Contacts of the helix formed by residues 138 - 151 (chain B) in PDB entry 3UXA
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 THR 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A GLU* 4.1 14.7 + - - +
2B PRO 4.1 16.2 - - - +
3B ARG* 4.1 11.7 - - + +
137B LEU* 1.3 77.5 - - - +
139B GLU* 1.3 64.9 + - - +
140B ARG* 3.0 9.2 + - - +
141B GLU* 2.8 50.6 + - + +
142B LEU* 3.0 19.5 + - - +
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Residues in contact with GLU 139 (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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212A GLY 5.4 6.5 - - - +
213A ILE 5.3 1.0 - - - +
214A SER* 3.5 31.4 - - - +
235A SER* 4.9 8.8 - - - -
3B ARG* 5.7 0.6 - - - +
137B LEU 3.7 1.0 + - - -
138B THR* 1.3 73.3 - - - +
140B ARG* 1.3 61.2 + - - +
142B LEU* 3.5 7.4 - - - +
143B GLU* 3.1 24.8 + - - +
168B ILE* 4.5 35.2 - - + +
171B ARG* 3.0 43.1 + - + +
172B ILE* 4.9 4.9 - - + +
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LYS* 5.0 7.8 - - + +
212A GLY 5.9 1.1 - - - -
214A SER* 4.0 6.6 + - - +
215A GLU* 3.3 34.8 + - - +
217A ASN* 3.6 22.6 - - - +
218A GLU* 3.5 36.8 + - + +
221A GLU* 3.2 32.9 + - - +
138B THR* 3.0 8.0 + - - +
139B GLU* 1.3 76.1 - - - +
141B GLU* 1.3 57.6 + - + +
143B GLU* 3.0 7.4 + - - +
144B SER* 2.8 39.9 + - - -
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Residues in contact with GLU 141 (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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2B PRO* 2.5 42.9 - - - +
114B VAL 5.2 4.7 - - - +
137B LEU* 3.4 18.4 - - + -
138B THR* 2.8 45.8 + - + +
140B ARG* 1.3 74.1 - - + +
142B LEU* 1.3 57.3 + - - +
144B SER* 3.1 8.2 + - - -
145B LEU* 2.9 38.5 + - + +
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Residues in contact with LEU 142 (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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132B LEU* 3.9 33.3 - - + +
134B VAL* 4.1 19.7 - - + -
137B LEU* 3.7 23.6 - - + +
138B THR 3.0 17.4 + - - +
139B GLU* 3.5 5.6 - - - +
141B GLU* 1.3 76.9 - - - +
143B GLU* 1.3 60.2 + - - +
145B LEU 3.7 0.2 + - - -
146B LEU* 3.2 22.0 + - - +
158B ILE* 4.7 4.7 - - + -
168B ILE* 3.5 32.3 - - + -
172B ILE* 3.5 30.1 - - + -
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Residues in contact with GLU 143 (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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189A ILE* 3.1 53.3 - - + +
191A LYS* 3.3 24.1 - - - +
212A GLY* 5.7 2.7 - - - +
139B GLU* 3.1 14.3 + - + +
140B ARG* 3.0 7.1 + - - +
142B LEU* 1.3 78.7 - - - +
144B SER* 1.3 62.9 + - - +
146B LEU* 3.7 9.0 + - + +
147B GLU* 3.1 38.8 + - - +
172B ILE* 4.5 21.5 - - + -
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Residues in contact with SER 144 (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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116B GLU* 4.5 11.0 + - - +
140B ARG* 2.8 20.4 + - - -
141B GLU* 3.1 9.2 + - - -
143B GLU* 1.3 83.3 + - - +
145B LEU* 1.3 63.5 + - - +
147B GLU* 3.4 6.7 + - - +
148B TYR* 3.1 26.0 + - - +
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Residues in contact with LEU 145 (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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113B ILE* 4.6 3.1 - - + +
114B VAL* 4.0 18.6 - - - +
115B LYS* 3.5 6.1 - - - +
116B GLU* 3.3 44.9 - - + +
119B ILE* 3.3 25.3 - - + +
132B LEU* 4.2 13.9 - - + -
137B LEU* 3.8 30.5 - - + -
141B GLU* 2.9 21.4 + - + +
142B LEU 4.5 0.7 - - - +
144B SER* 1.3 77.1 - - - +
146B LEU* 1.3 61.5 + - - +
148B TYR* 3.2 1.7 + - - -
149B ALA* 2.9 26.7 + - - +
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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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132B LEU* 3.8 11.5 - - + +
142B LEU 3.2 19.2 + - - +
143B GLU* 3.8 9.2 - - - +
144B SER 3.2 0.2 - - - -
145B LEU* 1.3 78.0 - - - +
147B GLU* 1.3 64.7 + - - +
149B ALA* 3.3 2.6 + - - +
150B ARG* 3.0 55.9 + - - +
155B GLU* 4.6 1.6 - - - +
156B PRO* 3.7 30.7 - - + +
158B ILE* 4.7 9.0 - - + -
172B ILE* 3.8 48.0 - - + +
173B GLY 5.5 0.4 - - - +
174B ALA* 5.6 1.8 - - - +
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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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189A ILE 3.8 13.5 - - - +
190A ASN* 3.5 16.8 + - - +
191A LYS* 2.7 28.8 + - - +
192A GLU* 3.2 34.8 + - - +
195A ARG* 4.8 2.4 + - - -
143B GLU* 3.1 37.2 + - - +
144B SER* 3.6 7.6 - - - +
145B LEU 3.3 0.2 - - - -
146B LEU* 1.3 76.0 - - - +
148B TYR* 1.3 58.6 + - - +
150B ARG* 3.2 12.4 + - + +
151B SER* 3.1 25.0 + - - -
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Residues in contact with TYR 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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116B GLU* 3.6 52.1 - - + +
119B ILE* 3.7 18.2 - - + -
120B ASP* 2.6 35.9 + - - -
144B SER 3.1 16.6 + - - +
145B LEU* 3.6 7.4 - - - +
146B LEU 3.2 0.2 - - - -
147B GLU* 1.3 73.7 - - - +
149B ALA* 1.3 62.9 + - - +
151B SER* 2.3 33.2 + - - -
152B TYR* 3.8 20.8 + + - -
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Residues in contact with ALA 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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119B ILE* 3.9 25.4 - - + -
130B VAL* 4.6 4.0 - - + -
132B LEU* 5.7 0.2 - - + -
145B LEU 2.9 17.2 + - - +
146B LEU 3.9 0.4 - - - +
148B TYR* 1.3 76.9 - - - +
150B ARG* 1.3 60.6 + - - +
152B TYR* 3.1 10.0 + - - +
154B MET* 3.0 36.8 + - + +
156B PRO* 3.6 27.4 - - + -
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Residues in contact with ARG 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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188A GLU* 3.9 30.6 - - - +
189A ILE 4.4 9.3 + - - +
146B LEU* 3.0 47.6 + - + +
147B GLU* 3.4 13.8 - - + +
149B ALA* 1.3 78.8 - - - +
151B SER* 1.3 55.9 + - - +
152B TYR 3.1 0.2 - - - -
153B GLY* 3.0 18.9 + - - -
154B MET 3.3 17.5 - - - +
155B GLU* 3.0 35.1 + - - +
172B ILE 4.6 1.0 + - - -
173B GLY 3.6 21.8 + - - -
174B ALA* 5.0 0.4 - - - +
175B ARG* 3.9 8.8 - - - +
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Residues in contact with SER 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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147B GLU 3.1 10.9 + - - -
148B TYR* 2.3 38.5 + - - -
150B ARG* 1.3 75.3 - - - +
152B TYR* 1.3 62.3 + - - +
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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