Contacts of the helix formed by residues 936 - 953 (chain B) in PDB entry 2XWU
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 ASN 936 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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890B PHE* 4.1 0.2 - - - -
935B VAL* 1.3 75.1 - - - +
937B LYS* 1.3 53.9 + - - +
938B ARG* 2.7 15.9 + - + +
939B ARG* 2.4 48.3 + - - +
940B VAL* 3.3 4.3 + - - +
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Residues in contact with LYS 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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886B ALA 6.3 0.4 - - - -
887B ASP* 3.6 29.2 + - - +
890B PHE* 3.3 57.3 - - + -
936B ASN* 1.3 70.5 - - - +
938B ARG* 1.3 59.2 + - - +
939B ARG 3.1 0.6 + - - -
940B VAL* 3.5 10.7 + - + +
941B LYS* 3.5 31.1 + - + +
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Residues in contact with ARG 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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936B ASN* 2.7 16.7 + - + +
937B LYS* 1.3 79.5 - - - +
939B ARG* 1.3 57.3 + - - +
941B LYS* 4.0 10.5 + - - +
942B GLU* 3.3 23.0 + - - +
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Residues in contact with ARG 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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932B ARG* 6.1 2.0 - - - +
935B VAL* 3.8 16.8 - - + -
936B ASN* 2.4 38.7 + - - +
938B ARG* 1.3 70.3 - - - +
940B VAL* 1.3 58.0 + - - +
941B LYS 3.2 1.6 - - - -
942B GLU* 2.9 26.7 + - + +
943B MET* 3.0 22.0 + - + +
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Residues in contact with VAL 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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886B ALA* 3.7 26.0 - - + +
889B LEU* 4.4 9.2 - - + -
890B PHE* 3.6 30.3 - - + +
893B ASN* 6.2 0.4 - - + -
930B ILE* 5.9 4.9 - - + -
935B VAL* 3.6 33.9 - - + -
936B ASN 3.8 4.3 - - - +
937B LYS* 3.5 6.7 + - + +
939B ARG* 1.3 76.2 - - - +
941B LYS* 1.3 62.1 + - + +
943B MET* 3.4 17.1 + - + +
944B VAL* 3.0 32.2 + - + +
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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
----------------------------------------------------------
882B MET* 6.1 0.3 - - - +
883B ASP* 3.7 44.4 + - - +
886B ALA* 3.8 20.4 - - + -
887B ASP* 3.4 28.0 + - - +
937B LYS* 3.5 29.9 + - + +
938B ARG* 4.0 9.4 - - - +
939B ARG 3.2 0.4 - - - -
940B VAL* 1.3 77.5 - - + +
942B GLU* 1.3 58.1 + - + +
944B VAL* 3.4 2.3 + - - +
945B LYS* 2.9 28.5 + - - +
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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
----------------------------------------------------------
938B ARG 3.3 18.6 - - - +
939B ARG* 2.9 15.9 + - + +
941B LYS* 1.3 77.9 - - + +
943B MET* 1.3 58.6 + - + +
945B LYS* 3.0 27.4 + - - +
946B GLU* 2.9 31.6 + - - +
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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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926B PHE* 3.7 9.8 - - + -
929B GLN* 2.9 65.9 - - + +
930B ILE* 3.2 23.8 - - + +
932B ARG* 5.4 4.3 - - - -
935B VAL* 4.5 12.3 - - - -
939B ARG* 3.0 22.2 + - + +
940B VAL* 3.4 20.6 + - + +
942B GLU* 1.3 75.9 - - + +
944B VAL* 1.3 65.2 + - + +
946B GLU* 3.9 5.0 - - - +
947B PHE* 3.0 26.5 + - - +
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Residues in contact with VAL 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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873B ILE* 3.6 25.4 - - + -
882B MET* 3.6 34.1 - - + +
886B ALA* 3.5 23.1 - - + -
889B LEU* 4.1 19.3 - - + -
926B PHE* 4.4 6.3 - - + -
930B ILE* 5.5 0.2 - - + -
940B VAL* 3.0 19.4 + - + +
941B LYS 3.7 4.7 - - - +
943B MET* 1.3 74.5 - - + +
945B LYS* 1.3 60.9 + - - +
947B PHE* 3.8 4.2 - - - +
948B THR* 2.9 30.7 + - - -
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Residues in contact with LYS 945 (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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882B MET* 5.6 5.1 - - + +
941B LYS 2.9 15.3 + - - +
942B GLU* 3.3 28.9 - - - +
944B VAL* 1.3 77.0 - - - +
946B GLU* 1.3 70.8 + - - +
948B THR* 3.2 16.6 - - + +
949B LEU* 3.1 44.3 - - + +
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Residues in contact with GLU 946 (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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929B GLN* 6.2 0.2 - - - +
942B GLU 2.9 14.5 + - - +
943B MET* 3.9 6.5 - - - +
945B LYS* 1.3 83.0 - - - +
947B PHE* 1.3 62.9 + - - +
949B LEU* 3.4 18.1 + - - +
950B LEU* 3.5 18.6 + - - +
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Residues in contact with PHE 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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870B LEU* 5.0 1.3 - - + -
873B ILE* 3.5 28.3 - - + -
908B LEU* 5.1 4.0 - - + -
914B PRO* 4.4 17.3 - - + -
918B LEU* 3.3 40.2 - - + -
922B GLN 4.6 8.3 - - - -
923B LYS* 4.9 3.6 - - - -
926B PHE* 3.6 57.2 - + + -
943B MET 3.0 19.1 + - - +
944B VAL 3.8 2.2 - - - +
946B GLU* 1.3 72.5 - - - +
948B THR* 1.3 64.1 + - - +
949B LEU 3.0 2.2 - - - -
950B LEU* 3.1 24.6 + - + +
951B CYS* 3.1 26.1 + - - -
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Residues in contact with THR 948 (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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873B ILE* 2.7 27.3 + - - -
879B ARG* 5.4 4.0 - - + +
882B MET* 2.8 36.1 - - + +
944B VAL 2.9 18.4 + - - +
945B LYS* 3.2 18.8 - - + +
947B PHE* 1.3 74.7 - - - +
949B LEU* 1.3 71.1 + - + +
951B CYS* 3.7 1.4 + - - +
952B ARG* 3.0 52.8 + - - +
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Residues in contact with LEU 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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879B ARG* 3.9 30.1 - - - +
945B LYS* 3.1 43.9 + - + +
946B GLU* 3.5 9.4 - - - +
947B PHE 3.0 0.6 - - - -
948B THR* 1.3 89.8 - - + +
950B LEU* 1.3 56.9 + - + +
952B ARG* 4.8 3.4 - - + -
953B GLY* 2.6 46.6 + - - +
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Residues in contact with LEU 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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917B ARG* 3.7 17.7 - - - +
918B LEU* 4.1 13.9 - - + -
922B GLN* 3.9 36.3 - - + +
946B GLU 3.6 15.0 - - - +
947B PHE* 3.1 16.7 + - + +
949B LEU* 1.3 79.6 - - + +
951B CYS* 1.3 65.1 + - - +
952B ARG 3.2 0.7 + - - -
953B GLY* 3.5 7.6 + - - +
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Residues in contact with CYS 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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873B ILE 4.0 2.0 - - - +
874B GLY* 3.1 38.5 - - - +
915B SER* 2.8 28.6 + - - -
917B ARG* 3.3 14.5 + - - -
918B LEU* 3.7 21.5 - - - +
947B PHE* 3.1 44.2 + - - -
948B THR 3.9 5.6 - - - +
950B LEU* 1.3 78.3 - - - +
952B ARG* 1.3 58.4 + - - +
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Residues in contact with ARG 952 (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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872B ALA 3.4 16.2 + - - -
874B GLY 4.3 8.3 - - - +
875B GLY* 3.2 27.1 + - - -
877B ALA 2.7 26.2 + - - -
878B SER* 5.2 0.2 - - - +
879B ARG* 3.8 33.4 - - - +
882B MET* 3.9 8.7 - - - -
917B ARG* 3.4 23.2 + - - +
948B THR* 3.0 39.8 + - - +
949B LEU* 3.3 4.9 + - - +
950B LEU 3.1 0.4 - - - -
951B CYS* 1.3 81.4 - - - +
953B GLY* 1.3 61.4 + - - +
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Residues in contact with GLY 953 (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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917B ARG* 4.4 10.1 - - - -
949B LEU* 2.6 30.9 + - - +
950B LEU* 3.5 8.2 + - - -
952B ARG* 1.3 78.9 - - - +
954B LEU 1.2 49.4 + - - -
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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