40.6 + - + +
939B PHE* 4.0 4.5 - - - +
941B LYS* 1.3 73.8 - - - +
943B MET* 1.3 65.7 + - + +
948B ALA* 3.1 13.1 - - - +
949B PRO* 3.5 26.9 - - + +
950B ARG* 3.2 46.5 + - - +
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Residues in contact with MET 943 (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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795B TYR* 5.6 1.4 - - - +
796B GLN 4.4 3.1 - - - +
797B THR* 3.2 41.5 - - + +
804B GLU* 4.6 6.3 - - - +
939B PHE* 2.9 42.8 + - + +
942B GLU* 1.3 90.0 - - + +
944B LEU* 1.3 70.1 + - + +
948B ALA* 3.7 3.8 - - - -
950B ARG* 3.6 51.9 - - + +
951B ARG* 3.2 26.7 - - - +
952B HIS* 4.0 4.7 + - + +
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Residues in contact with LEU 944 (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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795B TYR* 3.7 32.4 - - + -
796B GLN 5.9 0.4 - - - +
797B THR* 4.3 16.4 - - + -
808B LEU* 5.9 1.6 - - + -
811B PHE* 3.6 40.6 - - + -
846B LEU* 4.3 15.9 - - + -
867B LEU* 4.5 7.1 - - + +
939B PHE* 3.8 20.6 - - + -
940B TYR* 3.0 24.4 + - + +
943B MET* 1.3 82.1 - - + +
945B ALA* 1.3 71.6 + - - +
951B ARG* 2.9 25.9 + - - +
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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