Contacts of the helix formed by residues 843 - 849 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840A GLU* 5.9 0.4 + - - -
841A ARG 3.3 0.6 + - - -
842A GLU* 1.3 75.5 - - - +
844A GLU* 1.3 58.7 + - - +
845A CYS 3.4 2.2 - - - -
846A GLN* 3.5 13.6 + - - +
847A ARG* 3.0 26.7 + - - +
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Residues in contact with GLU 844 (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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841A ARG* 3.0 59.3 + - + +
842A GLU 3.2 1.4 - - - -
843A GLY* 1.3 76.3 - - - +
845A CYS* 1.3 62.5 + - - +
847A ARG* 3.2 28.3 + - - +
848A TYR* 2.9 27.4 + - - +
876A GLY* 4.4 1.2 - - - -
877A LEU 5.2 0.3 + - - -
997A VAL* 3.8 12.8 - - - +
998A ASN* 2.9 13.8 + - - +
999A LEU* 2.6 47.8 + - - +
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Residues in contact with CYS 845 (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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840A GLU* 4.1 32.3 - - - +
841A ARG 5.5 0.4 - - - -
843A GLY 3.4 0.4 - - - -
844A GLU* 1.3 80.8 - - - +
846A GLN* 1.3 59.9 + - - +
848A TYR* 3.2 10.4 + - - +
849A LYS* 3.2 26.2 + - - +
998A ASN* 3.5 27.4 - - - -
1000A LYS* 5.1 5.6 - - - -
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Residues in contact with GLN 846 (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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843A GLY* 3.5 16.1 - - - +
845A CYS* 1.3 76.2 - - - +
847A ARG* 1.3 66.2 + - - +
849A LYS* 2.7 54.3 + - - +
850A PRO* 4.3 2.1 - - - +
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Residues in contact with ARG 847 (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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841A ARG* 3.5 29.0 - - - +
843A GLY 3.0 15.0 + - - +
844A GLU* 3.3 27.9 + - - +
846A GLN* 1.3 75.4 - - - +
848A TYR* 1.3 59.7 + - - +
849A LYS 3.5 0.2 + - - -
850A PRO* 3.5 11.1 - - - +
875A GLN 4.5 7.7 + - - -
876A GLY* 5.0 1.4 - - - -
877A LEU 4.8 7.1 + - - +
994A ILE* 3.2 50.3 + - - +
995A ALA* 3.6 34.0 - - + +
997A VAL* 4.0 6.1 + - - +
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Residues in contact with TYR 848 (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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844A GLU 2.9 16.3 + - - +
845A CYS* 3.5 8.3 - - - +
846A GLN 3.2 0.4 - - - -
847A ARG* 1.3 73.9 - - - +
849A LYS* 1.3 64.9 + - - +
850A PRO* 3.3 2.5 - - - -
851A PHE* 2.8 31.7 + - + -
852A LYS* 3.2 26.0 + - + -
857A ARG* 3.7 15.1 - - - +
923A GLU* 2.7 53.2 + - + +
925A ALA* 3.8 6.9 + - + +
995A ALA 3.3 19.5 - - - +
996A GLN 3.6 22.7 - - - -
997A VAL 4.1 2.5 - - - +
998A ASN* 3.8 28.0 - - + -
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Residues in contact with LYS 849 (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 CYS 3.2 14.6 + - - -
846A GLN* 2.7 53.4 + - - +
848A TYR* 1.3 75.7 - - - +
850A PRO* 1.4 68.0 - - + +
851A PHE 3.0 1.4 + - - -
852A LYS* 3.2 51.3 + - + +
853A GLN 4.9 0.2 + - - -
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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