Contacts of the helix formed by residues 110 - 118 (chain B) in PDB entry 6UZA
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 ASN 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ALA* 2.9 26.1 + - + +
108B TYR* 3.6 1.6 + - + -
109B GLY* 1.3 72.3 - - - +
111B ILE* 1.3 63.0 + - - +
112B PRO* 3.6 13.2 - - - +
113B VAL* 3.4 30.2 + - - +
114B VAL* 3.2 25.7 + - - +
148B ILE* 4.5 0.4 - - - -
896B TYR* 3.8 42.3 - - + +
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLY* 2.9 11.1 + - - +
110B ASN* 1.3 71.6 - - - +
112B PRO* 1.4 66.0 - - + +
114B VAL* 3.3 3.5 + - - +
115B ARG* 2.9 46.7 + - - +
147B GLU* 3.3 41.5 - - + +
148B ILE* 3.8 22.0 - - + -
151B LEU* 4.3 13.4 - - + +
893B SER* 3.6 16.6 - - - +
896B TYR* 5.0 0.6 - - - +
897B GLU* 3.6 25.1 - - + +
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Residues in contact with PRO 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASN* 3.6 12.1 - - - +
111B ILE* 1.4 91.9 - - + +
113B VAL* 1.3 58.0 + - + +
115B ARG* 3.3 20.7 + - + +
116B LYS* 2.9 29.1 + - - +
896B TYR 4.6 11.9 - - - +
897B GLU* 4.8 5.4 - - - -
900B GLU* 3.4 51.6 - - + +
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Residues in contact with VAL 113 (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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101B ARG* 3.9 20.9 - - - +
105B ALA* 3.8 16.2 - - + -
110B ASN* 3.4 35.6 + - - +
111B ILE 3.3 0.6 - - - -
112B PRO* 1.3 78.4 - - + +
114B VAL* 1.3 57.8 + - - +
116B LYS* 3.8 10.2 - - - +
117B MET* 2.9 51.7 + - + +
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Residues in contact with VAL 114 (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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102B PHE* 4.1 26.6 - - + -
105B ALA* 3.8 28.3 - - + +
106B ALA* 4.1 7.9 - - + +
110B ASN 3.2 16.7 + - - +
111B ILE* 3.7 8.7 - - - +
112B PRO 3.3 0.4 - - - -
113B VAL* 1.3 76.2 - - - +
115B ARG* 1.3 56.6 + - - +
117B MET* 3.8 0.4 - - - -
118B LEU* 2.9 45.5 + - + +
148B ILE* 4.3 19.3 - - + -
151B LEU* 3.7 18.8 - - + -
152B LEU* 5.0 3.8 - - + -
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Residues in contact with ARG 115 (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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111B ILE* 2.9 28.3 + - - +
112B PRO* 3.6 30.9 - - + +
114B VAL* 1.3 77.8 - - - +
116B LYS* 1.3 61.8 + - - +
118B LEU* 4.3 3.7 - - - +
119B GLU* 3.7 20.6 + - - +
151B LEU* 3.7 31.9 - - + -
897B GLU* 4.7 13.1 + - - +
900B GLU* 4.4 8.5 + - - -
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Residues in contact with LYS 116 (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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101B ARG* 3.1 32.3 - - - +
112B PRO 2.9 17.8 + - - +
113B VAL* 3.8 12.2 - - - +
115B ARG* 1.3 77.9 - - - +
117B MET* 1.3 78.0 + - - +
119B GLU* 4.4 0.6 - - - +
120B GLU* 2.9 44.2 + - + +
121B CYS* 5.1 2.6 - - - -
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Residues in contact with MET 117 (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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98B GLU* 3.3 30.7 - - + +
101B ARG* 3.4 28.7 - - - +
102B PHE* 3.7 40.2 - - + +
113B VAL* 2.9 34.1 + - - +
114B VAL 4.4 0.7 - - - +
116B LYS* 1.3 92.1 - - - +
118B LEU* 1.3 59.1 + - - +
119B GLU 3.3 0.4 - - - -
121B CYS* 3.3 40.7 + - - +
124B LEU* 3.5 19.3 - - + +
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Residues in contact with LEU 118 (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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102B PHE* 3.8 21.1 - - + -
114B VAL* 2.9 24.2 + - + +
115B ARG* 4.4 3.4 - - - +
116B LYS 3.2 0.4 - - - -
117B MET* 1.3 77.8 - - - +
119B GLU* 1.3 57.6 + - - +
121B CYS 5.1 2.9 - - - -
124B LEU* 4.9 1.6 - - + -
126B VAL* 3.8 29.2 - - + -
151B LEU* 3.5 42.0 - - + +
152B LEU* 4.1 9.4 - - + -
155B LYS* 3.2 42.1 + - - +
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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