Contacts of the helix formed by residues 837 - 853 (chain A) in PDB entry 2O8C
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 PRO 837 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835A ASN 4.6 1.3 - - - +
836A PHE* 1.3 89.9 - - + +
838A LYS* 1.3 66.0 + - - +
839A HIS* 4.5 14.8 - - + +
840A VAL* 3.1 32.5 + - + +
841A ILE* 3.2 11.8 + - - +
1198B ALA 5.1 2.5 - - - +
1201B LEU* 3.8 42.4 - - + +
1202B MET* 5.0 4.7 - - + +
1234B GLU* 4.3 6.5 - - - +
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Residues in contact with LYS 838 (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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836A PHE 3.7 1.4 + - - -
837A PRO* 1.3 71.9 - - - +
839A HIS* 1.3 74.7 + - + +
840A VAL 3.5 2.1 + - - -
841A ILE* 3.6 10.7 - - - +
842A GLU* 3.4 32.7 - - - +
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Residues in contact with HIS 839 (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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837A PRO* 3.3 10.3 - - + -
838A LYS* 1.3 93.6 - - + +
840A VAL* 1.3 59.1 + - - +
842A GLU* 4.6 6.1 - - - +
843A CYS* 3.9 13.6 - - - +
1234B GLU* 2.7 36.1 + - + +
1238B THR* 4.9 13.4 - - + +
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Residues in contact with VAL 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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836A PHE* 3.7 25.6 - - + -
837A PRO* 3.1 26.0 + - + +
839A HIS* 1.3 79.5 - - - +
841A ILE* 1.3 65.8 + - - +
842A GLU 3.3 1.3 - - - -
843A CYS* 3.3 7.6 + - - +
844A ALA* 3.2 18.9 + - - +
1201B LEU* 3.9 11.2 - - + -
1230B ALA* 3.6 27.6 - - + +
1231B VAL* 4.7 1.3 - - - +
1234B GLU* 3.1 41.5 - - + +
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Residues in contact with ILE 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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828A ILE* 3.4 36.8 - - + +
831A ALA* 3.8 11.2 - - + -
832A GLU* 3.8 37.5 - - + +
836A PHE* 4.3 14.1 - - + +
837A PRO 3.2 16.7 + - - +
838A LYS* 3.6 13.2 - - - +
840A VAL* 1.3 81.9 - - - +
842A GLU* 1.3 68.2 + - + +
844A ALA* 3.5 6.1 + - + +
845A LYS* 3.4 29.8 + - - +
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Residues in contact with GLU 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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838A LYS* 3.4 23.3 + - - +
839A HIS* 5.0 3.8 - - - -
840A VAL 3.3 0.6 - - - +
841A ILE* 1.3 80.5 - - + +
843A CYS* 1.3 64.3 + - - +
844A ALA 3.2 0.7 - - - -
845A LYS* 3.3 32.8 + - + +
846A GLN* 3.3 22.5 + - - +
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Residues in contact with CYS 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 HIS 3.9 16.7 + - - +
840A VAL* 3.4 12.0 - - - +
841A ILE 3.3 0.2 - - - -
842A GLU* 1.3 77.6 - - - +
844A ALA* 1.3 62.0 + - - +
845A LYS 3.2 0.4 - - - -
846A GLN* 3.4 13.3 + - - +
847A LYS* 3.4 27.0 + - - +
1229B ASN* 5.1 1.8 - - - -
1230B ALA* 3.8 21.3 - - + +
1233B LYS* 3.7 32.8 - - - -
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Residues in contact with ALA 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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828A ILE* 4.2 18.0 - - + +
831A ALA* 6.5 0.2 - - + -
840A VAL 3.2 11.8 + - - +
841A ILE* 3.7 14.6 - - + +
842A GLU 3.2 0.2 - - - -
843A CYS* 1.3 76.4 - - - +
845A LYS* 1.3 61.4 + - - +
847A LYS* 4.1 1.3 - - - +
848A ALA* 3.3 23.2 + - - +
1226B ALA* 3.8 34.2 - - + +
1227B ILE* 4.6 8.1 - - + +
1230B ALA* 4.0 3.8 - - + +
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Residues in contact with LYS 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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828A ILE* 4.7 12.8 - - + -
832A GLU* 4.9 14.5 + - - -
841A ILE* 3.4 24.0 - - - +
842A GLU* 3.3 26.9 + - + +
843A CYS 3.2 0.4 - - - -
844A ALA* 1.3 78.6 - - - +
846A GLN* 1.3 62.2 + - + +
848A ALA* 3.7 5.3 + - - +
849A LEU* 3.4 30.1 + - + +
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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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842A GLU* 3.3 17.8 + - - +
843A CYS* 3.4 13.6 + - - +
844A ALA 3.3 0.4 - - - -
845A LYS* 1.3 78.1 - - + +
847A LYS* 1.3 64.9 + - + +
849A LEU* 3.5 10.6 + - + +
850A GLU* 3.4 29.8 + - - +
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Residues in contact with LYS 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 CYS* 3.4 18.0 + - - +
844A ALA 3.9 2.9 + - - +
846A GLN* 1.3 78.7 - - + +
848A ALA* 1.3 63.2 + - - +
850A GLU* 3.3 36.1 + - + +
851A LEU* 3.4 26.0 + - + +
1226B ALA* 4.6 18.4 - - - +
1229B ASN* 3.3 29.2 - - + +
1255B ASP* 4.0 16.2 - - - +
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Residues in contact with ALA 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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828A ILE* 3.7 24.9 - - + -
844A ALA 3.3 19.7 + - - +
845A LYS* 3.9 6.3 - - - +
846A GLN 3.2 0.2 - - - -
847A LYS* 1.3 77.9 - - - +
849A LEU* 1.3 63.8 + - + +
851A LEU* 3.4 9.2 + - - -
852A GLU* 3.4 11.2 - - - +
1222B PHE* 3.4 32.2 - - + -
1226B ALA* 4.5 7.4 - - + -
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Residues in contact with LEU 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 LYS* 3.4 18.2 - - + +
846A GLN* 3.5 10.2 + - + +
847A LYS 3.4 0.4 - - - -
848A ALA* 1.3 78.9 - - + +
850A GLU* 1.3 61.2 + - + +
851A LEU 3.2 1.8 + - - -
852A GLU* 3.6 29.9 + - - +
853A GLU* 3.8 14.4 + - - +
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Residues in contact with GLU 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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846A GLN* 3.4 20.4 + - - +
847A LYS* 3.3 43.3 + - + +
848A ALA 3.2 1.0 - - - -
849A LEU* 1.3 79.7 - - + +
851A LEU* 1.3 61.6 + - + +
852A GLU 3.6 0.2 - - - -
853A GLU* 3.4 30.9 - - - +
854A PHE* 4.4 6.4 - - - +
1330B LEU* 4.6 19.7 - - + +
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Residues in contact with LEU 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 LYS* 3.4 18.6 - - + +
848A ALA* 3.4 3.3 + - - +
849A LEU 3.2 0.6 - - - -
850A GLU* 1.3 83.4 - - + +
852A GLU* 1.3 62.9 + - - +
853A GLU 3.2 2.0 - - - -
854A PHE* 3.4 7.9 + - + +
855A GLN* 3.3 25.8 + - - +
1222B PHE* 3.7 36.1 - - + +
1225B THR* 3.3 29.4 - - + +
1226B ALA* 5.1 2.2 - - + +
1251B SER* 6.3 2.9 - - - -
1327B ASN* 6.0 4.9 - - - +
1330B LEU* 5.9 6.1 - - + -
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Residues in contact with GLU 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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823A ASP 5.8 0.4 - - - +
848A ALA* 3.4 16.2 + - - +
849A LEU* 3.6 26.2 + - - +
851A LEU* 1.3 78.8 - - - +
853A GLU* 1.3 59.0 + - - +
854A PHE 3.3 0.6 + - - -
855A GLN* 3.7 16.6 + - - +
1222B PHE* 3.7 26.1 - - + -
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Residues in contact with GLU 853 (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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849A LEU 3.8 6.8 + - - +
850A GLU* 3.4 43.7 - - - +
852A GLU* 1.3 80.0 - - - +
854A PHE* 1.3 58.4 + - + +
855A GLN 3.5 0.8 - - - -
1326B MET* 4.6 5.5 - - - +
1330B LEU* 4.4 13.4 - - + +
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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