Contacts of the helix formed by residues 818 - 828 (chain A) in PDB entry 5CGD
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 PHE 818 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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597A VAL* 3.8 18.6 - - + -
601A PHE* 3.4 26.9 - + + -
618A CYS* 4.4 18.6 - - + -
621A ILE* 3.5 34.1 - - + -
622A LEU* 3.8 23.6 - - + -
625A ILE* 4.0 8.7 - - + -
813A ALA 3.4 21.1 - - - -
814A LEU* 3.4 20.0 + - + +
817A MET* 1.3 95.9 - - + +
819A VAL* 1.3 60.3 + - - +
820A PRO 3.3 1.8 - - - -
821A LYS* 3.0 12.5 + - - +
822A VAL* 2.8 32.1 + - - +
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Residues in contact with VAL 819 (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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597A VAL* 5.2 9.2 - - + -
814A LEU* 3.3 17.0 + - + +
815A GLY* 3.3 24.0 - - - +
818A PHE* 1.3 77.2 - - - +
820A PRO* 1.4 59.4 - - + +
822A VAL* 3.3 8.4 + - + +
823A TYR* 2.9 31.0 + - + +
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Residues in contact with PRO 820 (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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773A TYR* 3.7 35.0 - - + +
815A GLY 3.4 15.9 - - - +
816A CYS* 3.5 24.5 - - - +
817A MET 3.8 3.4 - - - +
818A PHE 3.5 6.7 - - - +
819A VAL* 1.4 92.4 - - + +
821A LYS* 1.3 57.4 + - + +
823A TYR* 3.5 8.2 + - + +
824A ILE* 3.2 36.7 + - + +
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Residues in contact with LYS 821 (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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601A PHE* 3.9 28.6 - - + -
609A VAL* 4.3 36.5 + - + +
610A VAL* 5.3 4.8 - - - +
613A SER* 4.6 6.5 - - - -
618A CYS* 4.2 23.4 - - - -
665A LYS* 5.2 0.2 - - - +
767A ASN* 6.0 3.1 - - + +
770A GLU* 4.3 27.7 + - + +
817A MET 3.5 21.5 - - - +
818A PHE* 3.0 10.6 + - - +
820A PRO* 1.3 77.6 - - + +
822A VAL* 1.3 65.6 + - - +
824A ILE* 3.5 9.2 + - + +
825A ILE* 3.1 25.5 + - - +
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Residues in contact with VAL 822 (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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596A PHE* 4.0 18.8 - - + -
597A VAL* 4.0 29.6 - - + -
600A VAL* 4.3 15.7 - - + -
601A PHE* 4.2 10.1 - - + -
818A PHE 2.8 24.0 + - - +
819A VAL* 3.7 7.0 - - - +
821A LYS* 1.3 75.4 - - - +
823A TYR* 1.3 64.1 + - - +
825A ILE* 3.2 9.2 - - - +
826A LEU* 3.1 42.1 + - + +
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Residues in contact with TYR 823 (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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819A VAL* 2.9 21.0 + - + +
820A PRO* 3.6 10.3 - - + +
822A VAL* 1.3 77.5 - - - +
824A ILE* 1.3 65.6 + - + +
826A LEU* 3.3 3.5 + - - +
827A ALA* 2.8 57.0 + - + +
828A LYS* 3.6 28.2 + - + -
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Residues in contact with ILE 824 (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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609A VAL* 4.5 18.2 - - + -
768A PHE* 4.3 42.8 - - + +
773A TYR* 5.8 5.8 - - + +
820A PRO* 3.2 22.3 + - + +
821A LYS* 3.8 9.2 - - + +
822A VAL 3.3 0.2 - - - -
823A TYR* 1.3 84.8 - - + +
825A ILE* 1.3 59.9 + - - +
828A LYS* 3.0 51.4 + - + +
831A ARG* 5.0 3.4 - - + -
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Residues in contact with ILE 825 (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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600A VAL* 3.8 20.4 - - + -
601A PHE* 5.0 0.9 - - + -
604A TYR* 3.4 42.6 - - + +
607A THR* 4.0 13.9 - - + -
609A VAL* 3.6 15.9 - - + -
610A VAL* 3.5 29.4 - - + -
821A LYS 3.1 15.5 + - - +
822A VAL* 3.2 17.3 - - - +
823A TYR 3.2 0.4 - - - -
824A ILE* 1.3 79.3 - - - +
826A LEU* 1.3 75.8 + - + +
828A LYS 4.7 1.1 - - - -
829A PRO* 4.9 9.9 - - - +
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Residues in contact with LEU 826 (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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596A PHE* 4.2 19.1 - - + -
600A VAL* 4.8 6.5 - - + -
604A TYR* 4.2 26.0 - - + +
822A VAL* 3.1 33.5 + - + +
823A TYR* 4.2 2.5 - - - +
825A ILE* 1.3 95.1 - - + +
827A ALA* 1.3 62.0 + - + +
828A LYS 3.6 0.7 - - - -
829A PRO* 4.1 11.5 - - - +
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Residues in contact with ALA 827 (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 TYR* 2.8 45.3 + - + +
826A LEU* 1.3 77.0 - - + +
828A LYS* 1.3 75.3 + - - +
829A PRO* 3.4 10.7 - - - +
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Residues in contact with LYS 828 (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 TYR* 3.6 30.1 + - + +
824A ILE* 3.0 38.5 + - + +
825A ILE* 5.3 0.2 - - - -
827A ALA* 1.3 95.3 + - + +
829A PRO* 1.3 59.3 - - - +
830A GLU* 3.1 7.9 + - - +
831A ARG* 3.3 41.4 + - + +
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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