Contacts of the helix formed by residues 838 - 850 (chain A) in PDB entry 5J67
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 838 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836A GLU* 3.0 16.2 + - - +
837A SER* 1.3 75.0 - - - +
839A ARG* 1.3 60.3 + - - +
840A GLU* 4.0 4.5 + - - +
841A GLU* 3.5 36.3 + - - +
842A LEU* 3.2 35.7 + - - +
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Residues in contact with ARG 839 (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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838A SER* 1.3 69.5 + - - +
840A GLU* 1.3 73.3 + - + +
841A GLU 3.1 2.1 + - - -
842A LEU* 3.2 5.0 + - - +
843A LEU* 3.1 44.2 + - + +
974A ALA 5.4 0.2 + - - -
977A SER* 3.8 28.9 + - - -
978A ALA* 3.8 15.9 - - - +
981A SER* 3.3 27.1 + - - -
987A GLY 5.3 3.1 + - - +
989A GLY 3.9 2.0 + - - +
990A ASP* 2.6 38.1 + - - -
999A ASP* 5.6 1.2 + - - -
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Residues in contact with GLU 840 (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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838A SER* 4.0 4.1 + - - +
839A ARG* 1.3 82.9 - - + +
841A GLU* 1.3 59.1 + - - +
843A LEU* 3.7 17.0 + - - +
844A SER* 3.4 24.3 + - - -
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Residues in contact with GLU 841 (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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832A ILE* 4.9 1.2 - - - +
833A LEU* 3.2 37.7 - - + +
836A GLU* 3.2 39.2 - - - +
838A SER* 3.5 21.9 + - - +
839A ARG 3.1 0.4 - - - -
840A GLU* 1.3 78.6 - - - +
842A LEU* 1.3 65.4 + - + +
843A LEU 3.2 0.2 - - - -
844A SER* 3.3 9.4 + - - -
845A PHE* 3.2 19.2 + - - +
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Residues in contact with LEU 842 (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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833A LEU* 4.5 21.5 - - + +
836A GLU 5.3 2.7 - - - +
837A SER* 5.5 2.5 - - - -
838A SER 3.2 30.6 + - - +
839A ARG* 3.2 6.8 + - - +
841A GLU* 1.3 78.4 - - + +
843A LEU* 1.3 60.8 + - - +
845A PHE* 3.5 8.2 - - - +
846A ILE* 3.4 27.1 + - - +
971A THR* 5.4 8.1 - - + -
974A ALA* 3.5 33.9 - - + +
975A PHE* 3.7 32.7 - - + +
978A ALA* 3.8 17.5 - - + -
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Residues in contact with LEU 843 (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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839A ARG* 3.1 36.6 + - + +
840A GLU* 3.9 19.1 - - - +
841A GLU 3.2 0.2 - - - -
842A LEU* 1.3 71.2 - - - +
844A SER* 1.3 61.2 + - - +
845A PHE 3.2 1.3 - - - -
846A ILE* 3.1 7.8 + - + +
847A GLN* 2.9 39.7 + - + +
978A ALA* 3.6 25.4 - - + +
981A SER* 4.9 0.7 - - - +
982A SER* 3.8 24.0 - - - +
987A GLY* 3.7 26.2 - - - +
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Residues in contact with SER 844 (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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840A GLU 3.4 12.0 + - - -
841A GLU* 3.3 12.9 + - - -
843A LEU* 1.3 78.2 - - - +
845A PHE* 1.3 60.8 + - - +
847A GLN* 3.7 17.5 + - - +
848A HIS* 3.4 21.5 + - - +
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Residues in contact with PHE 845 (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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826A PHE* 3.7 29.8 - + - -
829A VAL* 3.9 19.7 - - + -
830A LEU* 4.4 19.1 - - + -
833A LEU* 3.8 32.8 - - + -
841A GLU 3.2 4.8 + - - +
842A LEU* 3.5 10.1 - - - +
843A LEU 3.2 0.2 - - - -
844A SER* 1.3 74.5 - - - +
846A ILE* 1.3 56.2 + - - +
848A HIS* 3.2 2.8 + - - -
849A TYR* 2.7 65.9 + + + +
850A GLY 4.9 0.2 - - - -
962A LEU* 4.4 9.2 - - + -
975A PHE* 3.4 37.2 - + + -
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Residues in contact with ILE 846 (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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731A ASN* 4.6 12.1 + - - +
842A LEU 3.4 18.4 + - - +
843A LEU* 3.1 12.1 + - + +
845A PHE* 1.3 72.3 - - - +
847A GLN* 1.3 63.6 + - - +
850A GLY* 2.7 49.5 + - - +
851A SER* 4.6 1.8 - - - +
975A PHE* 4.0 24.5 - - + -
978A ALA* 4.0 8.1 - - + +
979A LEU* 3.7 49.8 - - + +
982A SER* 4.1 12.8 - - - +
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Residues in contact with GLN 847 (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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731A ASN* 5.6 3.2 + - - +
739A GLN* 3.0 22.2 - - - +
843A LEU* 2.9 22.5 + - + +
844A SER* 3.7 20.1 + - - +
846A ILE* 1.3 76.3 - - - +
848A HIS* 1.3 55.9 + - - +
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Residues in contact with HIS 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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739A GLN* 3.1 25.6 - - - +
740A GLY* 3.2 21.9 + - - -
741A GLN 5.3 0.2 - - - -
844A SER 3.4 13.1 + - - +
845A PHE* 3.2 4.2 + - - +
847A GLN* 1.3 82.2 - - + +
849A TYR* 1.3 90.5 + + + +
850A GLY 3.5 0.2 - - - -
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Residues in contact with TYR 849 (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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729A GLY* 4.4 8.3 - - - -
739A GLN* 3.3 18.3 - - - +
740A GLY* 4.1 2.2 - - - -
741A GLN 3.8 32.8 - - - -
742A VAL* 4.6 2.8 - - + +
825A GLY* 3.4 22.7 + - - -
826A PHE* 3.6 25.1 - + + -
829A VAL* 3.6 28.4 - - + +
845A PHE* 2.7 54.1 + + + +
848A HIS* 1.3 97.3 + + + +
850A GLY* 1.3 60.3 + - - +
851A SER 4.0 0.2 + - - -
962A LEU* 3.4 14.9 - - + +
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Residues in contact with GLY 850 (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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730A TYR 4.1 6.3 - - - -
731A ASN* 4.3 11.7 - - - -
739A GLN* 3.9 12.1 - - - +
845A PHE* 4.9 0.3 - - - -
846A ILE* 2.7 45.5 + - - +
847A GLN 4.5 0.2 - - - -
848A HIS 3.5 1.8 - - - -
849A TYR* 1.3 78.2 - - - +
851A SER* 1.3 58.5 + - - -
962A LEU* 3.6 8.5 - - - +
975A PHE* 4.9 2.4 - - - -
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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