Contacts of the helix formed by residues 812 - 822 (chain B) in PDB entry 3T1N
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 812 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797B ILE* 3.7 9.3 - - - +
798B GLY 4.3 1.3 - - - +
811B LEU* 1.3 77.5 - - - +
813B GLU* 1.3 67.4 + - - +
814B LYS* 3.7 13.0 + - - +
815B TRP* 3.2 17.7 + - - +
816B VAL 4.2 0.5 + - - -
831B TYR* 2.7 32.2 + - - +
832B LEU 5.4 0.2 - - - -
833B LEU* 3.1 31.2 - - - -
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Residues in contact with GLU 813 (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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768B SER* 3.2 6.1 - - - -
769B SER* 3.1 45.2 + - - +
770B PRO* 4.4 5.8 - - + -
775B LEU* 3.6 26.7 - - + -
797B ILE* 3.7 10.2 - - + +
798B GLY* 3.0 25.5 - - - -
799B PRO* 3.5 4.4 - - - +
812B SER* 1.3 77.1 - - - +
814B LYS* 1.3 64.5 + - - +
816B VAL* 2.8 19.6 + - - +
817B LEU* 3.3 15.5 + - + +
833B LEU* 4.9 5.4 - - - +
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Residues in contact with LYS 814 (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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693B ARG* 4.1 13.9 - - - +
812B SER* 3.2 9.1 + - - +
813B GLU* 1.3 78.1 - - - +
815B TRP* 1.3 57.9 + - - +
817B LEU* 3.1 12.8 + - + +
818B ASP* 2.8 71.6 + - - +
831B TYR* 3.6 12.3 - - + -
824D PHE* 5.0 4.0 + - - +
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Residues in contact with TRP 815 (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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756B PHE* 4.6 9.9 - + - -
759B GLN* 4.0 20.9 - - - -
762B MET* 4.0 29.6 - - + -
795B ILE* 4.1 11.7 - - + -
797B ILE* 4.6 5.2 - - + -
811B LEU* 3.8 20.4 - - + -
812B SER 3.2 14.7 + - - +
813B GLU 3.0 0.4 - - - -
814B LYS* 1.3 76.3 - - - +
816B VAL* 1.3 80.0 + - + +
818B ASP* 4.4 0.7 - - - +
819B SER* 2.7 39.1 + - - -
825B VAL* 3.8 20.9 - - + -
826B CYS* 3.3 26.8 + - + +
828B PRO* 3.7 25.7 - - + +
831B TYR* 3.2 49.1 - + + -
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Residues in contact with VAL 816 (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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756B PHE* 4.2 16.3 - - + -
762B MET* 5.2 1.1 - - - -
764B VAL* 6.5 0.2 - - + -
775B LEU* 3.8 30.1 - - + -
778B LEU* 4.8 2.9 - - + -
779B VAL* 4.3 17.5 - - + -
797B ILE* 4.2 20.4 - - + -
813B GLU 2.8 11.0 + - - +
815B TRP* 1.3 98.8 - - + +
817B LEU* 1.3 64.2 + - + +
819B SER* 3.8 1.7 - - - -
820B ILE* 3.0 48.5 + - + +
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Residues in contact with LEU 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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693B ARG* 3.7 19.5 - - - +
698B LEU* 4.4 18.1 - - + +
770B PRO* 4.7 21.3 - - + -
775B LEU* 5.3 2.7 - - + -
778B LEU* 4.4 23.1 - - + -
813B GLU* 3.5 13.7 - - + +
814B LYS* 3.1 17.2 + - - +
816B VAL* 1.3 79.3 - - + +
818B ASP* 1.3 59.7 + - - +
820B ILE* 3.1 9.6 + - - +
821B THR* 3.0 29.6 + - - -
824D PHE* 3.1 39.0 - - + +
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Residues in contact with ASP 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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693B ARG* 3.0 32.7 + - - +
814B LYS* 2.8 48.7 + - - +
815B TRP 4.4 0.2 - - - +
817B LEU* 1.3 71.0 - - - +
819B SER* 1.3 53.3 + - - +
821B THR* 3.7 2.1 - - - -
822B GLN* 2.8 46.5 + - - +
826B CYS* 4.0 10.1 - - - -
831B TYR* 2.7 29.9 + - + +
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Residues in contact with SER 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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755B LEU* 3.4 5.9 - - - +
756B PHE* 4.2 20.4 - - - -
815B TRP* 2.7 29.3 + - - -
816B VAL 3.8 4.3 - - - -
817B LEU 3.2 0.6 - - - -
818B ASP* 1.3 78.3 - - - +
820B ILE* 1.3 58.4 + - - +
823B HIS* 2.9 23.0 + - - -
824B LYS 3.0 25.0 + - - -
825B VAL* 3.9 3.3 - - - -
826B CYS* 3.3 25.4 + - - +
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Residues in contact with ILE 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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698B LEU* 4.4 17.9 - - + +
701B ILE* 4.0 24.8 - - + +
702B ALA* 4.8 2.5 - - + +
736B ALA* 3.2 17.3 - - - +
755B LEU* 3.9 7.3 - - + +
756B PHE* 4.3 9.6 - - + -
778B LEU* 4.2 27.8 - - + -
782B CYS* 4.1 24.9 - - - -
816B VAL* 3.0 37.4 + - + +
817B LEU* 3.1 9.3 + - - +
819B SER* 1.3 78.3 - - - +
821B THR* 1.3 63.0 + - - +
823B HIS* 3.3 8.0 + - - -
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Residues in contact with THR 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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693B ARG* 3.4 38.7 + - - +
698B LEU* 4.1 6.8 - - - +
701B ILE* 4.6 9.2 - - + +
733B HIS 5.4 1.3 - - - +
734B PHE* 5.2 8.8 - - + -
735B PRO* 3.8 21.7 - - + +
736B ALA* 3.2 27.2 + - - +
817B LEU 3.0 13.2 + - - -
818B ASP* 3.8 4.0 - - - -
820B ILE* 1.3 77.4 - - - +
822B GLN* 1.3 64.2 + - + +
823B HIS 3.2 0.4 - - - -
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Residues in contact with GLN 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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735B PRO* 5.4 6.9 - - + +
736B ALA* 5.5 0.2 - - - -
739B LEU* 5.6 0.5 - - - +
818B ASP* 2.8 27.1 + - + +
819B SER 4.4 0.7 - - - +
821B THR* 1.3 77.6 - - + +
823B HIS* 1.3 71.3 + - - +
824B LYS* 3.1 45.2 + - + +
826B CYS* 3.5 23.2 - - - -
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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