Contacts of the helix formed by residues 145 - 153 (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 HIS 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B ALA 3.6 15.3 - - - -
107B GLU 3.0 27.1 + - - -
109B GLY* 3.5 23.8 + - - -
140B ALA* 3.0 14.2 + - + +
143B ASN* 3.7 16.3 - - + +
144B GLU* 1.3 78.4 + - - +
146B LEU* 1.3 55.7 + - - +
147B GLU* 3.3 8.1 + - - +
148B ILE* 4.1 21.5 - - + -
149B THR* 2.7 35.8 + - - -
176B ILE* 4.1 1.7 - - - +
889B GLN* 3.6 40.9 + - + -
890B ASP* 5.7 0.2 + - - -
893B SER* 4.2 8.5 + - - -
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Residues in contact with LEU 146 (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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144B GLU* 3.8 12.9 + - - +
145B HIS* 1.3 71.7 - - - +
147B GLU* 1.3 73.6 + - + +
149B THR* 3.4 5.0 + - - -
150B GLU* 2.9 42.2 + - + +
175B ARG* 3.5 74.3 - - + +
176B ILE* 4.3 14.3 - - + +
179B ALA* 4.1 15.9 - - + -
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Residues in contact with GLU 147 (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* 3.3 36.5 - - + +
145B HIS* 3.3 5.2 + - - +
146B LEU* 1.3 93.6 + - + +
148B ILE* 1.3 60.1 + - - +
150B GLU* 3.5 8.8 + - - +
151B LEU* 2.9 30.6 + - - +
893B SER* 3.8 9.7 + - - -
897B GLU* 5.2 0.4 - - - +
895C ARG* 3.7 38.1 + - - +
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Residues in contact with ILE 148 (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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105B ALA 3.6 22.4 - - - +
106B ALA* 3.9 16.6 - - - +
109B GLY* 3.7 25.8 - - - -
110B ASN 4.2 1.1 - - - +
111B ILE* 3.8 25.1 - - + +
114B VAL* 4.3 16.6 - - + -
140B ALA* 3.9 10.3 - - + -
145B HIS* 3.7 19.4 + - + -
147B GLU* 1.3 74.6 - - - +
149B THR* 1.3 58.8 + - - +
151B LEU* 3.6 6.9 - - - +
152B LEU* 2.9 48.0 + - + +
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Residues in contact with THR 149 (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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137B LEU* 4.1 19.6 - - + +
140B ALA* 3.8 17.1 + - - +
141B VAL* 4.0 15.9 - - + +
145B HIS 2.7 23.6 + - - -
146B LEU* 3.6 8.1 - - - -
147B GLU 3.3 0.2 - - - -
148B ILE* 1.3 77.9 - - - +
150B GLU* 1.3 56.6 + - - +
152B LEU* 3.3 1.0 + - - +
153B LEU* 2.9 49.1 + - + +
176B ILE* 4.4 11.0 - - + +
179B ALA* 5.2 5.4 - - + -
180B ILE* 4.3 9.4 - - + -
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Residues in contact with GLU 150 (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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146B LEU* 2.9 35.1 + - + +
147B GLU* 4.0 7.3 - - - +
149B THR* 1.3 75.8 - - - +
151B LEU* 1.3 57.5 + - - +
153B LEU* 4.1 9.6 + - + +
154B LYS* 3.3 28.6 + - - +
179B ALA* 4.0 26.8 - - + +
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Residues in contact with LEU 151 (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* 4.3 17.5 - - + +
114B VAL* 3.7 26.0 - - + -
115B ARG* 3.7 37.7 - - + +
118B LEU* 3.5 23.7 - - + +
147B GLU 2.9 17.3 + - - +
148B ILE* 3.6 6.7 - - - +
150B GLU* 1.3 78.7 - - - +
152B LEU* 1.3 61.1 + - - +
154B LYS* 4.0 28.5 + - - +
155B LYS* 5.6 0.9 - - - +
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Residues in contact with LEU 152 (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* 3.9 25.6 - - + -
106B ALA* 5.1 0.7 - - + -
114B VAL* 5.0 3.1 - - + -
118B LEU* 4.1 18.2 - - + -
126B VAL* 4.9 4.0 - - + -
136B ALA* 3.9 35.2 - - + +
137B LEU* 4.2 9.6 - - + +
140B ALA* 4.7 1.6 - - + -
148B ILE* 2.9 37.9 + - + +
149B THR 4.0 2.7 - - - +
151B LEU* 1.3 73.7 - - - +
153B LEU* 1.3 61.8 + - - +
154B LYS 3.1 6.8 + - - -
155B LYS* 3.3 18.9 - - + +
158B LEU* 3.3 38.2 - - + +
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Residues in contact with LEU 153 (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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137B LEU* 4.5 8.7 - - + -
149B THR* 2.9 39.8 + - + +
150B GLU* 4.1 7.2 + - + +
151B LEU 3.5 0.6 - - - -
152B LEU* 1.3 75.4 - - - +
154B LYS* 1.3 57.5 + - + +
155B LYS 3.3 4.0 + - - -
156B GLU 4.7 1.2 + - - -
158B LEU* 4.1 14.8 - - + -
161B VAL* 4.2 21.3 - - + -
179B ALA* 3.5 28.7 - - + +
180B ILE* 3.9 12.6 - - + +
183B HIS* 3.8 42.2 + - + +
184B PRO* 5.7 1.0 - - - +
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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