Contacts of the helix formed by residues 737 - 745 (chain C) in PDB entry 3V53
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 HIS 737 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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736C LYS* 1.3 89.9 + - - +
738C ILE* 1.3 61.1 + - - +
739C LYS* 3.6 1.8 - - - -
740C SER* 4.4 17.2 - - - +
741C LEU* 3.9 25.1 + - - +
839C ILE* 5.4 12.3 - - + -
789D THR* 5.2 4.3 - - - -
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Residues in contact with ILE 738 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736C LYS* 2.8 38.5 + - + +
737C HIS* 1.3 72.1 - - - +
739C LYS* 1.3 67.6 + - - +
740C SER 3.4 0.4 - - - -
741C LEU* 3.3 13.6 + - + +
742C ILE* 3.0 25.1 + - + +
832C TYR* 4.1 12.6 - - - +
783D ILE* 4.2 20.6 - - + -
787D GLU* 4.8 6.5 - - + -
789D THR* 4.4 3.7 + - - +
790D LEU* 4.0 19.5 - - + -
814D VAL* 3.6 45.5 - - + -
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Residues in contact with LYS 739 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737C HIS* 4.6 0.2 - - - +
738C ILE* 1.3 80.0 - - - +
740C SER* 1.3 64.6 + - - +
742C ILE* 3.1 19.3 + - - +
743C GLU* 2.9 46.8 + - - +
789D THR* 3.4 44.0 + - + +
790D LEU* 5.3 2.2 - - - +
792D ASP* 5.0 3.8 - - + -
793D PHE* 3.7 38.5 - - + +
796D SER* 5.7 3.1 - - - -
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Residues in contact with SER 740 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737C HIS* 4.4 21.0 - - - +
738C ILE 3.4 0.4 - - - -
739C LYS* 1.3 78.4 - - - +
741C LEU* 1.3 61.6 + - - +
743C GLU* 3.4 15.3 + - - +
744C LYS* 3.2 36.5 + - - +
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Residues in contact with LEU 741 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736C LYS* 6.5 1.3 - - + -
737C HIS 3.9 16.2 + - - +
738C ILE* 3.3 11.9 + - + +
739C LYS 3.2 1.0 + - - -
740C SER* 1.3 74.4 - - - +
742C ILE* 1.3 66.0 + - - +
744C LYS* 3.2 24.0 + - + +
745C ILE* 3.3 19.2 - - + +
832C TYR* 3.4 55.2 - - + +
835C GLU* 3.7 23.3 - - + +
836C ALA* 3.8 26.0 - - + +
839C ILE* 5.2 6.7 - - + -
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Residues in contact with ILE 742 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738C ILE* 3.0 28.6 + - + +
739C LYS* 3.1 10.1 + - - +
741C LEU* 1.3 77.9 - - - +
743C GLU* 1.3 59.2 + - - +
745C ILE* 3.1 34.7 + - - +
828C ARG* 4.2 2.6 + - - -
832C TYR* 4.1 11.2 - - + -
790D LEU* 5.1 5.2 - - + -
793D PHE* 3.5 35.7 - - + -
810D ASP* 3.5 38.6 - - + +
811D VAL* 5.9 0.2 - - - -
813D MET* 5.2 3.6 - - + -
814D VAL* 3.6 28.9 - - + -
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Residues in contact with GLU 743 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739C LYS* 2.9 46.6 + - - +
740C SER* 3.7 19.5 - - - +
741C LEU 3.2 0.4 - - - -
742C ILE* 1.3 75.1 - - + +
744C LYS* 1.3 63.3 + - - +
745C ILE 3.3 3.6 - - - +
793D PHE* 4.2 18.0 - - + -
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Residues in contact with LYS 744 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740C SER* 3.2 25.2 + - - +
741C LEU* 3.4 20.5 - - + +
743C GLU* 1.3 80.2 - - - +
745C ILE* 1.3 61.3 + - + +
746C PRO* 3.3 10.0 - - - +
755C TYR* 4.2 22.6 - - + +
831C ILE* 5.9 0.7 - - + -
835C GLU* 5.1 19.1 + - + +
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Residues in contact with ILE 745 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741C LEU* 3.3 19.3 - - + +
742C ILE* 3.1 15.4 + - - +
743C GLU 4.3 3.7 - - - +
744C LYS* 1.3 77.8 - - + +
746C PRO* 1.3 73.0 - - + +
747C THR* 3.8 3.3 + - - +
752C LEU* 4.1 2.5 - - + -
828C ARG* 3.1 55.2 + - + +
831C ILE* 4.0 21.1 - - + -
832C TYR* 3.5 39.7 - - + +
813D MET* 3.7 14.8 - - - -
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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