Contacts of the helix formed by residues 138 - 152 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A PRO 4.1 16.2 - - - +
3A ARG* 4.0 11.5 - - + +
137A LEU* 1.3 77.2 - - - +
139A GLU* 1.3 66.3 + - - +
140A ARG* 3.4 10.2 + - - +
141A GLU* 2.8 48.1 + - - +
142A LEU* 3.0 20.5 + - - +
168A ILE* 6.2 0.2 - - - -
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ARG* 5.4 0.6 - - - +
137A LEU 3.8 1.0 + - - -
138A THR* 1.3 72.3 - - - +
140A ARG* 1.3 63.8 + - - +
142A LEU* 3.6 6.4 + - - +
143A GLU* 3.0 25.6 + - - +
168A ILE* 4.5 32.5 - - + +
171A ARG* 3.1 46.7 + - + +
172A ILE* 4.8 6.1 - - + +
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A THR* 3.0 11.0 + - - +
139A GLU* 1.3 79.9 - - - +
141A GLU* 1.3 53.5 - - + +
143A GLU* 3.1 7.7 + - - +
144A SER* 2.8 38.6 + - - -
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 2.4 43.7 - - - +
114A VAL 5.3 5.4 - - - +
137A LEU* 3.5 17.3 - - + +
138A THR* 2.8 43.3 + - - +
140A ARG* 1.3 77.2 - - + +
142A LEU* 1.3 57.0 + - - +
144A SER* 3.1 7.8 + - - -
145A LEU* 2.9 42.8 + - + +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 4.0 31.5 - - + +
134A VAL* 4.1 21.3 - - + -
137A LEU* 3.7 23.9 - - + +
138A THR 3.0 17.5 + - - +
139A GLU 3.6 3.8 - - - +
141A GLU* 1.3 75.3 - - - +
143A GLU* 1.3 61.5 + - - +
145A LEU* 5.0 0.4 - - - -
146A LEU* 3.2 20.4 + - - +
158A ILE* 4.6 4.7 - - + -
168A ILE* 3.6 31.9 - - + -
172A ILE* 3.8 30.8 - - + +
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLU* 3.0 19.5 + - + +
140A ARG* 3.5 6.6 - - - +
142A LEU* 1.3 76.2 - - - +
144A SER* 1.3 68.3 + - - +
146A LEU* 3.4 9.2 + - + +
147A GLU* 2.9 50.6 + - - +
172A ILE* 4.3 23.1 - - + +
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Residues in contact with SER 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLU* 4.9 9.1 + - - +
140A ARG* 2.8 20.2 + - - +
141A GLU* 3.4 10.5 - - - -
143A GLU* 1.3 85.0 - - - +
145A LEU* 1.3 60.3 + - - +
147A GLU* 3.7 5.9 + - - +
148A TYR* 3.2 24.1 + - - +
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE* 4.3 8.5 - - + +
114A VAL* 4.1 23.6 - - - +
115A LYS* 3.6 4.9 - - - +
116A GLU* 3.4 39.9 - - + +
119A ILE* 3.4 27.3 - - + +
132A LEU* 4.0 12.9 - - + +
137A LEU* 4.1 23.6 - - + -
141A GLU* 2.9 21.3 + - + +
142A LEU* 4.5 0.4 - - - +
144A SER* 1.3 77.5 - - - +
146A LEU* 1.3 61.3 + - - +
148A TYR* 3.7 3.4 - - - -
149A ALA* 2.9 24.4 + - - +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 3.8 9.1 - - + +
142A LEU 3.2 19.3 + - - +
143A GLU* 3.8 10.3 - - - +
144A SER 3.3 0.2 - - - -
145A LEU* 1.3 77.1 - - - +
147A GLU* 1.3 64.8 + - - +
149A ALA* 3.5 2.9 + - - +
150A ARG* 3.1 61.4 + - - +
155A GLU* 4.6 1.6 - - - +
156A PRO* 3.6 35.2 - - + +
158A ILE* 4.3 14.1 - - + -
172A ILE* 4.0 33.2 - - + +
173A GLY 5.3 0.4 - - - +
174A ALA* 6.0 1.3 - - - -
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLU* 2.9 47.3 + - - +
144A SER* 3.7 6.7 - - - +
146A LEU* 1.3 77.1 - - - +
148A TYR* 1.3 57.8 + - - +
150A ARG* 3.0 25.5 + - - +
151A SER* 3.0 13.8 + - - -
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Residues in contact with TYR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLU* 3.6 53.1 + - + +
119A ILE* 3.6 17.3 - - + -
120A ASP* 2.7 32.6 + - - -
144A SER 3.2 16.1 + - - +
145A LEU* 3.7 8.3 - - - +
146A LEU 3.2 0.2 - - - -
147A GLU* 1.3 77.4 - - - +
149A ALA* 1.3 63.9 + - - +
151A SER* 2.7 31.5 + - - -
152A TYR* 3.6 22.5 + + - -
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Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ILE* 4.0 23.8 - - + -
130A VAL* 4.6 4.9 - - + -
145A LEU 2.9 16.5 + - - +
146A LEU 3.8 1.1 - - - +
148A TYR* 1.3 76.3 - - - +
150A ARG* 1.3 59.7 + - - +
151A SER 3.4 0.7 + - - -
152A TYR* 3.5 6.2 + - - +
154A MET* 2.9 37.5 + - + +
156A PRO* 3.4 32.3 - - + -
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Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 3.1 48.5 + - - +
147A GLU* 3.0 15.0 + - - +
149A ALA* 1.3 76.5 - - - +
151A SER* 1.3 59.0 + - - +
153A GLY* 3.0 17.3 + - - -
154A MET 3.3 18.8 - - - +
155A GLU* 2.7 36.5 + - - +
156A PRO* 4.5 2.2 - - + -
172A ILE 4.7 4.0 + - - -
173A GLY 3.6 21.4 + - - -
174A ALA* 5.0 0.8 - - - +
175A ARG* 3.6 33.4 - - - +
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Residues in contact with SER 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLU 3.0 10.6 + - - -
148A TYR* 2.7 32.0 + - - -
150A ARG* 1.3 77.1 - - - +
152A TYR* 1.3 65.3 + - - +
153A GLY 3.5 0.7 + - - -
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Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.3 15.4 - - - +
119A ILE* 4.1 12.8 - - + -
120A ASP* 2.8 42.3 + - - +
123A TYR* 3.3 59.9 + + + -
124A ASN* 4.8 4.4 + - - -
148A TYR* 3.7 30.5 + + - -
149A ALA 3.5 8.4 + - - +
151A SER* 1.3 84.2 + - - +
153A GLY* 1.3 56.3 + - - +
154A MET* 4.1 9.2 - - + -
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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