Contacts of the helix formed by residues 816 - 826 (chain B) in PDB entry 7CN9
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 816 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804B GLN 3.7 11.0 - - - -
805B ILE* 3.7 17.0 - - - -
807B PRO* 6.2 0.2 - - - -
815B ARG* 1.3 76.7 - - - +
817B PHE* 1.3 57.8 + - - +
818B ILE* 3.2 7.2 + - - +
819B GLU* 2.4 65.5 + - - +
820B ASP* 2.9 11.3 - - - +
1054B GLN* 3.6 21.2 + - - -
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Residues in contact with PHE 817 (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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803B SER 4.2 5.6 + - - +
804B GLN* 3.0 46.1 + - + +
815B ARG 4.1 1.4 + - - -
816B SER* 1.3 70.2 - - - +
818B ILE* 1.3 64.7 + - + +
820B ASP* 3.1 15.0 + - - +
821B LEU* 3.1 23.0 + - + +
935B GLN* 3.8 36.6 - - + -
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Residues in contact with ILE 818 (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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804B GLN* 3.2 22.9 - - + +
805B ILE* 3.5 30.3 - - + -
816B SER* 3.0 4.5 - - - +
817B PHE* 1.3 76.9 - - + +
819B GLU* 1.3 57.1 + - - +
821B LEU* 3.2 12.0 + - + +
822B LEU* 2.8 39.8 + - + +
931B ILE* 5.6 4.5 - - + -
934B ILE* 5.8 6.5 - - + -
935B GLN* 6.3 2.7 - - + -
938B LEU* 4.3 23.8 - - + -
1054B GLN* 4.2 19.3 - - + +
1063B LEU* 4.7 20.9 - - + -
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Residues in contact with GLU 819 (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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815B ARG* 2.1 64.2 + - - +
816B SER* 2.4 43.6 + - - +
818B ILE* 1.3 67.1 - - - +
820B ASP* 1.3 60.4 + - - +
822B LEU* 2.9 26.5 + - + +
823B PHE* 2.9 35.7 + - + -
871B ALA* 5.0 7.5 - - - +
1054B GLN* 4.8 4.9 - - - +
1055B SER* 5.3 16.0 + - - +
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Residues in contact with ASP 820 (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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812B PRO* 4.2 22.2 - - - +
815B ARG* 4.7 9.9 - - - +
816B SER 2.9 20.5 + - - +
817B PHE* 3.1 18.1 + - + +
819B GLU* 1.3 73.9 - - - +
821B LEU* 1.3 66.6 + - - +
822B LEU 2.9 1.2 + - - -
823B PHE* 3.0 24.3 + - - +
824B ASN 4.2 3.3 + - - -
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Residues in contact with LEU 821 (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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817B PHE* 3.1 15.1 + - + +
818B ILE* 3.2 15.9 + - + +
820B ASP* 1.3 78.4 - - - +
822B LEU* 1.3 59.3 + - - +
825B LYS* 3.1 48.9 + - + +
935B GLN* 3.6 35.0 - - + +
938B LEU* 3.6 31.9 - - + -
939B SER* 4.1 18.2 - - - -
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Residues in contact with LEU 822 (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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818B ILE* 2.8 30.6 + - + +
819B GLU* 2.9 22.7 + - + +
821B LEU* 1.3 77.8 - - - +
823B PHE* 1.3 69.0 + - - +
825B LYS* 3.0 16.1 + - - +
826B VAL* 3.0 15.8 + - + +
938B LEU* 4.6 17.9 - - + -
945B LEU* 4.6 19.0 - - + +
1054B GLN* 4.3 14.4 - - + -
1055B SER 3.4 25.1 - - - +
1056B ALA* 5.5 3.1 - - + -
1057B PRO* 5.4 8.7 - - + -
1061B VAL* 4.9 16.6 - - + -
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Residues in contact with PHE 823 (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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815B ARG* 3.7 14.1 - - - -
819B GLU* 2.9 62.8 + - + -
820B ASP* 3.0 14.0 + - - +
822B LEU* 1.3 73.5 - - + +
824B ASN* 1.3 58.7 + - + +
826B VAL* 2.6 39.4 + - - +
828B LEU* 5.2 14.3 - - + +
867B ASP* 5.4 11.2 - - + -
1055B SER* 6.2 0.2 - - - -
1057B PRO* 4.9 22.1 - - + +
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Residues in contact with ASN 824 (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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820B ASP 4.2 4.5 + - - +
823B PHE* 1.3 81.4 - - - +
825B LYS* 1.3 60.1 + - - +
826B VAL 2.8 16.1 - - - +
827B THR* 4.0 5.0 + - - +
828B LEU* 5.0 10.0 - - - +
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Residues in contact with LYS 825 (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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821B LEU* 3.1 42.6 + - + +
822B LEU* 3.0 14.7 + - - +
824B ASN* 1.3 79.0 - - - +
826B VAL* 1.3 54.9 + - - +
827B THR* 3.8 5.0 + - - +
938B LEU* 2.2 42.6 + - - +
939B SER* 4.3 5.0 + - - +
941B THR 3.7 13.9 + - - -
942B ALA* 4.7 5.3 - - - +
945B LEU* 3.5 41.7 - - + +
949B GLN* 5.1 1.9 + - - +
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Residues in contact with VAL 826 (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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822B LEU* 3.0 10.2 + - + +
823B PHE 2.6 28.9 + - - +
824B ASN* 2.8 15.5 - - - +
825B LYS* 1.3 73.2 - - - +
827B THR* 1.3 60.2 + - - +
828B LEU* 3.0 27.8 + - + +
945B LEU* 4.4 13.9 - - + -
948B LEU* 6.2 5.4 - - + -
949B GLN* 3.9 18.8 - - + +
952B VAL* 4.9 10.1 - - + -
1057B PRO* 3.5 38.8 - - + -
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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