Contacts of the helix formed by residues 1004 - 1010 (chain B) in PDB entry 4TU6
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 LYS1004 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002B ILE 3.3 6.6 + - - +
1003B ASP* 1.3 74.9 + - - +
1005B ARG* 1.3 64.2 + - + +
1006B PHE 3.0 1.4 + - - -
1007B ARG* 3.4 17.4 + - - +
1077B ARG* 5.1 4.4 + - - -
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Residues in contact with ARG1005 (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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1003B ASP* 2.9 34.5 + - - +
1004B LYS* 1.3 78.0 - - + +
1006B PHE* 1.3 82.3 + - + +
1007B ARG 3.5 0.8 + - - -
1008B VAL* 4.4 3.5 - - - +
1076B HIS* 6.3 0.2 - - - -
1077B ARG* 3.4 44.2 + - + +
1080B ALA* 3.7 22.3 - - - +
1084B THR* 3.4 25.3 + - - +
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Residues in contact with PHE1006 (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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1000B LEU* 3.4 41.7 - - + +
1003B ASP* 2.9 30.9 + - + -
1005B ARG* 1.3 112.7 - - + +
1007B ARG* 1.3 67.5 + - - +
1008B VAL 3.1 2.9 - - - -
1009B PHE* 2.8 26.7 + + + -
1010B THR* 3.4 11.1 + - - +
1031B LEU* 4.4 8.9 - - + +
1077B ARG 3.4 13.2 - - - -
1080B ALA* 3.7 8.3 - - + -
1081B LEU* 3.3 54.7 - - + -
1084B THR* 4.0 1.6 - - - -
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Residues in contact with ARG1007 (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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1001B ALA 5.4 1.3 - - - -
1003B ASP 3.8 3.4 + - - +
1004B LYS* 3.4 15.5 + - - +
1005B ARG 3.5 0.6 - - - -
1006B PHE* 1.3 76.0 - - - +
1008B VAL* 1.3 56.8 + - - +
1010B THR* 2.6 43.4 + - + +
1011B LYS* 4.3 1.2 + - - +
998C HIS* 3.0 31.8 + - - -
1002C ILE* 3.8 36.4 - - - +
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Residues in contact with VAL1008 (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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1005B ARG 4.4 9.6 + - - +
1006B PHE 3.0 0.2 + - - -
1007B ARG* 1.3 78.1 - - - +
1009B PHE* 1.3 92.7 + - + +
1010B THR 3.4 0.6 + - - -
1011B LYS* 4.2 9.6 + - - +
1013B VAL* 5.9 2.6 - - - +
1074B ILE* 3.9 25.4 - - + -
1077B ARG* 4.6 17.9 - - - +
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Residues in contact with PHE1009 (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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1006B PHE* 2.8 28.1 + + - +
1008B VAL* 1.3 96.2 - - + +
1010B THR* 1.3 57.6 + - - -
1011B LYS 3.4 3.8 - - - -
1030B ASP* 3.5 5.6 - - - +
1031B LEU* 2.9 35.9 + - + +
1056B ILE* 3.9 26.7 - - + -
1060B ALA* 4.1 18.2 - - + -
1074B ILE* 3.9 16.6 - - + -
1077B ARG* 3.7 12.3 - - + -
1078B ALA* 3.6 43.7 - - + -
1081B LEU* 3.8 15.3 - - + -
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Residues in contact with THR1010 (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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1001B ALA* 3.5 39.3 - - + +
1006B PHE 3.6 13.5 - - - +
1007B ARG* 2.6 28.8 + - + +
1009B PHE* 1.3 76.1 - - - +
1011B LYS* 1.3 61.9 + - - +
1030B ASP* 2.9 14.9 - - - +
1031B LEU* 4.1 7.6 - - + -
1032B SER* 3.3 18.0 + - - -
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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