Contacts of the helix formed by residues 145 - 160 (chain A) in PDB entry 1O1L
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 SER 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A VAL 3.4 4.0 + - - -
144A LEU* 1.3 75.4 - - - +
146A PRO* 1.3 75.8 - - - +
147A ALA* 3.3 9.4 + - - +
148A ASP* 3.0 33.9 + - - -
149A LYS* 3.0 21.3 + - - +
269A LYS* 4.9 2.0 - - - -
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Residues in contact with PRO 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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145A SER* 1.3 90.3 - - - +
147A ALA* 1.3 60.5 + - - +
149A LYS* 3.4 11.6 + - + +
150A THR* 2.8 30.9 + - - +
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Residues in contact with ALA 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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145A SER* 3.1 7.8 + - - +
146A PRO* 1.3 81.8 - - - +
148A ASP* 1.3 61.6 + - - +
150A THR* 3.3 7.7 + - - -
151A ASN* 3.0 36.4 + - - +
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Residues in contact with ASP 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 LEU* 4.1 14.4 - - + -
145A SER* 3.0 33.0 + - - +
147A ALA* 1.3 78.3 - - - +
149A LYS* 1.3 63.1 + - - +
151A ASN* 3.2 2.1 + - - +
152A VAL* 2.9 29.9 + - - +
265A ALA* 5.8 0.5 - - - +
266A SER* 2.6 38.8 + - - +
269A LYS* 2.5 41.9 + - - +
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Residues in contact with LYS 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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143A VAL* 6.1 1.1 - - - -
144A LEU* 3.3 35.8 + - + -
145A SER 3.0 14.6 + - - +
146A PRO* 3.9 7.9 - - + +
148A ASP* 1.3 77.5 - - - +
150A THR* 1.3 57.6 + - - +
152A VAL* 3.5 5.3 + - - +
153A LYS* 3.0 48.9 + - - +
215A VAL* 3.6 41.1 - - + -
216A ASP* 2.5 30.9 + - - +
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Residues in contact with THR 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 PRO* 2.8 22.3 + - - +
147A ALA* 3.5 7.6 - - - -
149A LYS* 1.3 74.7 - - - +
151A ASN* 1.3 59.3 + - - +
153A LYS* 3.3 8.2 + - - +
154A ALA* 2.8 38.2 + - + +
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Residues in contact with ASN 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 ALA* 3.0 24.9 + - - +
148A ASP 3.6 4.5 - - - +
150A THR* 1.3 76.9 - - - +
152A VAL* 1.3 59.6 + - - +
154A ALA* 3.3 7.0 + - - +
155A ALA* 2.9 31.9 + - - +
262A ALA* 3.8 17.4 + - - +
263A VAL* 3.8 28.8 - - + +
266A SER* 3.1 28.2 + - - +
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Residues in contact with VAL 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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144A LEU* 5.5 2.0 - - + -
148A ASP* 2.9 22.7 + - + +
149A LYS* 3.9 5.2 - - - +
151A ASN* 1.3 76.6 - - - +
153A LYS* 1.3 59.4 + - + +
155A ALA* 3.4 0.9 + - - +
156A TRP* 2.9 30.6 + - + +
212A VAL* 4.0 27.1 - - + -
215A VAL* 5.7 3.8 - - + -
266A SER 3.8 15.3 - - - +
267A LEU* 4.0 18.6 - - + +
270A PHE* 3.8 43.3 - - + -
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Residues in contact with LYS 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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149A LYS* 3.0 33.0 + - - +
150A THR* 3.9 6.8 + - - +
152A VAL* 1.3 76.9 - - + +
154A ALA* 1.3 58.8 + - - +
157A GLY* 2.8 29.1 + - - -
212A VAL* 4.0 30.1 - - + +
213A ALA* 6.2 0.4 - - - -
215A VAL* 4.3 23.3 - - + +
216A ASP* 5.9 0.4 + - - -
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Residues in contact with ALA 154 (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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150A THR* 2.8 24.9 + - + +
151A ASN* 3.7 7.6 - - - +
153A LYS* 1.3 74.0 - - - +
155A ALA* 1.3 61.1 + - - +
157A GLY* 3.9 1.1 - - - -
158A LYS* 3.2 20.6 + - - +
258A GLU* 5.4 1.8 - - - +
263A VAL* 6.2 2.0 - - + -
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Residues in contact with ALA 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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151A ASN 2.9 19.2 + - - +
152A VAL 4.0 1.6 - - - +
154A ALA* 1.3 73.2 - - - +
156A TRP* 1.3 61.6 + - + +
158A LYS* 3.2 9.5 + - - +
159A VAL* 3.1 24.0 + - - +
251A LEU* 5.8 1.6 - - + -
255A LEU* 4.0 15.4 - - + +
258A GLU* 5.1 7.6 - - + -
263A VAL* 4.1 22.8 - - + +
267A LEU* 4.3 17.7 - - + -
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Residues in contact with TRP 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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152A VAL* 2.9 19.1 + - + +
153A LYS 4.3 1.1 - - - +
155A ALA* 1.3 74.8 - - - +
157A GLY* 1.3 66.6 + - - +
159A VAL* 3.1 30.6 + - + +
160A GLY* 3.2 10.3 + - - -
163A ALA* 4.5 15.6 - - + +
205A ALA* 3.8 24.9 - - + -
208A LEU* 3.8 31.2 - - + -
209A THR* 2.9 33.5 + - + +
212A VAL* 3.9 31.6 - - + -
247A LEU* 5.6 5.8 - - + -
251A LEU* 4.6 21.5 - - + -
267A LEU* 5.6 7.0 - - + -
270A PHE* 5.8 5.2 - + - -
271A LEU* 6.3 2.0 - - + -
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Residues in contact with GLY 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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153A LYS 2.8 18.9 + - - -
154A ALA 3.9 1.3 - - - -
156A TRP* 1.3 77.6 - - - +
158A LYS* 1.3 61.7 - - - +
160A GLY* 3.1 15.8 + - - -
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Residues in contact with LYS 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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154A ALA 3.2 12.6 + - - +
155A ALA 3.2 10.2 + - - +
156A TRP 3.2 0.8 - - - -
157A GLY* 1.3 72.9 - - - +
159A VAL* 1.3 66.6 + - - +
160A GLY* 4.3 0.3 - - - -
162A HIS* 4.7 5.7 - - - -
254A HIS 5.5 1.2 + - - -
255A LEU* 3.3 24.3 - - + +
258A GLU* 3.4 34.9 + - + +
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Residues in contact with VAL 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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155A ALA 3.1 15.1 + - - +
156A TRP* 3.1 30.2 + - + +
158A LYS* 1.3 75.9 - - - +
160A GLY* 1.3 63.3 + - - +
162A HIS* 3.0 29.3 + - - -
163A ALA* 3.6 32.8 - - + +
166A TYR* 3.7 23.3 - - + -
251A LEU* 3.9 27.4 - - + -
255A LEU* 4.3 8.7 - - + -
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Residues in contact with GLY 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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156A TRP* 3.2 5.9 + - - -
157A GLY* 3.1 16.3 + - - -
158A LYS 4.3 0.7 - - - -
159A VAL* 1.3 77.3 - - - +
161A ALA* 1.3 62.2 + - - -
162A HIS* 3.1 1.4 + - - -
163A ALA* 3.3 19.1 + - - +
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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