Contacts of the helix formed by residues 102 - 110 (chain B) in PDB entry 3ZUU
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 LEU 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B GLY 3.7 2.4 + - - -
101B GLU* 1.3 71.2 - - - +
103B PHE* 1.3 56.8 + - - +
105B ARG* 3.3 2.3 + - - +
106B ILE* 3.0 32.7 + - + +
112B PHE* 4.0 25.8 - - + -
120B PHE* 4.2 15.7 - - + -
146B THR* 3.0 36.6 + - + +
148B LEU* 3.9 33.2 - - + +
156B LEU* 4.2 7.6 - - + -
206B THR* 4.0 25.4 - - + -
210B MET* 4.4 12.8 - - + -
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Residues in contact with PHE 103 (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 GLU* 3.1 18.0 - - + +
102B LEU* 1.3 77.1 - - - +
104B GLU* 1.3 71.7 + - - +
106B ILE* 3.2 13.4 + - + +
107B CYS* 3.0 53.3 + - - -
144B GLU 6.0 2.0 - - - +
145B ASN* 5.0 4.9 - - - +
146B THR 4.7 0.6 + - - -
209B VAL* 4.2 20.4 - - + -
213B GLY 5.5 4.3 - - - -
214B ALA* 6.1 0.9 - - - -
215B TYR* 3.6 40.6 - + - +
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Residues in contact with GLU 104 (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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104A GLU* 5.5 14.0 - - - +
100B GLY* 5.9 0.7 - - - -
101B GLU* 3.0 32.9 + - + +
103B PHE* 1.3 92.8 - - - +
105B ARG* 1.3 58.0 + - - +
107B CYS* 3.3 11.1 + - - +
108B ASN* 2.9 48.1 + - - +
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Residues in contact with ARG 105 (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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150A GLY 5.7 2.8 + - - -
101B GLU 3.4 2.0 + - - -
102B LEU* 3.3 10.0 + - - +
103B PHE 3.2 0.2 - - - -
104B GLU* 1.3 76.2 - - - +
106B ILE* 1.3 64.9 + - - +
108B ASN* 3.4 11.2 + - + +
109B ALA* 3.0 22.4 + - + +
112B PHE* 3.7 13.0 - - + -
116B GLU* 3.3 28.1 + - - -
120B PHE* 3.8 13.9 - - - -
148B LEU* 3.6 29.6 - - + +
154B PRO* 3.6 30.1 - - - +
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Residues in contact with ILE 106 (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 LEU* 3.0 22.6 + - + +
103B PHE* 3.2 17.0 + - + +
105B ARG* 1.3 77.2 - - - +
107B CYS* 1.3 59.0 + - - +
109B ALA* 2.9 5.9 + - - +
110B GLY 2.9 27.4 + - - +
111B ARG* 4.7 2.0 - - - -
112B PHE* 3.7 23.1 - - + -
209B VAL* 3.7 35.2 - - + +
210B MET* 3.5 40.2 - - + +
213B GLY* 3.9 17.9 - - - +
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Residues in contact with CYS 107 (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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27A ILE* 5.5 5.2 - - - +
37A LEU* 5.0 1.6 - - - +
96A TYR* 4.0 5.2 + - - -
103B PHE* 3.0 49.5 + - - +
104B GLU* 3.6 16.2 - - - +
106B ILE* 1.3 76.8 - - - +
108B ASN* 1.3 65.2 + - - +
110B GLY* 3.2 12.6 + - - +
213B GLY 5.5 6.1 - - - -
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Residues in contact with ASN 108 (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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96A TYR* 2.6 37.3 + - - -
98A SER* 3.2 21.8 - - - +
99A GLY* 3.7 7.1 + - - -
100A GLY* 3.6 32.9 - - - +
104B GLU* 2.9 34.4 + - - +
105B ARG* 3.6 10.3 - - + +
107B CYS* 1.3 77.4 - - - +
109B ALA* 1.3 56.7 + - - +
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Residues in contact with ALA 109 (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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24A VAL* 3.8 11.4 - - - +
37A LEU* 4.2 2.8 - - - +
46A LEU* 4.0 14.8 - - + +
98A SER* 5.0 7.2 - - - -
105B ARG* 3.0 16.8 + - + +
106B ILE 2.9 6.9 + - - +
108B ASN* 1.3 76.1 - - - +
110B GLY* 1.3 56.2 + - - +
111B ARG 3.0 26.0 + - - +
112B PHE* 3.6 17.9 - - + -
116B GLU* 5.7 1.1 - - - +
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Residues in contact with GLY 110 (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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24A VAL* 4.1 0.9 - - - -
25A LYS* 3.9 26.5 + - - +
27A ILE* 5.6 0.9 - - - -
37A LEU* 3.8 18.5 - - - +
106B ILE* 2.9 11.5 + - - +
107B CYS* 3.2 12.8 + - - -
108B ASN 3.4 0.8 + - - -
109B ALA* 1.3 74.7 - - - +
111B ARG* 1.3 60.4 + - - +
213B GLY* 3.3 19.6 - - - +
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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