Contacts of the helix formed by residues 915 - 923 (chain B) in PDB entry 4YZ9
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 PRO 915 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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885B ASP* 5.7 2.9 - - + -
913B GLU 4.5 0.9 - - - +
914B LEU* 1.3 106.2 - - + +
916B ALA* 1.3 65.1 + - - +
917B GLU* 3.5 7.6 - - + +
918B VAL* 3.4 26.8 + - + +
919B ARG* 3.2 18.7 + - - +
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Residues in contact with ALA 916 (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 LEU 3.8 0.6 + - - -
915B PRO* 1.3 74.0 - - - +
917B GLU* 1.3 64.8 + - - +
919B ARG* 3.1 21.8 + - - +
920B GLU* 3.3 6.1 + - - +
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Residues in contact with GLU 917 (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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881B PRO* 4.4 28.7 - - + +
915B PRO* 4.9 6.7 - - + +
916B ALA* 1.3 79.7 - - - +
918B VAL* 1.3 73.4 + - + +
920B GLU* 3.1 22.9 + - - +
921B THR* 3.7 8.5 + - - +
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Residues in contact with VAL 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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881B PRO* 4.1 26.9 - - + +
882B LEU* 4.8 20.0 - - + -
885B ASP* 4.2 9.6 - - + -
911B TYR* 5.6 0.2 - - - -
914B LEU* 4.3 25.4 - - + -
915B PRO* 3.4 30.9 + - + +
916B ALA 3.2 1.0 - - - -
917B GLU* 1.3 85.1 - - + +
919B ARG* 1.3 62.4 + - - +
921B THR* 2.5 30.4 + - - +
922B LEU* 3.7 10.0 + - + +
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Residues in contact with ARG 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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911B TYR* 4.1 28.0 - - + +
914B LEU* 5.4 4.2 - - + +
915B PRO 3.2 11.8 + - - +
916B ALA* 3.1 14.7 + - - +
918B VAL* 1.3 76.3 - - - +
920B GLU* 1.3 50.5 + - - +
922B LEU 2.7 9.7 + - - -
923B GLY* 2.5 36.3 + - - -
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Residues in contact with GLU 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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916B ALA 3.3 4.5 + - - +
917B GLU* 3.1 17.1 + - - +
919B ARG* 1.3 77.5 - - - +
921B THR* 1.3 64.8 + - + +
923B GLY* 3.5 9.7 + - - +
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Residues in contact with THR 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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879B THR* 3.6 28.1 - - + +
881B PRO* 4.1 15.5 - - + -
882B LEU* 5.6 3.5 - - - +
917B GLU 4.1 10.3 - - - +
918B VAL* 2.5 23.7 + - - +
920B GLU* 1.3 80.9 - - + +
922B LEU* 1.3 78.5 + - - +
923B GLY 3.7 0.5 + - - -
928B ASP* 5.1 4.7 - - - +
932B TYR* 4.1 19.6 - - - +
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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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882B LEU* 5.3 10.5 - - + -
907B LYS* 5.1 6.7 - - + -
911B TYR* 3.8 13.0 + - + -
914B LEU* 5.8 2.9 - - + -
918B VAL* 4.1 12.8 - - + +
919B ARG 2.7 9.3 + - - +
921B THR* 1.3 82.6 + - - +
923B GLY* 1.3 63.5 + - - +
924B SER 3.1 3.8 + - - -
925B LEU* 3.5 10.2 + - - -
928B ASP* 4.4 5.2 - - - -
929B PHE* 3.5 53.1 + - + +
932B TYR* 3.1 51.4 - - + -
933B PHE* 4.6 8.3 - - + -
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Residues in contact with GLY 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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911B TYR* 2.3 26.7 + - - -
919B ARG* 2.5 28.2 + - - -
920B GLU* 3.5 8.1 + - - -
921B THR 3.4 4.2 + - - -
922B LEU* 1.3 69.4 - - - +
924B SER* 1.3 65.9 + - - +
928B ASP* 4.8 1.2 + - - +
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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