Contacts of the helix formed by residues 106 - 111 (chain K) in PDB entry 6T9L
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 ILE 106 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3K ILE* 4.1 19.7 - - + -
7K ILE* 3.8 14.1 - - + -
11K PHE* 3.8 28.9 - - + -
103K ILE* 3.8 19.9 - - + +
104K GLY* 3.7 1.2 - - - -
105K ASN* 1.3 90.6 - - - +
107K ASP* 1.3 62.0 + - - +
108K LEU* 3.3 27.8 + - + +
109K ILE* 3.3 25.3 - - + +
110K ASN* 2.9 21.9 + - - +
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Residues in contact with ASP 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105K ASN 4.1 1.6 + - - -
106K ILE* 1.3 70.8 - - - +
108K LEU* 1.3 68.3 + - - +
109K ILE 3.5 0.2 - - - -
110K ASN* 3.7 13.3 - - + +
111K ASP* 2.9 25.8 + - + +
118K TRP* 3.1 33.6 - - + -
127K VAL* 5.3 4.5 - - - +
37M LEU* 6.0 2.8 - - + +
41M ARG* 4.7 16.2 + - - +
76N ARG* 4.4 14.8 + - - +
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Residues in contact with LEU 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K PHE* 4.3 19.7 - - + -
17K LYS* 4.0 22.0 - - + +
21K LEU* 3.9 33.0 - - + -
106K ILE* 3.1 12.6 - - + -
107K ASP* 1.3 82.0 + - - +
109K ILE* 1.3 60.0 + - + +
111K ASP 3.2 4.0 - - - -
112K ALA* 3.1 26.7 + - - +
115K ALA* 5.0 4.9 - - + -
118K TRP* 3.6 50.9 - - + +
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Residues in contact with ILE 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ILE* 5.6 2.9 - - + -
11K PHE* 4.7 13.7 - - + -
21K LEU* 4.2 15.9 - - + -
24K CYS* 5.4 4.7 - - - -
28K ARG* 3.3 26.5 + - - +
94K LEU* 4.6 27.1 - - + +
103K ILE* 3.4 45.8 - - + +
106K ILE* 3.3 23.5 - - + +
108K LEU* 1.3 76.4 - - + +
110K ASN* 1.3 70.4 + - - +
111K ASP 3.5 0.2 + - - -
112K ALA* 3.5 15.2 + - - +
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Residues in contact with ASN 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K ARG* 4.0 17.7 + - - +
93K LEU* 5.4 7.3 - - - +
103K ILE 4.6 4.2 - - - +
104K GLY* 4.8 12.1 + - - -
105K ASN 5.2 0.4 - - - -
106K ILE 2.9 29.3 + - - +
107K ASP* 3.5 9.4 + - + +
108K LEU 3.2 0.8 - - - -
109K ILE* 1.3 89.3 - - - +
111K ASP* 1.3 56.9 + - + +
112K ALA 3.5 1.0 + - - -
113K ILE* 5.7 1.4 - - - +
37M LEU* 4.9 15.0 - - - +
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Residues in contact with ASP 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K ASP* 2.9 17.8 + - + +
108K LEU 3.2 5.6 - - - +
110K ASN* 1.3 77.5 - - + +
112K ALA* 1.3 61.4 + - - +
113K ILE* 3.1 15.4 - - - +
114K LEU* 3.3 35.5 + - - +
115K ALA* 3.8 0.3 + - - -
118K TRP* 3.5 24.1 - - + -
121K VAL* 4.8 7.4 - - - +
76N ARG* 5.4 2.8 - - - -
87N LEU* 3.5 33.2 - - + +
90N ILE* 5.2 0.9 - - - +
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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