Contacts of the helix formed by residues 140 - 160 (chain A) in PDB entry 1A81
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 GLY 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A LEU 4.2 0.2 + - - -
139A GLN* 1.3 73.6 - - - +
141A GLN* 1.3 68.7 - - - +
143A LEU* 3.7 15.6 - - - +
144A GLU* 4.0 8.8 + - - +
197G ARG* 4.5 34.5 + - - -
198G ASP* 3.8 11.6 + - - +
202G SER* 4.7 5.2 - - - -
217G ARG* 5.2 0.8 + - - -
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Residues in contact with GLN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLN* 3.0 6.3 + - - +
140A GLY* 1.3 76.7 - - - +
142A ALA* 1.3 65.1 + - - +
143A LEU 3.5 0.2 + - - -
144A GLU* 3.5 11.9 + - - +
145A GLN* 3.1 28.1 + - - +
199G ASN* 3.6 38.6 + - - +
201G GLY* 4.1 4.5 - - - -
202G SER* 3.4 36.0 + - - +
217G ARG* 4.6 8.3 - - - +
219G ASP* 5.5 3.8 - - + -
220G LYS 6.0 0.4 - - - +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.4 16.9 - - + +
139A GLN* 2.6 42.0 + - + +
141A GLN* 1.3 70.7 - - - +
143A LEU* 1.3 66.7 + - - +
145A GLN* 3.1 18.0 + - - +
146A ALA 3.2 9.9 + - - -
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 4.2 30.5 - - - +
132A VAL* 3.2 37.0 - - + -
133A LYS* 3.8 26.9 - - + +
138A LEU* 3.4 20.8 - - + +
139A GLN 3.0 8.0 + - - +
140A GLY* 3.7 12.1 - - - +
142A ALA* 1.3 75.3 - - - +
144A GLU* 1.3 69.1 + - - +
145A GLN 2.9 1.6 + - - -
146A ALA* 3.0 11.3 + - - +
147A ILE* 2.9 30.0 + - + +
197G ARG* 6.0 2.5 - - - +
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Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 4.6 12.5 + - - -
140A GLY 4.0 11.4 + - - +
141A GLN* 3.5 9.6 + - - +
142A ALA 3.4 0.4 - - - -
143A LEU* 1.3 79.3 - - - +
145A GLN* 1.3 73.4 + - - +
147A ILE* 3.0 25.0 - - - +
148A ILE* 2.8 22.0 - - + +
197G ARG* 5.3 4.4 + - - +
217G ARG* 3.7 42.0 + - - +
170H PTR 5.8 1.7 - - - -
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Residues in contact with GLN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLN* 3.1 21.1 - - - +
142A ALA* 3.3 11.2 - - - +
143A LEU 2.9 1.0 + - - -
144A GLU* 1.3 78.7 - - - +
146A ALA* 1.3 57.2 + - - +
147A ILE 2.4 16.1 + - - -
148A ILE* 2.6 41.2 + - + +
149A SER* 2.9 8.4 + - - +
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Residues in contact with ALA 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 VAL* 4.0 6.1 - - + -
136A TRP* 3.9 24.2 - - + -
138A LEU* 3.4 25.6 - - + -
142A ALA 3.2 1.6 + - - +
143A LEU 3.0 9.8 + - - +
145A GLN* 1.3 77.2 - - - +
147A ILE* 1.3 56.8 + - - +
149A SER* 3.4 6.9 + - - -
150A GLN* 2.8 36.1 + - - +
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Residues in contact with ILE 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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128A ILE* 3.5 32.3 - - + -
129A ARG* 4.6 15.0 - - + -
132A VAL* 5.0 9.2 - - + +
143A LEU* 2.9 35.0 - - + +
144A GLU* 3.0 31.4 - - - +
145A GLN 2.4 6.1 + - - -
146A ALA* 1.3 69.3 - - - +
148A ILE* 1.3 60.6 + - + +
150A GLN* 5.0 0.4 - - - -
151A LYS* 2.4 46.2 + - + +
154A LEU* 5.1 2.2 - - + -
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Residues in contact with ILE 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 GLU* 2.8 24.2 - - + +
145A GLN* 2.6 52.7 + - + +
147A ILE* 1.3 75.6 - - + +
149A SER* 1.3 76.6 + - - +
151A LYS* 3.9 7.6 + - - +
152A PRO* 4.0 8.3 - - - +
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Residues in contact with SER 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 GLN* 2.9 25.8 + - - +
146A ALA* 3.4 6.4 + - - -
148A ILE* 1.3 89.7 - - - +
150A GLN* 1.3 72.8 + - - +
152A PRO* 4.0 9.5 - - - +
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Residues in contact with GLN 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TRP* 3.3 29.8 - - + -
146A ALA 2.8 21.4 + - - +
149A SER* 1.3 83.7 + - - +
151A LYS* 1.3 49.7 + - - +
152A PRO* 2.7 8.7 - - - +
153A GLN* 2.5 58.8 + - - +
154A LEU* 2.8 21.6 - - + +
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Residues in contact with LYS 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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125A GLU* 3.1 32.7 + - - -
128A ILE* 5.8 8.1 - - + -
147A ILE* 2.4 40.7 + - + +
148A ILE* 4.2 4.9 - - - +
150A GLN* 1.3 63.4 - - - +
152A PRO* 1.3 68.4 - - + +
153A GLN 2.7 1.2 + - - -
154A LEU* 3.0 22.5 + - - +
155A GLU* 2.2 59.7 + - + +
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Residues in contact with PRO 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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68A ARG* 4.8 20.6 + - - +
148A ILE 4.0 11.0 - - - +
149A SER 4.1 7.4 - - - +
150A GLN* 3.0 13.0 - - - +
151A LYS* 1.3 95.5 - - + +
153A GLN* 1.3 58.6 + - + +
155A GLU* 2.9 19.0 - - - +
156A LYS* 3.9 5.5 + - - +
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Residues in contact with GLN 153 (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 TRP* 5.3 6.5 - - - -
150A GLN* 2.5 43.0 + - - +
152A PRO* 1.3 72.6 - - + +
154A LEU* 1.3 72.5 + - + +
156A LYS* 2.9 21.3 + - + +
157A LEU* 3.2 32.1 + - - +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 4.4 20.9 - - + -
131A TYR* 4.7 13.0 - - + -
132A VAL* 3.6 31.4 - - + -
136A TRP* 4.5 12.1 - - + -
146A ALA 5.7 0.2 - - - +
147A ILE* 5.1 2.7 - - + +
150A GLN* 2.8 49.1 - - + +
151A LYS* 3.0 10.1 + - - +
153A GLN* 1.3 71.2 - - + +
155A GLU* 1.3 57.0 + - + +
157A LEU* 2.3 45.1 + - + +
158A ILE* 2.9 19.7 + - + -
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Residues in contact with GLU 155 (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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48A LEU* 5.6 4.7 - - + -
128A ILE* 5.4 5.4 - - + +
151A LYS* 2.2 77.4 + - - +
152A PRO* 2.9 14.2 - - - +
154A LEU* 1.3 79.0 - - + +
156A LYS* 1.3 62.8 + - - +
158A ILE* 4.6 6.3 - - - -
159A ALA* 3.0 28.0 + - - +
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Residues in contact with LYS 156 (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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48A LEU* 4.9 22.6 - - + +
152A PRO 3.9 5.3 + - - +
153A GLN* 2.9 20.5 + - + +
154A LEU 2.8 1.6 + - - -
155A GLU* 1.3 75.9 - - - +
157A LEU* 1.3 49.2 - - - +
159A ALA* 4.6 2.0 - - - +
160A THR* 2.5 37.8 + - + +
235A ASP* 4.8 11.7 + - - -
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Residues in contact with LEU 157 (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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131A TYR* 4.7 23.6 - - + +
136A TRP* 6.6 0.7 - - + -
153A GLN* 3.2 39.3 + - - +
154A LEU* 2.3 30.7 + - + +
156A LYS* 1.3 65.1 - - + +
158A ILE* 1.3 76.2 + - + +
160A THR* 2.5 24.5 + - - +
161A THR* 3.3 13.6 + - + +
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Residues in contact with ILE 158 (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 LYS* 4.9 8.1 - - + -
127A LEU* 4.0 26.2 - - + +
128A ILE* 3.0 46.4 - - + +
131A TYR* 4.6 20.9 - - + -
154A LEU* 2.9 31.0 + - + +
155A GLU* 4.0 3.6 - - - +
157A LEU* 1.3 81.8 - - + +
159A ALA* 1.3 64.0 + - - +
161A THR* 3.2 24.8 - - - +
162A ALA* 3.3 6.4 + - + +
238A TRP* 5.9 2.5 - - + -
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Residues in contact with ALA 159 (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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48A LEU* 4.1 23.8 - - + -
155A GLU 3.0 17.5 + - - +
156A LYS 4.6 1.6 - - - +
158A ILE* 1.3 76.4 - - - +
160A THR* 1.3 62.2 + - - +
161A THR 2.9 6.6 + - - -
162A ALA* 3.7 14.3 + - - +
163A HIS* 5.0 1.2 + - - -
236A THR* 4.1 18.3 + - + +
238A TRP* 4.6 28.1 - - + +
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Residues in contact with THR 160 (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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48A LEU* 6.4 0.7 - - + -
156A LYS* 2.5 20.0 + - + +
157A LEU* 2.5 26.2 + - - +
159A ALA* 1.3 74.8 - - - +
161A THR* 1.3 67.2 + - - +
163A HIS* 3.0 18.4 + - - -
220A LYS* 5.9 4.7 - - - +
235A ASP 5.6 4.0 - - - +
236A THR* 4.7 14.6 - - + +
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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