Contacts of the helix formed by residues 917 - 925 (chain B) in PDB entry 3E0D
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 917 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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915B PHE* 3.6 1.2 - - - +
916B LYS* 1.3 81.2 + - - +
918B LEU* 1.3 58.3 + - - +
920B ASP* 3.2 13.7 + - - +
921B PHE* 3.0 26.5 + - - +
947B PHE* 3.6 21.0 - - - -
984B GLU* 2.6 37.8 + - - -
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Residues in contact with LEU 918 (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 SER* 1.3 72.4 - - - +
919B GLY* 1.3 65.7 + - - +
921B PHE* 3.2 10.1 + - + +
922B LEU* 3.0 39.5 + - + +
935B LEU* 5.8 1.1 - - + -
939B VAL* 5.5 1.1 - - + -
944B LEU* 4.6 26.5 - - + -
947B PHE* 3.9 13.8 - - + +
953B LEU* 3.7 47.1 - - + +
956B SER* 4.1 1.6 - - - -
957B LEU* 4.3 19.7 - - + -
960B LEU* 3.7 22.9 - - + -
984B GLU* 4.5 0.4 + - - +
987B LEU* 4.1 12.1 - - + -
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Residues in contact with GLY 919 (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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918B LEU* 1.3 75.8 - - - +
920B ASP* 1.3 64.5 + - - +
922B LEU* 2.9 16.2 + - - -
923B LYS* 3.0 15.4 + - - +
960B LEU* 4.7 7.4 - - - +
963B TRP* 3.6 26.5 - - - -
984B GLU* 3.0 24.0 + - - -
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Residues in contact with ASP 920 (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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914B PRO 4.3 0.5 - - - +
915B PHE* 3.8 5.4 - - - -
916B LYS* 2.8 36.0 + - + +
917B SER* 3.2 26.5 + - - +
919B GLY* 1.3 74.5 - - - +
921B PHE* 1.3 59.5 + - - +
923B LYS* 3.7 24.4 - - - +
924B ARG* 3.1 49.1 + - - +
963B TRP* 5.0 0.2 - - - -
984B GLU* 4.1 1.4 + - - -
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Residues in contact with PHE 921 (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 VAL* 3.8 22.4 - - + -
905B ILE* 4.1 8.3 - - + -
915B PHE* 3.4 39.5 - + + -
917B SER 3.0 13.4 + - - +
918B LEU* 3.3 14.4 - - + +
919B GLY 3.1 0.2 - - - -
920B ASP* 1.3 77.2 - - - +
922B LEU* 1.3 61.1 + - + +
924B ARG* 3.5 2.1 + - - +
925B LEU* 3.0 58.1 + - + +
930B VAL* 4.7 3.4 - - + -
935B LEU* 3.7 31.2 - - + -
938B LEU* 4.0 21.8 - - + -
944B LEU* 4.3 17.0 - - + -
947B PHE* 4.8 2.7 - - + -
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Residues in contact with LEU 922 (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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918B LEU* 3.0 34.8 + - + +
919B GLY* 2.9 7.3 + - - +
921B PHE* 1.3 80.4 - - + +
923B LYS* 1.3 56.8 + - - +
925B LEU 2.9 23.1 - - - +
926B PRO* 4.1 0.3 - - - +
927B GLU 5.1 0.5 + - - -
935B LEU* 3.6 42.8 - - + -
957B LEU* 4.6 10.8 - - + +
960B LEU* 3.6 36.1 - - + +
961B LEU* 4.1 11.9 - - + +
964B ALA* 3.9 15.4 - - + +
968B ARG* 3.0 12.9 + - - -
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Residues in contact with LYS 923 (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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919B GLY 3.0 13.8 + - - +
920B ASP* 3.7 32.1 + - - +
922B LEU* 1.3 75.0 - - - +
924B ARG* 1.3 68.6 + - + +
963B TRP* 4.0 20.4 - - + -
964B ALA* 4.1 8.7 - - + +
967B THR* 5.4 9.0 - - + -
968B ARG* 2.8 33.6 + - + +
981B GLU* 2.9 35.5 + - - +
983B GLU* 5.0 11.1 + - - +
984B GLU* 5.9 1.4 - - - +
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Residues in contact with ARG 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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908B GLU* 3.2 60.6 + - + +
912B GLY* 3.3 16.3 - - - -
913B GLY 3.0 28.7 + - - +
914B PRO 3.4 3.8 + - - -
915B PHE* 3.3 46.0 - - + +
920B ASP* 3.1 38.5 + - - +
921B PHE 3.9 2.7 - - - +
923B LYS* 1.3 82.8 - - + +
925B LEU* 1.3 61.5 + - - +
926B PRO* 3.4 9.1 - - - +
968B ARG* 5.1 0.2 + - - -
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Residues in contact with LEU 925 (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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904B ALA* 4.1 9.9 - - + +
905B ILE* 3.8 25.4 - - + +
908B GLU* 3.9 26.7 - - + +
915B PHE* 4.0 14.4 - - + -
921B PHE* 3.0 53.1 + - + +
922B LEU* 2.9 21.2 - - - +
924B ARG* 1.3 79.1 - - - +
926B PRO* 1.3 70.8 - - + +
927B GLU* 4.7 0.2 - - - -
929B VAL* 4.7 5.8 - - + -
930B VAL* 4.0 22.2 - - + +
935B LEU* 6.0 0.5 - - - +
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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