Contacts of the helix formed by residues 856 - 864 (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 GLY 856 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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852A GLU* 5.0 6.5 - - - -
853A SER* 2.9 22.1 + - - -
855A ASP* 1.3 83.4 - - - +
857A PRO* 1.3 74.6 - - - +
858A ILE 3.3 2.2 - - - -
859A VAL 3.7 3.0 + - - -
860A LYS* 3.1 19.1 + - - +
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Residues in contact with PRO 857 (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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852A GLU* 5.3 3.1 - - - +
856A GLY* 1.3 83.1 - - - +
858A ILE* 1.3 71.9 + - + +
860A LYS* 3.4 6.5 + - + +
861A GLN* 3.0 29.9 + - + +
950A LEU* 5.5 10.1 - - + -
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Residues in contact with ILE 858 (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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848A ARG* 3.1 38.6 - - - +
849A ILE* 3.8 27.4 - - + -
852A GLU* 4.2 17.5 - - - +
856A GLY 3.3 0.8 - - - -
857A PRO* 1.3 84.8 - - + +
859A VAL* 1.3 65.0 + - + +
861A GLN* 3.2 6.0 + - - +
862A LEU* 3.1 20.1 + - - +
947A ALA 5.2 1.9 - - - +
948A MET* 3.9 21.2 - - + +
950A LEU* 4.6 15.0 - - + -
951A CYS* 3.4 17.3 - - - -
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Residues in contact with VAL 859 (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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849A ILE* 4.1 22.2 - - + -
852A GLU* 3.8 28.9 + - + -
853A SER 3.6 16.2 - - - +
854A LEU* 3.7 27.4 - - + +
856A GLY 3.7 2.4 + - - +
857A PRO 3.5 0.2 - - - -
858A ILE* 1.3 75.9 - - - +
860A LYS* 1.3 62.7 + - - +
862A LEU* 3.4 7.5 + - + +
863A GLU* 3.0 36.8 + - + +
898A ARG* 4.1 22.9 - - + +
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Residues in contact with LYS 860 (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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854A LEU 4.1 10.8 - - - +
855A ASP* 3.3 41.0 + - - +
856A GLY 3.1 16.1 + - - +
857A PRO* 3.4 8.5 - - + +
858A ILE 3.2 0.2 - - - -
859A VAL* 1.3 77.3 - - - +
861A GLN* 1.3 57.6 + - + +
863A GLU* 3.2 5.4 + - - +
864A ARG* 3.0 41.0 + - - +
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Residues in contact with GLN 861 (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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857A PRO* 3.0 15.8 + - + +
858A ILE 3.5 8.3 - - - +
860A LYS* 1.3 76.7 - - - +
862A LEU* 1.3 62.8 + - - +
863A GLU 3.4 0.7 + - - -
864A ARG* 3.4 45.5 + - - +
943A HIS* 4.3 2.4 - - - -
946A ARG 5.2 0.7 - - - +
947A ALA* 3.7 30.2 - - + +
950A LEU* 3.6 28.7 - - + +
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Residues in contact with LEU 862 (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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845A VAL* 5.0 1.8 - - + -
849A ILE* 3.4 37.7 - - + -
858A ILE 3.1 10.1 + - - +
859A VAL* 3.6 11.0 - - - +
860A LYS 3.2 0.2 - - - -
861A GLN* 1.3 79.6 - - - +
863A GLU* 1.3 59.6 + - + +
897A VAL* 3.7 36.3 - - + +
898A ARG* 4.2 11.9 - - + +
901A LEU* 4.2 4.9 - - + -
943A HIS* 2.7 24.7 + - + -
944A THR* 3.9 29.4 - - + +
947A ALA* 3.7 18.4 - - + +
948A MET* 4.7 9.2 - - + -
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Residues in contact with GLU 863 (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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854A LEU* 5.4 7.5 - - + +
859A VAL* 3.0 29.9 + - + +
860A LYS* 3.2 4.7 + - - +
862A LEU* 1.3 78.0 - - + +
864A ARG* 1.3 54.6 + - - +
865A GLY 3.1 0.9 + - - -
866A GLY* 2.7 28.1 + - - -
895A GLY 4.2 4.2 - - - +
896A SER* 2.9 32.7 + - - -
897A VAL* 2.9 29.0 + - - +
898A ARG* 3.1 15.0 + - - +
1006A SO4 3.8 8.9 + - - -
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Residues in contact with ARG 864 (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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860A LYS* 3.0 28.7 + - - +
861A GLN* 3.4 34.4 + - - +
863A GLU* 1.3 72.1 - - - +
865A GLY* 1.3 59.9 + - - +
943A HIS* 3.2 21.7 - - - -
1006A SO4 4.0 6.3 - - - +
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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