Contacts of the helix formed by residues 915 - 923 (chain A) in PDB entry 4U6R
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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885A ASP* 4.8 10.8 - - - +
913A GLU 4.1 3.4 - - - +
914A LEU* 1.3 90.4 - - + +
916A ALA* 1.3 67.3 + - - +
917A GLU* 4.6 8.7 - - + +
918A VAL* 2.9 32.8 + - + +
919A ARG 3.1 8.7 + - - -
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Residues in contact with ALA 916 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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915A PRO* 1.3 70.6 - - - +
917A GLU* 1.3 56.9 + - - +
919A ARG* 3.2 34.7 + - - +
920A GLU* 2.9 27.9 + - - +
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Residues in contact with GLU 917 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881A PRO* 4.0 22.1 - - + +
915A PRO* 3.0 8.8 + - + +
916A ALA* 1.3 75.9 - - - +
918A VAL* 1.3 67.3 + - + +
920A GLU* 3.8 10.7 - - - +
921A THR* 3.2 26.5 + - - +
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Residues in contact with VAL 918 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881A PRO* 4.1 22.7 - - + +
882A LEU* 4.1 18.8 - - + -
885A ASP* 4.2 17.5 - - + +
914A LEU* 3.9 27.8 - - + -
915A PRO* 2.9 28.8 + - + +
917A GLU* 1.3 79.8 - - + +
919A ARG* 1.3 66.7 + - - +
921A THR* 3.1 11.5 - - + +
922A LEU* 3.1 31.0 + - + +
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Residues in contact with ARG 919 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911A TYR* 3.2 66.8 + - + +
912A ARG* 3.8 21.4 + - - +
914A LEU* 2.5 39.6 + - + +
915A PRO* 3.1 2.1 + - - +
916A ALA* 3.4 36.6 + - - +
918A VAL* 1.3 79.2 - - - +
920A GLU* 1.3 57.0 + - - +
922A LEU* 3.5 1.5 + - - +
923A GLY* 3.1 23.2 + - - +
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Residues in contact with GLU 920 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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916A ALA 2.9 16.1 + - - +
917A GLU* 4.2 9.1 - - - +
918A VAL 3.2 0.2 - - - -
919A ARG* 1.3 75.0 - - - +
921A THR* 1.3 64.4 + - - +
923A GLY* 3.5 10.4 + - - +
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Residues in contact with THR 921 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879A THR* 2.7 38.5 + - - +
881A PRO* 4.3 16.8 - - + +
882A LEU* 4.5 10.3 - - + +
917A GLU 3.2 16.7 + - - +
918A VAL* 3.1 22.9 - - - +
920A GLU* 1.3 77.7 - - - +
922A LEU* 1.3 68.1 + - + +
923A GLY* 4.6 0.2 - - - -
932A TYR* 3.2 18.5 - - + -
936A ARG* 5.3 0.3 + - - -
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Residues in contact with LEU 922 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882A LEU* 3.9 27.1 - - + -
907A LYS* 4.1 7.0 - - + -
911A TYR* 4.2 6.1 - - + -
914A LEU* 3.9 25.1 - - + -
918A VAL* 3.1 27.4 + - + +
919A ARG 3.9 3.6 - - - +
921A THR* 1.3 79.1 - - + +
923A GLY* 1.3 65.1 + - - +
928A ASP* 3.5 20.8 - - - +
929A PHE* 3.5 32.2 - - + -
932A TYR* 3.9 19.0 - - + +
933A PHE* 4.0 21.8 - - + -
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Residues in contact with GLY 923 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911A TYR* 2.6 28.9 + - - -
919A ARG 3.1 9.6 + - - -
920A GLU* 3.5 8.2 + - - -
921A THR 3.3 3.8 + - - -
922A LEU* 1.3 81.7 - - - +
924A THR* 1.3 61.7 + - - +
928A ASP* 3.9 10.8 - - - -
929A PHE* 4.5 1.6 + - - +
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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