Contacts of the helix formed by residues 130 - 149 (chain A) in PDB entry 1EUB
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A THR* 4.4 8.5 - - + -
128A ASP 5.0 0.9 + - - -
129A MET* 1.3 76.9 - - - +
131A HIS* 1.3 71.0 + - + +
132A SER* 2.6 11.5 + - - +
133A GLU* 2.3 45.7 + - - -
134A VAL* 3.0 12.0 + - - +
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Residues in contact with HIS 131 (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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122A ILE* 6.4 2.0 - - + -
126A THR* 4.5 11.1 - - + +
130A THR* 1.3 78.3 - - + +
132A SER* 1.3 62.5 + - - +
134A VAL* 4.0 12.2 - - + +
135A GLU* 3.0 39.0 + - + +
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 2.6 9.1 + - - +
131A HIS* 1.3 77.1 - - - +
133A GLU* 1.3 73.1 + - - +
135A GLU* 2.8 32.5 + - - +
136A LYS* 3.1 6.4 + - - +
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A MET* 3.3 25.2 - - + -
130A THR* 2.3 53.5 + - - +
132A SER* 1.3 75.9 - - - +
134A VAL* 1.3 57.9 + - - +
135A GLU 2.8 0.9 - - - -
136A LYS* 2.4 33.3 + - + +
137A ALA* 2.7 12.2 + - - -
209A SER* 4.1 23.7 - - - +
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Residues in contact with VAL 134 (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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122A ILE* 5.2 3.6 - - + +
123A VAL* 4.9 8.1 - - - +
124A ASN* 3.9 23.8 - - + +
125A TYR 2.7 32.3 - - - +
126A THR* 4.9 1.3 - - + +
129A MET* 3.9 17.7 - - + +
130A THR 3.0 15.0 + - - +
131A HIS* 4.0 11.7 - - + +
133A GLU* 1.3 77.9 - - - +
135A GLU* 1.3 65.2 + - - +
137A ALA* 3.8 9.9 - - - -
138A PHE* 2.8 30.7 + - + -
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Residues in contact with GLU 135 (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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122A ILE* 5.6 2.0 - - + -
131A HIS* 3.0 29.5 + - + +
132A SER* 2.8 24.1 + - - +
133A GLU 2.7 0.2 + - - -
134A VAL* 1.3 77.9 - - - +
136A LYS* 1.3 55.0 + - - +
138A PHE* 3.0 19.8 - - + -
139A LYS* 2.8 35.1 + - + +
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Residues in contact with LYS 136 (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 SER 3.1 8.7 + - - +
133A GLU* 2.4 21.6 + - - +
135A GLU* 1.3 67.4 - - - +
137A ALA* 1.3 66.2 + - - +
139A LYS* 4.5 1.3 - - - -
140A LYS* 2.6 58.5 + - + +
209A SER* 3.9 7.0 - - - +
217A PHE* 3.3 28.3 - - + -
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Residues in contact with ALA 137 (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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124A ASN* 5.0 2.2 - - + -
129A MET* 4.9 0.2 - - + -
133A GLU 2.7 12.4 + - - +
134A VAL* 3.4 13.9 - - - +
136A LYS* 1.3 74.2 - - - +
138A PHE* 1.3 54.2 + - - +
141A ALA* 2.5 37.2 - - - +
165A ILE* 4.3 5.4 - - + -
209A SER* 5.2 0.2 - - - -
216A LEU* 2.7 52.2 - - + +
217A PHE* 3.4 8.8 - - - -
220A ALA* 4.3 0.3 - - - +
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Residues in contact with PHE 138 (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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120A TYR* 3.6 17.9 - + - -
122A ILE* 2.8 46.0 - - + -
134A VAL* 2.8 24.8 + - + +
135A GLU* 3.0 40.6 - - + -
137A ALA* 1.3 75.3 - - - +
139A LYS* 1.3 95.9 + - + +
141A ALA* 4.0 1.1 - - - +
142A PHE* 3.0 29.4 + - + +
155A ARG* 3.0 33.0 - - - -
165A ILE* 3.8 24.2 - - + +
224A PHE* 6.2 0.7 - - + -
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Residues in contact with LYS 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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120A TYR* 5.6 0.7 - - - +
135A GLU* 2.8 23.1 + - + +
136A LYS* 4.5 0.9 - - - -
138A PHE* 1.3 97.9 - - + +
140A LYS* 1.3 56.9 + - - +
142A PHE* 2.4 34.3 + - + +
143A LYS* 2.6 27.4 + - - +
153A PHE* 6.5 1.3 - - - -
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Residues in contact with LYS 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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136A LYS* 2.6 57.4 + - + +
139A LYS* 1.3 78.1 - - - +
141A ALA* 1.3 53.5 + - - +
143A LYS* 2.5 52.9 + - + +
144A VAL* 2.9 20.8 + - + +
217A PHE* 3.4 34.8 - - + -
249A LYS* 5.6 12.3 - - - -
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Residues in contact with ALA 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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136A LYS 3.3 0.2 + - - -
137A ALA 2.5 23.9 + - - +
138A PHE* 4.0 2.2 - - - +
140A LYS* 1.3 77.9 - - - +
142A PHE* 1.3 56.8 + - + +
144A VAL* 3.3 6.2 + - - +
145A TRP* 3.0 27.1 + - - +
216A LEU 3.5 22.0 - - - +
217A PHE* 3.5 20.2 - - - +
220A ALA* 3.9 9.9 - - + -
221A ALA* 3.9 10.5 - - - +
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Residues in contact with PHE 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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120A TYR* 2.9 52.3 - + + +
138A PHE* 3.0 22.4 + + - +
139A LYS* 2.4 28.5 + - + +
141A ALA* 1.3 69.4 - - + +
143A LYS* 1.3 57.5 + - - +
145A TRP* 3.5 21.4 - + + +
146A SER* 2.8 36.6 + - - -
153A PHE* 3.5 43.3 - + + -
163A ILE* 5.3 1.8 - - + -
224A PHE* 2.9 41.7 - + - -
228A LEU* 6.2 1.6 - - + -
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Residues in contact with LYS 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 LYS* 2.6 21.6 + - - +
140A LYS* 2.5 43.8 + - - +
142A PHE* 1.3 71.8 - - - +
144A VAL* 1.3 58.8 + - + +
146A SER* 3.4 6.6 + - - -
147A ASP* 2.9 38.5 + - - +
153A PHE* 6.2 0.2 - - - -
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Residues in contact with VAL 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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140A LYS* 2.9 27.7 + - + +
141A ALA* 3.5 10.8 - - - +
143A LYS* 1.3 78.8 - - + +
145A TRP* 1.3 69.5 + - - +
147A ASP* 2.8 22.2 + - + +
148A VAL* 3.0 21.9 + - + +
217A PHE* 5.4 2.9 - - + +
221A ALA* 4.9 9.4 - - + -
248A GLY* 4.2 31.4 - - - +
249A LYS* 5.1 8.3 - - + -
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Residues in contact with TRP 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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141A ALA 3.0 17.5 + - - +
142A PHE* 3.5 29.6 - + + +
144A VAL* 1.3 78.5 - - - +
146A SER* 1.3 61.3 + - - +
148A VAL* 2.6 32.2 - - + +
149A THR* 3.1 19.3 + - + +
151A LEU* 3.7 18.2 - - + +
153A PHE* 5.1 0.4 - + - -
221A ALA* 4.5 16.4 - - + +
224A PHE* 5.4 8.7 - + + +
225A GLY* 3.8 33.7 - - - -
228A LEU* 3.7 33.4 - - + +
229A GLY* 5.3 0.2 - - - -
239A LEU* 5.7 1.6 - - + -
240A MET* 6.3 0.9 - - - -
258A ASP* 4.7 10.5 - - + -
262A ILE* 3.2 48.5 - - + -
266A TYR* 3.9 12.6 - + - -
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Residues in contact with SER 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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142A PHE* 2.8 19.6 + - - -
143A LYS* 3.6 6.7 - - - -
145A TRP* 1.3 76.0 - - - +
147A ASP* 1.3 68.5 + - - +
149A THR 2.8 27.4 - - - +
150A PRO* 3.6 5.4 - - - +
151A LEU 4.7 0.7 - - - +
153A PHE* 2.7 41.7 - - - -
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Residues in contact with ASP 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 LYS* 2.9 25.6 + - - +
144A VAL* 2.8 20.3 + - + +
146A SER* 1.3 80.3 - - - +
148A VAL* 1.3 63.4 + - + +
149A THR* 4.5 0.2 - - - -
150A PRO* 5.8 0.2 - - - +
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Residues in contact with VAL 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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144A VAL* 3.0 16.6 + - + +
145A TRP* 2.6 44.6 - - + +
147A ASP* 1.3 79.8 - - + +
149A THR* 1.3 59.5 + - + +
150A PRO* 4.6 0.2 - - - +
253A MET* 6.0 0.2 - - + -
258A ASP* 4.7 4.9 - - - +
259A VAL* 3.8 38.5 - - + +
262A ILE* 3.6 23.6 - - + -
263A GLN* 2.8 32.1 - - - +
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Residues in contact with THR 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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145A TRP* 3.1 19.1 - - + +
146A SER* 2.8 24.7 + - - +
148A VAL* 1.3 83.3 - - + +
150A PRO* 1.3 63.7 - - - +
151A LEU* 2.6 32.7 + - + +
262A ILE* 3.0 45.1 + - + -
263A GLN* 3.4 6.3 - - - +
266A TYR 4.0 2.6 - - - -
267A GLY* 3.8 10.6 + - - -
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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
------------------------------------------------------------
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