Contacts of the helix formed by residues 940 - 951 (chain B) in PDB entry 4G5P
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 940 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700A ASN* 4.2 10.3 - - - +
701A GLN* 3.9 24.9 - - - +
935B GLN* 3.4 4.4 + - - +
939B CYS* 1.3 76.6 - - - +
941B ILE* 1.3 59.4 + - - +
942B ASP* 3.6 18.5 + - - +
943B VAL* 2.8 24.7 + - - +
944B TYR 3.1 10.0 + - - -
977B ARG 4.2 6.5 - - - +
978B TYR* 3.1 38.2 + - - +
979B LEU* 4.3 0.4 - - - +
980B VAL* 4.3 17.5 - - + -
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Residues in contact with ILE 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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700A ASN* 3.0 46.3 - - - +
702A ALA* 3.9 18.7 + - + +
704A LEU* 4.2 14.6 - - + -
764A TYR* 3.4 18.8 - - + +
767A ALA* 3.4 33.9 - - + -
768A SER* 4.4 0.7 - - - +
935B GLN* 3.2 11.8 - - - +
940B THR* 1.3 72.8 - - - +
942B ASP* 1.3 62.0 + - - +
944B TYR* 4.5 3.4 - - + +
945B MET* 2.9 56.2 + - + +
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Residues in contact with ASP 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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700A ASN* 3.9 13.9 + - - +
764A TYR* 2.9 33.4 + - - -
940B THR* 3.0 10.3 + - - +
941B ILE* 1.3 85.5 - - - +
943B VAL* 1.3 59.7 + - - +
945B MET* 3.8 3.1 - - - +
946B ILE* 3.5 24.8 + - - +
949B LYS* 5.4 0.3 + - - -
967B GLU* 5.3 0.2 - - - +
971B MET* 4.4 9.7 - - + +
977B ARG* 5.8 2.1 + - - -
978B TYR* 3.9 31.5 - - + -
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Residues in contact with VAL 943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815B LEU* 5.5 3.4 - - + -
904B VAL* 5.3 0.7 - - + -
908B MET* 4.4 13.9 - - + -
939B CYS* 4.3 13.0 - - + -
940B THR* 2.8 19.0 + - - +
942B ASP* 1.3 68.7 - - + +
944B TYR* 1.3 65.4 + - - +
945B MET 3.2 1.7 + - - -
946B ILE* 3.3 13.2 + - - +
947B MET* 3.2 37.9 + - + +
968B PHE* 5.2 9.3 - - + -
971B MET* 4.4 10.5 - - - -
978B TYR* 3.4 37.9 - - + +
979B LEU* 4.2 10.5 - - + -
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Residues in contact with TYR 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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704A LEU* 3.7 25.7 + - + -
706A ILE* 3.2 23.9 - - + +
905B TRP* 5.2 0.2 - + - -
932B ARG* 4.8 1.0 - - - +
933B LEU 2.4 27.8 + - - -
934B PRO* 3.3 9.2 - - - +
935B GLN* 3.2 62.0 + - + +
936B PRO* 3.5 10.8 - - + -
939B CYS* 5.0 1.1 - - + -
940B THR 3.1 8.7 + - - +
941B ILE* 4.4 3.4 - - + +
943B VAL* 1.3 79.6 - - - +
945B MET* 1.3 57.6 + - - +
947B MET* 3.2 19.0 - - + +
948B VAL* 2.8 55.4 + - + +
951B TRP* 4.5 9.2 - + - -
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Residues in contact with MET 945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A LEU* 3.6 25.6 - - + -
760A LEU* 3.8 28.3 - - - +
763A ALA* 5.0 1.1 - - + -
764A TYR* 3.7 28.0 - - + +
780A ILE* 6.5 0.2 - - - -
941B ILE* 2.9 53.7 + - + +
942B ASP* 3.8 6.1 - - - +
944B TYR* 1.3 74.0 - - - +
946B ILE* 1.3 66.1 + - - +
948B VAL* 3.2 10.4 + - - +
949B LYS* 3.0 50.7 + - - +
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Residues in contact with ILE 946 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900B TYR* 5.7 0.4 - - + -
942B ASP 3.5 10.5 - - - +
943B VAL* 3.3 10.9 + - - +
945B MET* 1.3 75.9 - - - +
947B MET* 1.3 57.9 + - + +
949B LYS* 2.8 46.2 + - - +
950B CYS* 3.4 9.4 + - - -
959B PRO* 4.8 2.7 - - + +
964B LEU* 3.8 28.7 - - + -
967B GLU* 3.6 28.3 - - + +
968B PHE* 4.8 21.5 - - + -
971B MET* 3.6 35.9 - - + -
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Residues in contact with MET 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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901B GLY* 4.3 5.4 - - - +
904B VAL* 3.8 35.9 - - + -
905B TRP* 4.1 16.6 - - - -
908B MET* 4.4 3.1 - - + -
936B PRO* 3.9 27.6 - - + -
939B CYS* 4.6 0.2 - - - -
943B VAL* 3.2 23.3 + - + +
944B TYR* 3.2 31.4 - - + +
946B ILE* 1.3 81.4 - - + +
948B VAL* 1.3 61.6 + - - +
950B CYS* 3.3 22.1 + - - +
951B TRP* 3.4 39.8 - - + -
968B PHE* 6.0 1.6 - - + -
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Residues in contact with VAL 948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A LEU* 5.0 5.8 - - + -
706A ILE* 4.6 11.2 - - + -
760A LEU* 4.8 11.0 - - + -
780A ILE* 6.1 1.1 - - + -
782A LEU* 3.7 31.9 - - + -
932B ARG* 6.0 1.3 - - + -
944B TYR* 2.8 59.4 + - + +
945B MET* 3.4 14.1 - - - +
947B MET* 1.3 74.2 - - - +
949B LYS* 1.3 57.1 + - - +
951B TRP* 2.7 44.8 + - + +
952B MET* 3.3 1.3 + - - +
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Residues in contact with LYS 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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760A LEU* 3.9 31.6 - - + -
761A ASP* 5.6 4.4 + - - -
942B ASP 5.4 0.2 + - - -
945B MET* 3.0 42.9 + - - +
946B ILE* 2.8 30.2 + - - +
948B VAL* 1.3 76.3 - - - +
950B CYS* 1.3 57.9 + - - +
952B MET* 3.3 19.1 - - + +
957B SER 4.6 4.5 - - - +
958B ARG* 3.3 21.8 - - - +
959B PRO* 3.6 18.2 - - + -
967B GLU* 5.4 3.6 + - - -
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Residues in contact with CYS 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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897B VAL* 3.4 38.8 - - + +
898B TRP* 3.3 14.0 - - - -
900B TYR* 4.6 9.6 - - - -
901B GLY* 4.4 7.9 - - - +
946B ILE* 3.5 17.0 - - - -
947B MET* 3.4 14.8 - - - +
948B VAL 3.0 0.4 + - - -
949B LYS* 1.3 77.6 - - - +
951B TRP* 1.3 66.1 + - + +
952B MET 3.2 1.1 - - - -
958B ARG* 3.3 24.0 - - - -
959B PRO* 4.0 15.0 - - - -
964B LEU* 4.8 4.9 - - - -
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Residues in contact with TRP 951 (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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782A LEU* 3.3 5.6 - - - +
898B TRP* 3.1 51.3 + + + -
901B GLY* 3.4 29.1 - - - -
902B VAL* 3.4 16.9 - - + +
905B TRP* 4.3 3.4 - + - -
915B TYR* 5.3 3.4 - - - -
932B ARG* 2.9 53.5 + - + +
933B LEU* 3.9 45.8 - - + -
944B TYR* 4.5 9.6 - + - -
947B MET* 3.4 33.7 - - + -
948B VAL* 2.7 20.3 + - + +
950B CYS* 1.3 82.6 - - - +
952B MET* 1.3 58.1 + - - +
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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