Contacts of the helix formed by residues 843 - 849 (chain B) in PDB entry 5WRZ
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 843 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840B GLU* 6.0 0.4 + - - -
841B ARG 3.3 0.8 + - - -
842B GLU* 1.3 75.3 - - - +
844B GLU* 1.3 62.5 + - - +
845B CYS 3.4 2.7 - - - +
846B GLN* 3.6 12.6 + - - +
847B ARG* 3.2 21.1 + - - +
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Residues in contact with GLU 844 (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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841B ARG* 3.0 59.5 + - + +
842B GLU 3.2 1.2 + - - -
843B GLY* 1.3 77.6 - - - +
845B CYS* 1.3 60.2 + - - +
847B ARG* 3.3 26.5 + - - +
848B TYR* 2.9 27.9 + - - +
876B GLY* 4.6 1.2 - - - -
877B LEU 5.4 0.3 + - - -
997B VAL* 3.8 12.5 - - - +
998B ASN* 2.9 14.4 + - - +
999B LEU* 2.6 46.8 + - - +
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Residues in contact with CYS 845 (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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840B GLU* 4.2 32.8 - - - +
841B ARG 4.5 0.4 + - - -
843B GLY 3.4 0.2 - - - -
844B GLU* 1.3 77.4 - - - +
846B GLN* 1.3 63.7 + - - +
848B TYR* 3.4 8.1 + - - +
849B LYS* 3.3 22.0 + - - +
998B ASN* 4.2 22.0 - - - +
1000B LYS* 5.6 3.1 - - - -
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Residues in contact with GLN 846 (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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843B GLY* 3.6 14.9 + - - +
845B CYS* 1.3 78.5 - - - +
847B ARG* 1.4 61.5 + - - +
849B LYS* 3.1 49.0 + - - +
850B PRO* 3.8 4.0 - - - +
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Residues in contact with ARG 847 (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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841B ARG* 3.4 29.3 - - - +
843B GLY 3.2 12.6 + - - +
844B GLU* 3.3 27.3 + - - +
846B GLN* 1.4 78.2 - - - +
848B TYR* 1.3 61.4 + - - +
850B PRO* 3.4 12.7 - - - +
875B GLN 4.8 6.7 + - - -
876B GLY* 5.1 2.0 - - - -
877B LEU 5.0 6.1 + - - +
994B ILE* 3.5 55.9 + - - +
995B ALA* 3.6 31.1 - - + +
997B VAL* 4.1 4.9 + - - +
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Residues in contact with TYR 848 (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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844B GLU 2.9 16.5 + - - +
845B CYS* 3.8 6.5 - - - +
846B GLN 3.2 0.4 - - - -
847B ARG* 1.3 79.6 - - - +
849B LYS* 1.3 54.2 + - - +
850B PRO* 3.3 1.1 - - - -
851B PHE* 2.7 29.4 + - + +
852B LYS* 3.1 31.4 + - + -
857B ARG* 3.5 13.5 - - - +
923B GLU* 2.7 46.8 + - + +
925B ALA* 3.8 16.0 + - + +
995B ALA* 3.3 19.5 - - - +
996B GLN 3.6 21.3 - - - -
997B VAL 3.9 14.1 - - - +
998B ASN* 3.8 25.6 - - + -
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Residues in contact with LYS 849 (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 CYS 3.3 10.3 + - - +
846B GLN* 3.1 46.7 + - - +
848B TYR* 1.3 75.3 - - - +
850B PRO* 1.4 69.5 - - + +
851B PHE 2.9 1.6 + - - -
852B LYS* 3.0 53.7 + - + +
853B GLN 4.6 0.3 + - - -
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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