Contacts of the helix formed by residues 3928 - 3939 (chain B) in PDB entry 5NUG
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 THR3928 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3924B ILE* 5.1 7.0 - - - -
3926B GLY 4.8 3.6 - - - +
3927B LEU* 1.3 77.8 - - - +
3929B VAL* 1.3 55.6 + - - +
3930B GLU* 3.8 9.8 + - - +
3931B GLN* 3.2 33.4 + - - +
3932B ALA* 2.7 35.3 + - - +
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Residues in contact with VAL3929 (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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3921B THR* 5.9 2.7 - - + -
3924B ILE* 4.6 19.5 - - + -
3928B THR* 1.3 74.2 - - - +
3930B GLU* 1.3 63.8 + - + +
3932B ALA* 4.4 4.2 - - - +
3933B GLU* 3.3 24.1 + - + +
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Residues in contact with GLU3930 (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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3928B THR* 3.3 8.4 + - - +
3929B VAL* 1.3 81.1 - - + +
3931B GLN* 1.3 64.1 + - + +
3933B GLU* 3.6 14.0 + - - +
3934B ALA* 4.2 3.8 + - - +
3995B ALA 4.8 2.1 - - - +
3998B PRO* 6.1 1.2 - - - +
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Residues in contact with GLN3931 (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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3926B GLY 4.5 3.6 + - - -
3927B LEU* 3.8 26.4 - - + +
3928B THR* 3.2 37.1 + - - +
3930B GLU* 1.3 77.5 - - + +
3932B ALA* 1.3 63.5 + - - +
3933B GLU 3.4 0.5 + - - -
3934B ALA* 3.5 9.5 + - - +
3935B VAL* 3.5 14.7 + - - +
3961B LEU* 4.0 21.1 + - - +
3995B ALA 3.8 17.5 - - - +
3996B PHE* 3.0 30.6 - - - +
3997B ARG* 5.2 2.3 + - - -
3998B PRO* 5.4 3.2 - - + +
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Residues in contact with ALA3932 (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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3921B THR* 6.3 0.9 - - + -
3922B PRO* 4.0 24.1 - - + +
3923B ARG 4.8 4.3 - - - +
3924B ILE* 5.4 4.7 - - + -
3927B LEU* 4.3 18.1 - - + +
3928B THR 2.7 23.5 + - - +
3929B VAL* 4.4 4.0 - - - +
3931B GLN* 1.3 70.8 - - - +
3933B GLU* 1.3 63.4 + - - +
3934B ALA 3.2 0.2 - - - -
3935B VAL* 3.3 24.0 + - - +
3936B VAL* 3.7 13.0 + - - +
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Residues in contact with GLU3933 (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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3916B LEU* 5.9 3.1 - - - +
3922B PRO* 6.0 0.2 - - - -
3929B VAL* 3.3 20.0 + - + +
3930B GLU* 3.6 9.6 - - - +
3931B GLN 3.3 0.6 - - - -
3932B ALA* 1.3 76.8 - - - +
3934B ALA* 1.3 58.3 + - - +
3935B VAL 3.5 0.4 + - - -
3936B VAL* 4.1 7.1 + - - +
3937B ARG* 4.1 11.8 + - - +
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Residues in contact with ALA3934 (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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3930B GLU 4.2 3.1 + - - +
3931B GLN 3.5 6.2 + - - +
3932B ALA 3.2 0.4 - - - -
3933B GLU* 1.3 74.8 - - - +
3935B VAL* 1.3 53.8 + - - +
3936B VAL 3.3 2.2 - - - -
3937B ARG* 3.2 10.6 + - + +
3938B LEU* 2.8 35.0 + - - +
3994B GLN 5.1 0.4 - - - +
3995B ALA* 3.4 36.1 - - + +
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Residues in contact with VAL3935 (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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3922B PRO* 5.0 5.8 - - + -
3927B LEU* 4.1 23.1 - - + -
3931B GLN 3.5 16.2 - - - +
3932B ALA* 3.3 11.1 + - + +
3934B ALA* 1.3 74.5 - - - +
3936B VAL* 1.3 59.2 + - - +
3938B LEU* 4.4 0.7 - - - -
3939B SER* 2.9 28.6 + - - -
3947B LEU* 3.5 22.2 - - + +
3948B ILE* 3.8 27.6 - - + +
3995B ALA* 4.9 1.1 - - + -
3996B PHE* 3.8 30.5 - - + -
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Residues in contact with VAL3936 (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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3916B LEU* 5.1 14.8 - - + -
3917B SER* 5.5 3.4 - - - +
3920B SER* 3.6 28.0 - - - +
3922B PRO* 3.4 34.1 - - + -
3932B ALA 3.7 4.4 + - - +
3933B GLU* 4.3 8.3 - - - +
3934B ALA 3.3 0.4 - - - -
3935B VAL* 1.3 77.6 - - - +
3937B ARG* 1.3 60.5 + - - +
3939B SER* 2.7 19.6 + - - +
3940B CYS* 3.4 13.8 - - - -
3948B ILE* 5.6 3.6 - - + -
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Residues in contact with ARG3937 (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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3907B HIS* 3.3 22.4 - - + +
3911B GLY 4.2 3.4 - - - +
3912B ASN* 5.8 2.5 - - - +
3914B ILE* 3.5 31.6 - - + -
3933B GLU 4.1 4.3 + - - +
3934B ALA* 3.2 18.8 + - + +
3936B VAL* 1.3 78.9 - - - +
3938B LEU* 1.3 60.9 + - - +
3940B CYS* 3.2 25.7 + - - +
3941B LEU* 4.4 0.7 + - - +
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Residues in contact with LEU3938 (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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3907B HIS* 3.9 14.1 - - + +
3934B ALA 2.8 20.4 + - - +
3937B ARG* 1.3 72.8 - - - +
3939B SER* 1.3 60.6 + - - +
3940B CYS 3.2 1.0 + - - -
3941B LEU* 3.5 30.5 + - + +
3944B PHE* 3.1 26.1 - - + +
3947B LEU* 3.6 31.2 - - + -
3991B LEU* 4.1 35.2 - - + +
3992B LEU* 4.4 16.6 - - + -
3995B ALA* 4.3 15.3 - - + -
3996B PHE* 5.0 2.0 - - + -
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Residues in contact with SER3939 (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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3935B VAL 2.9 15.5 + - - -
3936B VAL* 2.7 27.5 + - - +
3938B LEU* 1.3 75.4 - - - +
3940B CYS* 1.3 60.9 + - - +
3941B LEU 3.3 4.1 + - - +
3944B PHE 3.4 15.1 - - - +
3945B LYS* 4.0 19.9 - - - +
3947B LEU* 3.8 7.8 - - - +
3948B ILE* 4.6 17.1 - - - +
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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