Contacts of the helix formed by residues 901 - 914 (chain B) in PDB entry 6IEH
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 901 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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899B ASP 4.1 0.2 + - - -
900B LEU* 1.3 76.3 - - - +
902B ALA* 1.3 54.5 + - - +
903B GLU* 4.2 12.3 - - - -
904B GLN* 2.8 25.2 + - - +
905B ALA* 2.6 35.4 + - - +
927B GLN* 4.7 13.5 + - - +
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Residues in contact with ALA 902 (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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900B LEU 3.8 1.8 + - - -
901B SER* 1.3 71.9 - - - +
903B GLU* 1.3 67.3 + - + +
905B ALA* 3.4 7.6 + - - +
906B THR* 3.2 28.4 + - - +
1022B LYS* 4.6 22.4 - - + +
1025B GLU* 5.8 2.0 - - + -
1026B GLY* 4.7 7.5 - - - +
1029B LYS* 5.0 15.5 - - + +
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Residues in contact with GLU 903 (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 SER* 4.3 11.1 - - - -
902B ALA* 1.3 78.1 + - + +
904B GLN* 1.3 60.8 + - - +
906B THR* 3.5 2.5 + - - -
907B ALA* 2.9 29.9 + - - +
971B TYR* 4.5 10.2 - - + +
974B ALA* 4.1 24.0 - - + +
975B THR* 3.1 39.9 - - + +
1029B LYS* 5.0 9.7 - - + +
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Residues in contact with GLN 904 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900B LEU* 4.5 6.3 - - + -
901B SER* 2.8 35.8 + - - +
903B GLU* 1.3 77.0 - - - +
905B ALA* 1.3 65.5 + - - +
907B ALA* 4.3 4.9 - - - -
908B LEU* 2.8 28.7 + - - +
927B GLN 4.3 17.0 - - - +
928B LEU* 5.5 3.4 - - - +
931B PRO* 4.9 8.7 - - + -
971B TYR* 6.0 0.4 - - - -
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Residues in contact with ALA 905 (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 PHE* 4.3 10.5 - - + -
900B LEU* 4.3 8.5 - - + +
901B SER 2.6 17.5 + - - +
902B ALA* 3.5 9.6 - - - +
903B GLU 3.2 0.2 - - - -
904B GLN* 1.3 75.5 - - - +
906B THR* 1.3 62.8 + - + +
908B LEU* 3.8 2.8 - - - +
909B LEU* 3.2 27.3 + - - +
1022B LYS* 4.3 20.9 - - + +
1023B PHE* 4.3 20.4 - - + -
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Residues in contact with THR 906 (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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902B ALA 3.2 16.5 + - - +
903B GLU* 3.5 6.3 + - - -
905B ALA* 1.3 76.7 - - + +
907B ALA* 1.3 66.7 + - - +
909B LEU* 3.3 16.6 + - + +
910B SER 3.4 8.0 + - - -
970B VAL* 4.0 2.8 - - - +
974B ALA* 4.1 7.0 - - + +
1000B LEU* 3.5 12.7 - - - +
1004B LEU* 4.2 13.5 - - + -
1022B LYS 5.6 0.7 - - - +
1023B PHE* 5.5 2.5 - - + +
1026B GLY* 3.7 33.4 - - - +
1029B LYS* 6.2 0.4 - - + -
1030B ILE* 2.9 27.1 - - + +
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Residues in contact with ALA 907 (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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903B GLU 2.9 17.4 + - - +
904B GLN* 4.0 4.3 - - - +
906B THR* 1.3 82.8 + - - +
908B LEU* 1.3 62.6 + - - +
909B LEU 3.2 0.2 - - - -
910B SER* 3.2 19.8 + - - -
928B LEU* 5.6 4.9 - - + -
967B MET* 3.6 35.2 - - + +
970B VAL* 4.0 9.4 - - - -
971B TYR* 3.9 17.9 - - + +
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Residues in contact with LEU 908 (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 MET* 4.7 8.7 - - + -
896B LEU* 3.7 24.9 - - + -
897B PHE* 4.4 14.6 - - + -
900B LEU* 5.3 3.8 - - + -
904B GLN 2.8 18.4 + - - +
905B ALA 3.8 4.7 - - - +
907B ALA* 1.3 74.4 - - - +
909B LEU* 1.3 63.6 + - + +
910B SER 3.1 1.6 + - - -
911B CYS* 3.2 21.4 + - - +
912B PHE* 4.1 2.7 + - + -
931B PRO* 3.4 45.1 - - + +
932B LEU* 4.7 1.6 - - + -
935B MET* 4.4 21.3 - - + -
967B MET* 4.2 17.6 - - + +
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Residues in contact with LEU 909 (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 MET* 6.5 0.2 - - + -
897B PHE* 4.2 13.5 - - + -
905B ALA 3.2 19.5 - - - +
906B THR* 3.3 7.6 + - - +
907B ALA 3.2 0.2 - - - -
908B LEU* 1.3 74.0 - - + +
910B SER* 1.3 63.7 + - - +
911B CYS 3.2 0.4 - - - -
912B PHE* 2.9 37.7 + - + +
913B VAL* 3.3 6.1 + - - +
1000B LEU* 4.0 12.8 - - + -
1003B LEU* 4.0 22.8 - - + +
1004B LEU* 3.6 25.1 - - + -
1007B MET* 4.1 18.2 - - + -
1023B PHE* 3.7 23.6 - - + -
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Residues in contact with SER 910 (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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906B THR 3.4 3.6 + - - -
907B ALA 3.2 17.5 + - - -
908B LEU 3.1 0.8 + - - -
909B LEU* 1.3 74.6 - - - +
911B CYS* 1.3 60.7 + - - +
913B VAL* 3.0 4.5 + - - -
914B PHE* 2.7 33.1 + - - +
963B LYS 4.3 3.3 + - - -
966B LEU* 4.0 6.9 - - - +
967B MET* 3.9 19.6 + - - +
970B VAL* 3.7 26.5 - - - -
996B CYS* 4.8 6.1 - - - -
1000B LEU* 4.0 13.0 - - - -
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Residues in contact with CYS 911 (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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908B LEU* 3.2 15.2 + - + +
910B SER* 1.3 81.5 + - - +
912B PHE* 1.3 67.3 + - + +
914B PHE 3.9 6.3 + - - +
932B LEU* 5.3 5.8 - - - -
935B MET* 4.9 6.5 - - + -
961B SER 5.0 1.0 - - - +
962B PHE* 3.9 21.2 - - + -
963B LYS 3.0 37.4 + - - +
964B PRO* 3.1 28.7 - - - -
967B MET* 3.7 17.9 - - - -
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Residues in contact with PHE 912 (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 SER 5.2 0.5 - - - +
883B ALA* 4.0 18.9 - - + +
884B ASP 4.6 1.9 + - - -
887B LEU* 4.1 7.6 - - + -
888B LEU* 2.6 61.2 - - + -
891B MET* 3.6 24.2 - - + -
908B LEU* 4.8 4.5 - - + -
909B LEU* 2.9 28.8 + - + +
911B CYS* 1.3 78.0 - - + +
913B VAL* 1.3 56.9 + - - +
914B PHE 4.2 0.2 + - - -
935B MET* 3.1 34.1 - - + -
962B PHE* 3.9 19.4 - + - -
1003B LEU* 3.8 11.2 - - + -
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Residues in contact with VAL 913 (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 SER* 4.7 8.3 - - - +
883B ALA* 4.7 6.1 - - + -
909B LEU 3.3 1.3 + - - +
910B SER 3.0 8.1 + - - +
912B PHE* 1.3 80.2 - - - +
914B PHE* 1.3 59.7 + - - +
915B GLN* 3.6 5.7 + - - +
996B CYS* 3.5 32.8 - - - +
999B ARG* 3.9 28.0 - - + +
1000B LEU* 4.0 13.7 - - + +
1003B LEU* 3.6 37.5 - - + -
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Residues in contact with PHE 914 (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 SER* 2.7 25.1 + - - +
911B CYS 3.9 6.6 + - - +
912B PHE 3.8 1.0 - - - -
913B VAL* 1.3 72.1 - - - +
915B GLN* 1.3 61.1 + - - +
916B GLU* 3.2 45.1 - - + -
918B SER* 4.2 15.7 - - - -
962B PHE* 5.7 0.2 - - - -
963B LYS* 3.6 37.1 + - + +
965B HIS* 3.9 23.3 - + + -
966B LEU* 4.6 16.2 - - + -
988B VAL* 4.6 18.4 - - + -
992B SER 5.1 2.7 - - - -
993B ILE* 6.2 0.4 - - - -
996B CYS* 4.0 29.2 - - + -
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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