Contacts of the helix formed by residues 856 - 865 (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 GLY 856 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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852B GLU* 3.9 20.1 + - - -
853B SER* 4.6 1.6 - - - -
854B LEU 3.4 2.0 - - - +
855B ASP* 1.3 78.8 - - - +
857B PRO* 1.3 77.3 - - - +
858B ILE 3.4 2.2 - - - -
859B VAL* 3.7 2.7 + - - +
860B LYS* 2.9 26.4 + - - +
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Residues in contact with PRO 857 (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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852B GLU* 5.3 5.4 - - - +
856B GLY* 1.3 84.2 - - - +
858B ILE* 1.3 59.4 + - + +
860B LYS* 4.4 3.4 - - + -
861B GLN* 2.6 40.6 + - - +
950B LEU* 4.0 18.6 - - + -
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Residues in contact with ILE 858 (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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848B ARG* 3.0 44.0 - - + +
849B ILE* 4.9 8.5 - - + -
852B GLU* 3.3 28.5 + - + +
856B GLY 3.4 0.8 - - - -
857B PRO* 1.3 83.6 - - + +
859B VAL* 1.3 66.1 + - + +
861B GLN* 3.6 2.4 - - - +
862B LEU* 3.2 28.9 + - + +
947B ALA 5.0 2.6 - - - +
948B MET* 4.0 27.6 - - + -
950B LEU* 4.4 16.6 - - + -
951B CYS* 3.8 13.5 - - - -
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Residues in contact with VAL 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849B ILE* 4.8 3.1 - - + +
852B GLU* 3.1 34.3 - - + +
854B LEU* 4.0 34.1 - - + +
856B GLY 3.7 2.7 + - - +
858B ILE* 1.3 77.0 - - + +
860B LYS* 1.3 58.4 + - - +
862B LEU* 3.4 7.4 - - - +
863B GLU* 2.8 51.4 + - + +
898B ARG* 3.7 35.7 - - + +
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Residues in contact with LYS 860 (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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854B LEU 4.5 10.5 + - - +
855B ASP* 4.7 4.9 - - - +
856B GLY 2.9 23.2 + - - +
857B PRO* 3.9 2.9 - - + +
859B VAL* 1.3 77.7 - - - +
861B GLN* 1.3 61.8 + - - +
863B GLU* 3.8 5.3 - - - -
864B ARG* 3.0 24.3 + - - +
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Residues in contact with GLN 861 (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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857B PRO* 2.6 25.1 + - + +
858B ILE 3.2 4.5 + - - +
860B LYS* 1.3 76.0 - - - +
862B LEU* 1.3 62.1 + - - +
864B ARG* 3.3 17.0 + - - +
865B GLY 4.4 1.4 + - - -
943B HIS* 4.4 3.1 - - - -
946B ARG 5.0 3.6 + - - -
947B ALA* 3.4 32.2 - - - +
950B LEU* 4.5 13.5 - - + +
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Residues in contact with LEU 862 (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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845B VAL* 5.2 6.5 - - + -
849B ILE* 5.3 8.1 - - + -
858B ILE* 3.2 24.6 + - + +
859B VAL* 3.4 10.8 - - + +
861B GLN* 1.3 80.1 - - - +
863B GLU* 1.3 84.7 + - + +
865B GLY 3.8 0.5 + - - -
897B VAL* 3.8 23.8 - - + +
898B ARG* 4.0 14.4 - - + +
901B LEU* 5.8 2.9 - - + -
943B HIS* 2.4 31.5 + - + +
944B THR* 5.4 5.8 - - + -
947B ALA* 3.4 23.8 - - + -
948B MET* 4.1 23.3 - - + -
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Residues in contact with GLU 863 (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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859B VAL* 2.8 38.4 + - + +
860B LYS* 3.8 4.9 - - - +
862B LEU* 1.3 83.2 - - + +
864B ARG* 1.3 60.8 + - - +
865B GLY 3.3 0.4 - - - -
866B GLY* 2.8 25.1 + - - +
895B GLY 4.5 1.6 - - - +
896B SER* 2.2 33.9 + - - -
897B VAL* 3.3 17.9 + - - +
898B ARG* 2.9 18.2 + - - +
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Residues in contact with ARG 864 (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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860B LYS 3.0 13.1 + - - +
861B GLN* 3.4 17.0 - - - +
862B LEU 3.2 1.0 - - - -
863B GLU* 1.3 78.6 - - - +
865B GLY* 1.3 57.8 + - - +
866B GLY 3.4 3.8 + - - +
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Residues in contact with GLY 865 (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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864B ARG* 1.3 77.0 - - - +
866B GLY* 1.3 65.4 + - - +
868B ALA* 3.5 7.3 + - - +
869B VAL* 3.3 25.4 + - - +
943B HIS* 3.7 28.3 - - - -
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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