Contacts of the helix formed by residues 811 - 819 (chain A) in PDB entry 5AMN
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 811 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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809A TYR 3.9 0.7 + - - +
810A GLY* 1.3 74.7 - - - -
812A LEU* 1.3 62.9 + - - +
813A ARG* 3.7 6.4 + - - +
814A GLY* 3.3 18.0 + - - -
815A PHE* 3.0 19.9 + - - +
877A ALA 4.4 0.7 - - - -
878A ARG* 3.8 19.1 - - - -
880A ILE 3.2 11.7 - - - -
881A LEU* 3.8 10.6 - - - +
2018A DTQ 4.7 10.7 + - - -
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Residues in contact with LEU 812 (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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810A GLY 3.7 1.0 + - - -
811A SER* 1.3 70.0 - - - +
813A ARG* 1.3 61.1 + - - +
815A PHE* 3.8 4.9 - - + -
816A LEU* 3.0 45.9 + - + +
854A PHE* 4.2 14.6 - - + -
858A ILE* 4.2 22.7 - - + -
877A ALA* 3.5 16.8 - - + +
880A ILE* 2.7 23.3 + - + +
882A VAL* 3.6 26.2 - - + +
888A MET* 3.9 13.9 - - - -
940A LEU* 4.6 2.2 - - + -
944A ILE* 4.1 25.4 - - + -
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Residues in contact with ARG 813 (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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811A SER* 3.2 3.0 - - - +
812A LEU* 1.3 77.6 - - - +
814A GLY* 1.3 58.5 + - - +
816A LEU* 3.3 6.5 + - - +
817A ARG* 2.9 68.0 + - + +
877A ALA* 3.3 29.9 + - + +
878A ARG* 3.9 20.9 - - + +
917A TRP* 5.2 6.0 - - - -
943A GLU* 3.4 21.3 + - - -
948A GLY* 3.5 18.4 + - - -
949A GLY 3.6 8.5 + - - -
950A ASN* 2.6 26.8 + - - +
951A PRO* 5.2 0.2 - - - +
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Residues in contact with GLY 814 (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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809A TYR 5.6 0.9 - - - -
811A SER* 3.3 13.8 + - - -
813A ARG* 1.3 79.5 - - - +
815A PHE* 1.3 57.2 + - - +
817A ARG* 3.9 6.4 - - - +
818A GLU* 3.1 35.7 + - - +
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Residues in contact with PHE 815 (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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809A TYR* 3.5 53.3 + + + +
811A SER 3.0 18.1 + - - +
812A LEU* 3.7 20.9 - - + +
814A GLY* 1.3 76.9 - - - +
816A LEU* 1.3 67.2 + - + +
818A GLU* 3.5 5.8 + - + +
819A SER* 3.1 20.4 + - - -
846A LEU* 3.9 35.4 - - + -
854A PHE* 4.3 11.7 - + - -
882A VAL* 4.3 9.9 - - + -
886A ARG* 4.4 20.2 - - + -
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Residues in contact with LEU 816 (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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812A LEU* 3.0 50.3 + - + +
813A ARG* 3.3 4.2 + - - +
815A PHE* 1.3 78.5 - - + +
817A ARG* 1.3 63.0 + - - +
819A SER* 3.3 17.0 - - - -
820A ARG* 3.6 4.7 + - - -
846A LEU* 3.8 15.0 - - + -
851A LEU* 4.0 12.6 - - + -
854A PHE* 4.8 3.8 - - + -
877A ALA* 5.2 3.4 - - + -
943A GLU 4.1 0.9 - - - +
944A ILE* 3.7 31.0 - - + +
947A LEU* 3.6 47.0 - - + +
948A GLY* 4.0 11.0 - - - +
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Residues in contact with ARG 817 (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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813A ARG* 2.9 53.8 + - - +
814A GLY* 3.7 6.0 + - - +
816A LEU* 1.3 74.4 - - - +
818A GLU* 1.3 63.6 + - + +
819A SER 3.1 0.2 - - - -
820A ARG* 2.9 57.6 + - - +
821A LYS* 4.7 2.1 - - - +
947A LEU 3.9 12.6 - - - +
948A GLY* 3.2 22.1 + - - +
949A GLY* 5.2 1.0 - - - -
950A ASN* 4.2 13.1 + - - +
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Residues in contact with GLU 818 (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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814A GLY 3.1 25.7 + - - +
815A PHE* 3.9 6.5 - - - +
817A ARG* 1.3 76.3 - - + +
819A SER* 1.3 61.0 + - - +
820A ARG 3.1 1.4 + - - -
821A LYS* 3.4 22.5 + - - +
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Residues in contact with SER 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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815A PHE* 3.1 12.0 + - - -
816A LEU 3.3 13.7 - - - -
817A ARG 3.1 0.6 - - - -
818A GLU* 1.3 78.1 - - - +
820A ARG* 1.3 54.2 + - - +
821A LYS 3.3 7.9 + - - +
845A ALA* 6.2 0.2 - - - -
846A LEU* 3.3 38.0 + - - -
947A LEU* 5.0 6.2 - - - +
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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