Contacts of the helix formed by residues 145 - 157 (chain B) in PDB entry 4UT2
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 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B GLU* 2.8 37.2 + - - +
140B CYS* 3.0 15.0 + - - +
141B LYS* 4.5 4.7 - - - +
144B TYR* 1.3 82.1 + - - +
146B ILE* 1.3 66.3 + - - +
147B LYS* 3.2 15.3 + - - +
148B LEU* 2.9 42.5 + - - +
149B TRP 3.5 4.2 + - - -
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Residues in contact with ILE 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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137B TYR* 3.6 43.7 - - + +
141B LYS* 3.5 41.5 - - + +
145B ASN* 1.3 71.6 - - - +
147B LYS* 1.3 65.1 + - + +
149B TRP* 3.2 16.1 + - + +
150B LYS* 3.1 33.4 + - + +
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Residues in contact with LYS 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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32B GLU* 5.2 2.7 - - - +
145B ASN* 3.2 12.7 + - - +
146B ILE* 1.3 78.6 - - - +
148B LEU* 1.3 60.5 + - - +
150B LYS* 3.2 14.2 + - + +
151B THR* 3.1 24.8 + - - -
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Residues in contact with LEU 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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32B GLU* 4.2 17.7 + - + +
35B ILE* 3.9 33.4 - - + -
36B ARG* 4.1 21.8 - - + +
39B CYS* 5.5 0.4 - - - -
101B LEU* 4.8 3.4 - - + -
140B CYS* 5.1 3.4 - - - -
144B TYR* 3.6 41.5 - - + -
145B ASN* 2.9 22.5 + - - +
146B ILE 3.2 0.4 - - - -
147B LYS* 1.3 72.7 - - - +
149B TRP* 1.3 65.8 + - - +
151B THR* 3.1 12.3 + - - -
152B PHE* 3.0 34.3 + - + -
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Residues in contact with TRP 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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128B ALA* 3.6 30.3 - - + -
131B ASN* 2.8 29.4 + - - -
132B ARG* 3.8 25.6 - - + -
136B PHE* 3.7 22.2 - + - -
137B TYR* 3.7 43.8 - + + +
140B CYS* 3.7 24.1 - - + -
145B ASN 3.5 2.6 + - - +
146B ILE* 3.2 18.5 + - + +
148B LEU* 1.3 79.3 - - - +
150B LYS* 1.3 89.9 + - + +
152B PHE* 3.2 7.0 + - - +
153B THR* 3.1 27.1 + - - -
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Residues in contact with LYS 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 ILE* 3.1 28.3 + - + +
147B LYS* 3.5 14.6 - - + +
148B LEU 3.2 0.2 - - - -
149B TRP* 1.3 92.1 - - + +
151B THR* 1.3 62.3 + - - +
153B THR* 3.2 11.2 + - - -
154B ASP* 3.2 21.0 + - - +
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Residues in contact with THR 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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36B ARG* 4.1 30.2 - - + +
39B CYS* 3.6 25.2 - - + +
40B LEU* 4.7 11.7 - - + -
147B LYS 3.1 14.5 + - - -
148B LEU* 3.1 14.2 + - + -
150B LYS* 1.3 74.3 - - - +
152B PHE* 1.3 63.4 + - - +
154B ASP* 3.5 8.3 + - + +
155B CYS* 3.3 19.8 + - - +
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Residues in contact with PHE 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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35B ILE* 3.4 33.7 - - + -
39B CYS* 3.4 20.9 - - - -
101B LEU* 3.8 21.1 - - + -
104B ILE* 3.5 34.3 - - + -
105B CYS* 4.4 2.2 - - - -
108B LEU* 4.0 8.5 - - + -
136B PHE* 3.6 29.2 - + + -
140B CYS* 4.3 3.6 - - - -
148B LEU* 3.0 33.5 + - + -
149B TRP 3.2 7.4 + - - +
151B THR* 1.3 73.6 - - - +
153B THR* 1.3 55.9 + - - +
155B CYS* 3.1 5.2 + - + +
156B PHE* 2.8 56.9 + + + -
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Residues in contact with THR 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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128B ALA* 3.8 35.4 - - + +
131B ASN* 5.0 1.9 + - - -
149B TRP* 3.1 23.8 + - - -
150B LYS* 3.2 15.6 + - - +
152B PHE* 1.3 77.1 - - - +
154B ASP* 1.3 58.0 + - - +
156B PHE* 3.3 9.9 + - - +
157B ASN* 2.9 52.6 + - - +
194B ASP* 4.9 2.9 - - - +
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Residues in contact with ASP 154 (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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40B LEU* 6.1 1.2 - - - +
43B ARG* 2.9 45.6 + - - +
150B LYS 3.2 9.8 + - - +
151B THR* 3.8 11.4 - - + +
153B THR* 1.3 79.4 - - - +
155B CYS* 1.3 63.4 + - - +
157B ASN* 3.7 10.9 + - - +
158B CYS* 3.6 8.7 - - - -
192B PRO* 4.5 6.6 - - - +
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Residues in contact with CYS 155 (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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39B CYS* 3.6 22.7 - - + +
42B SER* 3.3 26.7 - - - -
43B ARG* 4.3 11.2 - - - +
46B PHE* 3.8 20.3 - - - -
108B LEU* 4.2 13.5 - - - -
151B THR 3.3 10.9 + - - +
152B PHE* 3.1 11.5 + - - +
154B ASP* 1.3 76.4 - - - +
156B PHE* 1.3 72.0 + - + +
158B CYS* 3.0 19.8 + - - +
159B LEU* 3.6 3.7 + - - +
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Residues in contact with PHE 156 (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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94B VAL* 4.2 11.9 - - + -
104B ILE* 3.8 35.7 - - + -
108B LEU* 5.6 1.1 - - + -
122B ARG* 3.4 15.6 + - - -
126B GLU* 3.8 43.7 - - + +
127B CSO 4.4 0.9 - - - -
128B ALA 5.9 0.2 - - - -
131B ASN* 3.6 28.3 - - - -
136B PHE* 3.9 24.7 - + - -
152B PHE* 2.8 34.0 + + + +
153B THR* 3.7 8.1 - - + +
155B CYS* 1.3 79.4 - - + +
157B ASN* 1.3 60.3 + - - +
158B CYS 3.0 5.2 + - - -
159B LEU* 3.1 26.1 + - + +
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Residues in contact with ASN 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 2.9 26.2 + - - +
127B CSO 4.4 3.1 + - - -
128B ALA 5.5 0.2 + - - -
153B THR* 2.9 36.1 + - - +
154B ASP* 3.8 11.3 + - - +
155B CYS 3.2 0.4 - - - -
156B PHE* 1.3 75.2 - - - +
158B CYS* 1.3 58.6 + - - +
159B LEU 3.6 0.6 - - - +
191B ARG* 3.9 7.3 - - - +
192B PRO* 3.3 13.0 - - + +
193B THR 3.3 37.2 + - - +
194B ASP* 2.8 28.9 + - - +
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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