Contacts of the helix formed by residues 923 - 934 (chain B) in PDB entry 5MJ6
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 LYS 923 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439B ARG* 3.8 7.8 - - - +
441B GLU* 3.2 22.8 + - - +
881B TYR* 4.1 13.2 - - - +
891B ASN* 2.8 31.7 + - - +
894B LEU* 3.7 29.6 - - + -
913B SER* 3.6 5.2 - - - +
919B PHE* 4.9 1.3 - - + -
920B ARG* 2.9 21.5 + - + +
922B GLN* 1.3 99.0 + - + +
924B LEU* 1.3 65.3 + - - +
925B SER 3.3 2.2 - - - -
926B PHE* 3.2 25.6 + - - +
927B ILE* 3.0 23.8 + - + +
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Residues in contact with LEU 924 (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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910B MET* 3.6 28.0 - - - +
913B SER* 3.2 20.3 + - - +
914B LEU* 3.5 36.6 - - + -
921B THR* 3.1 23.7 + - + +
922B GLN 3.3 0.4 - - - -
923B LYS* 1.3 78.3 - - - +
925B SER* 1.3 58.4 + - - +
927B ILE* 3.4 2.9 + - + +
928B ILE* 3.0 45.7 + - + +
944B PHE* 4.5 3.8 - - + -
952B LEU* 3.5 20.4 - - + -
956B PHE* 4.8 6.7 - - + -
966B ILE* 5.1 1.1 - - + -
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Residues in contact with SER 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B GLU* 4.8 4.6 + - - -
921B THR 4.8 0.4 + - - -
922B GLN 4.7 4.8 + - - -
924B LEU* 1.3 79.6 - - - +
926B PHE* 1.3 60.7 + - - +
928B ILE* 3.9 1.8 - - - +
929B ARG* 2.9 47.0 + - - +
956B PHE* 6.1 0.2 - - - -
962B THR* 4.0 21.0 - - - +
965B ASN* 4.2 12.4 + - - +
966B ILE* 3.8 29.4 - - - +
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Residues in contact with PHE 926 (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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891B ASN* 4.0 14.1 - - + -
894B LEU* 4.1 24.5 - - + -
895B GLU* 3.3 55.4 - - + -
898B ALA* 6.2 0.9 - - + -
922B GLN 5.4 0.9 + - - +
923B LYS* 3.4 27.6 - - - +
925B SER* 1.3 82.8 + - - +
927B ILE* 1.3 60.4 + - - +
929B ARG* 3.5 30.4 + - - +
930B THR* 2.9 45.0 + - - -
933B ARG* 5.4 3.6 - - - -
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Residues in contact with ILE 927 (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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894B LEU* 3.8 40.2 - - + -
898B ALA* 4.8 5.6 - - + -
909B LEU* 4.0 17.3 - - + +
910B MET* 3.6 32.3 - - + +
913B SER* 3.5 32.8 - - - +
919B PHE* 4.4 6.7 - - + -
923B LYS* 3.0 17.0 + - + +
924B LEU* 3.7 4.7 - - + +
926B PHE* 1.3 75.4 - - - +
928B ILE* 1.3 65.4 + - - +
930B THR* 3.3 5.6 + - - -
931B VAL* 2.9 29.1 + - + +
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Residues in contact with ILE 928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910B MET* 4.1 21.5 - - + -
924B LEU* 3.0 48.9 + - + +
925B SER* 4.0 3.8 - - - +
927B ILE* 1.3 74.8 - - - +
929B ARG* 1.3 57.3 + - - +
931B VAL* 3.4 0.6 + - - +
932B GLY* 3.0 27.7 + - - -
941B ALA* 3.9 16.6 - - + +
944B PHE* 4.3 14.6 - - + -
945B VAL* 4.0 21.3 - - + -
952B LEU* 5.0 3.1 - - + -
966B ILE* 4.0 33.0 - - + +
969B GLY 5.3 1.3 - - - +
970B SER* 4.5 8.9 - - - +
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Residues in contact with ARG 929 (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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925B SER* 2.9 32.8 + - - +
926B PHE* 3.6 34.5 - - - +
928B ILE* 1.3 77.3 - - - +
930B THR* 1.3 62.8 + - - +
932B GLY* 3.5 1.7 + - - -
933B ARG* 3.3 42.8 + - - +
961B TYR* 5.9 1.4 - - - -
965B ASN* 3.2 34.7 + - - +
969B GLY* 4.8 22.6 - - - +
972B TYR* 6.6 0.4 - - + -
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Residues in contact with THR 930 (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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865B LYS* 6.0 0.2 - - - -
895B GLU* 4.0 10.7 - - + +
898B ALA* 3.6 31.7 - - + +
899B SER* 3.7 18.4 - - - +
926B PHE* 2.9 39.1 + - - -
927B ILE 3.8 2.9 - - - -
929B ARG* 1.3 75.5 - - - +
931B VAL* 1.3 65.1 + - - +
932B GLY 3.4 0.2 + - - -
933B ARG* 3.4 28.1 + - - +
934B HIS* 3.6 18.7 + - + -
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Residues in contact with VAL 931 (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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898B ALA* 4.0 20.2 - - + +
906B LEU* 4.0 28.2 - - + +
909B LEU* 5.4 0.7 - - + -
910B MET* 4.2 23.8 - - + -
927B ILE* 2.9 34.8 + - + +
928B ILE 3.9 2.9 - - - +
930B THR* 1.3 75.6 - - - +
932B GLY* 1.3 60.9 + - - +
933B ARG 3.4 1.0 + - - -
934B HIS* 3.7 7.8 + - - +
937B GLY* 3.3 39.8 + - - +
940B LEU* 4.3 1.3 - - + -
941B ALA* 4.0 8.3 - - + -
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Residues in contact with GLY 932 (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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928B ILE 3.0 16.8 + - - -
929B ARG 4.0 2.2 - - - -
930B THR 3.2 0.4 - - - -
931B VAL* 1.3 78.5 - - - +
933B ARG* 1.3 60.7 + - - +
934B HIS 3.4 1.6 - - - -
937B GLY 3.9 4.7 - - - -
938B HIS* 3.4 28.2 - - - -
941B ALA* 3.8 17.0 - - - -
969B GLY 4.9 11.7 - - - +
970B SER* 5.5 1.9 - - - -
973B LEU* 4.2 4.3 - - - +
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Residues in contact with ARG 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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777B ASN* 3.8 20.6 - - - +
781B LYS* 2.7 28.1 + - - -
895B GLU* 5.4 7.9 + - - -
926B PHE* 5.4 2.6 - - - -
929B ARG* 3.3 33.1 + - - +
930B THR* 3.8 36.1 + - - +
931B VAL 3.3 1.4 - - - -
932B GLY* 1.3 77.6 - - - +
934B HIS* 1.3 73.3 + - + +
972B TYR* 4.2 22.3 + - + +
973B LEU* 3.7 7.9 - - + +
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Residues in contact with HIS 934 (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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904A ARG* 4.5 7.0 - - - +
776B TYR* 6.6 0.2 - + - -
777B ASN* 4.9 5.8 - - - -
780B GLU* 4.4 3.4 - - - -
781B LYS* 3.7 4.5 - - - +
829B THR* 4.6 20.2 - - + +
865B LYS* 5.7 5.1 + - - -
898B ALA 5.2 0.2 + - - -
899B SER* 4.0 28.8 + - - -
901B GLU* 5.9 0.9 - - - +
930B THR* 3.6 19.8 + - + -
931B VAL 3.7 5.2 + - - +
933B ARG* 1.3 103.6 + - + +
935B PHE* 1.3 67.7 + - - +
936B PRO* 3.4 11.3 - - + -
937B GLY 3.4 2.7 + - - +
938B HIS* 3.2 21.0 + - - +
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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