Contacts of the helix formed by residues 843 - 854 (chain A) in PDB entry 5G04
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 SER 843 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771A GLU* 4.0 7.5 + - - -
774A LYS* 5.8 0.5 - - - +
805A HIS* 3.3 34.3 + - - -
841A PRO 3.7 5.4 + - - -
842A PRO* 1.3 72.5 - - - +
844A ILE* 1.3 59.5 + - - +
845A TYR* 3.6 11.3 + - - +
846A GLN* 3.5 28.2 + - - +
847A TRP* 2.9 29.6 + - - +
860A TYR* 4.4 3.4 - - - -
1812A TRP* 5.4 2.1 - - - -
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Residues in contact with ILE 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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771A GLU* 4.0 33.2 + - + +
774A LYS* 4.7 11.9 - - + -
775A LEU* 5.0 10.8 - - + -
843A SER* 1.3 69.1 + - - +
845A TYR* 1.3 73.3 + - + +
847A TRP* 3.4 9.4 - - + +
848A VAL* 3.1 39.3 + - + +
860A TYR* 3.7 22.1 + - + +
870A SER* 3.5 25.4 - - - +
873A VAL* 3.8 25.1 - - + -
874A VAL* 4.0 15.9 - - + -
951A ILE* 5.6 5.6 - - + -
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Residues in contact with TYR 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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774A LYS* 3.5 51.5 + - + +
809A ASP* 4.1 2.9 - - - -
843A SER* 3.6 8.9 + - - +
844A ILE* 1.3 81.8 - - + +
846A GLN* 1.3 62.2 + - - +
848A VAL* 3.2 5.0 + - - +
849A SER* 3.2 23.6 + - - -
948A PRO* 4.4 8.7 - - + +
951A ILE* 3.7 26.9 - - + -
1809A SER* 4.0 12.3 + - - -
1812A TRP* 3.6 58.8 - + + -
1813A GLN* 4.1 17.2 + - + +
1816A LEU* 3.9 21.1 - - + +
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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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805A HIS* 6.2 0.2 - - + -
808A ARG* 5.7 6.1 - - - +
843A SER* 3.4 23.5 + - - +
845A TYR* 1.3 78.6 - - - +
847A TRP* 1.3 61.1 - - - +
849A SER* 3.0 19.3 + - - -
850A SER* 2.7 50.0 + - - +
1812A TRP* 4.3 18.2 - - + -
1815A LYS* 5.1 4.2 - - - +
1893A SER* 5.5 6.3 - - - +
1923A LYS* 5.9 2.3 - - - -
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Residues in contact with TRP 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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843A SER 2.9 17.9 + - - +
844A ILE* 3.4 11.2 - - + +
846A GLN* 1.3 76.6 - - - +
848A VAL* 1.3 73.3 + - + +
850A SER* 4.1 2.6 - - - -
851A CYS* 3.0 45.9 + - + +
856A GLY 4.9 3.1 + - - -
858A PRO* 2.8 52.5 + - + +
859A PRO 5.1 2.7 - - - -
860A TYR* 3.5 34.4 - + + +
874A VAL* 4.1 38.4 - - + -
877A ILE* 3.8 34.8 - - + -
878A ALA* 5.2 4.7 - - + -
882A LEU* 6.0 1.3 - - + -
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Residues in contact with VAL 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A ILE* 3.1 24.9 + - + +
845A TYR 3.2 4.9 + - - +
847A TRP* 1.3 85.7 - - + +
849A SER* 1.3 57.6 + - - +
851A CYS* 3.3 4.4 + - - +
852A LEU* 3.0 38.2 + - + +
873A VAL* 5.8 0.7 - - + -
877A ILE* 3.7 35.2 - - + -
881A ILE* 6.2 2.5 - - + -
951A ILE* 4.3 14.6 - - + -
954A PRO* 5.5 8.1 - - + -
1816A LEU* 3.8 21.8 - - + -
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Residues in contact with SER 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 TYR 3.2 13.3 + - - -
846A GLN* 3.0 25.8 + - - -
848A VAL* 1.3 76.9 - - - +
850A SER* 1.3 68.6 + - - +
852A LEU* 3.4 8.5 - - - +
853A LYS* 3.3 25.8 + - - +
1812A TRP* 4.7 2.3 - - - -
1815A LYS* 4.4 14.4 + - - -
1816A LEU* 3.6 14.5 - - - +
1819A GLU* 3.2 26.4 - - - +
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Residues in contact with SER 850 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A GLN* 2.7 38.2 + - - +
847A TRP* 4.1 3.6 - - - -
849A SER* 1.3 79.9 + - - +
851A CYS* 1.3 52.4 + - - +
853A LYS* 3.4 5.3 + - - +
854A GLY* 2.7 40.8 + - - +
856A GLY 5.5 0.7 - - - -
857A MET* 4.8 16.2 - - - -
858A PRO* 5.7 1.3 - - - -
1923A LYS* 5.1 16.4 + - - +
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Residues in contact with CYS 851 (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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847A TRP* 3.0 37.0 + - + +
848A VAL* 3.4 7.9 - - - +
850A SER* 1.3 75.2 - - - +
852A LEU* 1.3 62.4 + - - +
854A GLY 3.1 21.3 - - - +
855A GLU* 4.2 4.3 + - - -
856A GLY* 4.5 17.6 + - - +
877A ILE* 4.1 20.6 - - - -
881A ILE* 5.4 6.4 - - - +
882A LEU* 3.9 27.4 - - - -
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Residues in contact with LEU 852 (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 VAL* 3.0 28.1 + - + +
849A SER* 3.4 14.6 - - - +
851A CYS* 1.3 78.3 - - - +
853A LYS* 1.3 81.4 + - + +
881A ILE* 5.2 22.5 - - + +
954A PRO* 6.6 0.2 - - + -
1816A LEU* 4.5 5.6 - - + +
1819A GLU* 3.6 33.0 - - + +
1820A PHE* 4.0 29.8 - - + +
1823A SER* 3.8 11.6 - - - +
1824A ARG* 3.9 23.0 + - - +
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Residues in contact with LYS 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A SER* 3.3 13.7 + - - +
850A SER* 4.0 3.4 - - - +
852A LEU* 1.3 96.8 - - + +
854A GLY* 1.3 57.3 + - - +
1819A GLU* 3.2 33.3 + - + +
1823A SER* 5.7 4.0 - - - +
1824A ARG* 4.4 16.1 - - - +
1893A SER* 5.2 0.6 + - - -
1921A GLN* 3.4 34.6 + - - +
1922A LEU 5.1 0.8 + - - -
1923A LYS* 4.9 11.1 - - - +
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Residues in contact with GLY 854 (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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850A SER 2.7 31.4 + - - +
851A CYS* 3.1 9.7 - - - +
853A LYS* 1.3 75.9 - - - +
855A GLU* 1.3 67.3 + - - +
856A GLY 4.6 1.7 - - - +
857A MET* 5.1 2.3 - - - +
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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