Contacts of the helix formed by residues 811 - 819 (chain J) in PDB entry 1CQT
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 811 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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553B LEU 4.0 3.4 - - - +
554B ASN* 3.7 30.3 - - - +
555B LEU 3.7 10.3 - - - +
808J VAL* 3.1 22.9 - - + +
810J GLU* 1.3 83.5 - - - +
812J VAL* 1.3 60.6 + - - +
813J LYS* 4.2 4.5 - - + +
814J GLU* 2.9 39.7 + - + +
815J LEU* 2.9 14.0 - - - +
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Residues in contact with VAL 812 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B GLU* 6.6 0.2 - - - -
509B LEU* 4.2 18.8 - - + -
553B LEU* 3.4 21.2 + - + +
555B LEU 2.9 28.5 + - - +
556B SER 3.6 15.7 - - - +
557B PHE* 3.9 12.1 - - + -
560B MET* 3.7 30.7 - - + -
811J PRO* 1.3 72.0 - - - +
813J LYS* 1.3 60.2 + - - +
815J LEU* 3.5 8.0 + - + +
816J LEU* 3.1 36.8 + - + +
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Residues in contact with LYS 813 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B ALA* 3.8 18.7 + - - +
553B LEU* 2.9 28.1 + - + +
554B ASN* 4.2 10.8 - - - +
811J PRO* 3.1 6.0 - - + -
812J VAL* 1.3 77.5 - - - +
814J GLU* 1.3 61.0 + - - +
816J LEU* 3.4 8.5 - - + +
817J ARG* 3.2 22.6 + - + +
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Residues in contact with GLU 814 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810J GLU* 4.4 2.5 - - - -
811J PRO* 2.9 35.6 + - + +
813J LYS* 1.3 79.2 - - - +
815J LEU* 1.3 65.3 + - + +
817J ARG* 3.1 43.5 + - - +
818J ARG* 3.0 67.7 + - - +
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Residues in contact with LEU 815 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B PHE* 5.1 12.8 - - + -
810J GLU* 3.6 32.5 - - + +
811J PRO 2.9 30.7 + - - +
812J VAL* 3.5 12.1 + - + +
813J LYS 3.4 0.2 - - - -
814J GLU* 1.3 74.4 - - - +
816J LEU* 1.3 65.6 + - + +
817J ARG 2.9 9.1 + - - -
818J ARG* 3.4 22.5 + - - +
819J LYS* 3.1 31.2 + - + +
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Residues in contact with LEU 816 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B LEU 5.3 2.9 - - - +
507B GLU* 4.4 24.9 - - + +
510B GLU* 3.5 47.8 - - + +
553B LEU* 4.2 9.9 - - + -
812J VAL* 3.1 28.3 + - + +
813J LYS* 3.4 8.7 - - - +
814J GLU 3.2 0.2 - - - -
815J LEU* 1.3 81.9 - - + +
817J ARG* 1.3 55.6 + - - +
819J LYS* 4.5 10.5 - - + -
820J ARG* 3.2 45.6 + - - +
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Residues in contact with ARG 817 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813J LYS* 3.2 12.3 + - + +
814J GLU* 3.2 43.5 + - - +
815J LEU 2.9 0.4 - - - -
816J LEU* 1.3 78.9 - - - +
818J ARG* 1.3 62.0 + - - +
819J LYS 3.1 0.9 - - - -
820J ARG* 3.2 2.8 + - - -
821J GLY 2.7 49.7 + - - +
822J HIS* 4.1 24.5 + - + -
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Residues in contact with ARG 818 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810J GLU* 3.5 36.2 + - - +
814J GLU* 3.0 52.7 + - - +
815J LEU* 4.1 16.6 - - - +
817J ARG* 1.3 82.4 - - - +
819J LYS* 1.3 62.9 + - - +
821J GLY* 3.9 7.9 + - - +
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Residues in contact with LYS 819 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B GLU* 5.8 4.7 - - - +
815J LEU* 3.1 23.9 + - + +
816J LEU* 4.5 7.4 - - + -
818J ARG* 1.3 78.5 - - - +
820J ARG* 1.3 68.8 + - + +
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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