Contacts of the helix formed by residues 153 - 167 (chain L) in PDB entry 5U0A
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 ASN 153 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151L GLY 3.4 4.4 + - - -
152L LEU* 1.3 79.2 - - + +
154L ALA* 1.3 76.2 + - - +
155L ASP* 2.8 26.7 + - - +
156L SER* 4.1 3.7 - - - -
157L THR* 3.2 27.0 + - - +
32M C 3.6 34.2 + - - +
33M A 2.6 44.4 + - - -
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Residues in contact with ALA 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147L VAL* 3.6 25.1 - - + +
152L LEU 3.3 2.4 + - - -
153L ASN* 1.3 75.0 + - - +
155L ASP* 1.3 64.8 + - - +
156L SER 3.2 2.0 - - - -
157L THR* 3.5 8.3 - - - +
158L GLU* 2.9 27.4 + - - +
217L TYR* 4.0 5.5 + - - +
221L LEU* 4.9 9.4 - - + -
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Residues in contact with ASP 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153L ASN* 2.8 25.5 + - - +
154L ALA* 1.3 78.1 - - - +
156L SER* 1.3 82.0 + - - +
158L GLU* 3.9 9.7 - - - +
159L GLN* 3.6 25.5 + - - +
33M A 3.3 21.0 + - - +
34M T 5.7 7.2 + - - +
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Residues in contact with SER 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222F ASN* 5.3 2.9 + - - -
153L ASN* 3.8 6.9 + - - -
154L ALA 3.2 0.2 - - - -
155L ASP* 1.3 87.3 + - - +
157L THR* 1.3 60.4 + - - +
158L GLU 3.0 1.3 - - - -
159L GLN* 3.1 11.7 + - - +
160L ARG* 2.9 48.2 + - - +
32M C 3.4 33.6 + - - -
33M A 5.2 0.4 - - - -
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Residues in contact with THR 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143L LEU* 3.6 22.2 + - - +
147L VAL* 3.5 14.4 - - + -
152L LEU* 4.7 8.9 - - + +
153L ASN 3.2 22.9 + - - +
154L ALA 3.5 2.9 - - - +
156L SER* 1.3 78.3 - - - +
158L GLU* 1.3 59.7 + - - +
160L ARG* 3.3 27.0 + - - +
161L LEU* 3.0 26.3 + - - +
179L LEU* 4.5 2.1 - - - +
183L LEU* 5.9 0.7 - - - +
217L TYR* 3.2 25.6 - - + +
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Residues in contact with GLU 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J ARG* 4.1 19.1 - - - +
154L ALA 2.9 19.8 + - - +
155L ASP* 3.9 9.4 - - - +
156L SER 3.0 0.2 - - - -
157L THR* 1.3 76.7 - - - +
159L GLN* 1.3 62.3 + - + +
161L LEU* 3.0 7.7 + - + +
162L HIS* 2.9 55.9 + - + +
217L TYR* 4.5 11.0 - - + +
218L HIS* 2.9 32.2 - - + -
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Residues in contact with GLN 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ASP 5.5 4.5 + - - -
22F LEU* 4.2 17.5 - - + +
27K C 5.9 2.8 - - - +
155L ASP 3.6 14.9 + - - +
156L SER* 3.1 12.0 + - - +
158L GLU* 1.3 79.4 - - + +
160L ARG* 1.3 61.6 + - + +
162L HIS* 3.9 7.9 - - + +
163L LEU* 2.9 26.6 + - - +
34M T 6.0 4.4 - - - +
35M G 5.8 2.0 + - - -
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Residues in contact with ARG 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F ASN* 4.9 14.8 - - - +
152L LEU* 3.6 23.2 - - - +
153L ASN 4.4 0.6 + - - -
156L SER* 2.9 36.6 + - - +
157L THR* 3.3 38.6 + - - +
159L GLN* 1.3 77.0 - - + +
161L LEU* 1.3 62.1 + - - +
163L LEU* 3.5 9.8 + - + +
164L ILE* 3.0 31.6 + - + +
178L ARG* 6.4 3.1 - - - +
179L LEU* 3.9 27.2 - - + +
182L TYR* 4.0 16.9 - - - -
31M A 5.3 12.0 + - - +
32M C 3.9 8.9 + - - -
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Residues in contact with LEU 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L LEU* 5.9 4.0 - - + -
140L GLY* 4.9 4.3 - - - -
143L LEU* 3.8 20.2 - - + -
157L THR 3.0 14.0 + - - +
158L GLU* 3.0 10.0 + - + +
160L ARG* 1.3 77.6 - - - +
162L HIS* 1.3 61.1 + - + +
164L ILE* 3.0 10.8 + - - +
165L ALA* 2.9 24.2 + - + +
179L LEU* 4.8 0.2 - - - +
213L TRP* 4.7 9.6 - - + +
214L VAL* 3.5 42.4 - - + +
217L TYR* 3.5 46.4 - - + -
218L HIS* 5.6 0.4 - - - +
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Residues in contact with HIS 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LEU* 3.9 16.6 - - + -
45J LEU* 3.1 54.1 - - + +
46J ALA* 5.0 4.0 - - - -
49J ARG* 6.4 0.2 - - + -
158L GLU* 2.9 63.0 + - + +
159L GLN* 4.1 6.5 - - + +
161L LEU* 1.3 73.7 - - + +
163L LEU* 1.3 61.7 + - - +
165L ALA* 3.1 12.2 + - - +
166L ARG* 3.1 22.5 + - - +
214L VAL* 3.6 22.8 - - + +
218L HIS* 3.6 4.9 + - - -
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Residues in contact with LEU 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LEU* 3.4 47.9 - - + +
24F SER* 5.1 6.7 - - - +
225F GLN* 3.8 19.1 - - - +
159L GLN 2.9 19.3 + - - +
160L ARG* 3.8 8.7 - - + +
162L HIS* 1.3 77.3 - - - +
164L ILE* 1.3 61.0 + - + +
166L ARG* 3.8 4.0 + - - +
167L GLN* 3.4 26.7 - - - +
175L HIS* 3.5 39.0 - - + +
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Residues in contact with ILE 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L LEU* 5.7 3.8 - - + -
143L LEU* 6.2 0.2 - - + -
160L ARG* 3.0 16.3 + - + +
161L LEU* 3.0 10.6 + - - +
163L LEU* 1.3 79.7 - - + +
165L ALA* 1.3 64.0 + - - +
166L ARG 3.1 1.4 + - - -
167L GLN* 3.3 17.6 + - - +
172L VAL* 3.8 27.5 - - + +
175L HIS* 4.0 33.9 - - + +
176L LEU* 4.6 8.7 - - + -
179L LEU* 4.0 31.4 - - + -
202L TRP* 4.1 8.4 - - + -
213L TRP* 4.3 19.7 - - + -
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Residues in contact with ALA 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J LEU* 3.8 20.0 - - + -
161L LEU* 2.9 12.9 + - + +
162L HIS* 3.1 8.9 + - - +
164L ILE* 1.3 78.6 - - - +
166L ARG* 1.3 58.3 + - - +
202L TRP* 4.5 2.2 - - - -
207L ARG* 2.9 25.6 + - - -
210L ALA* 3.7 28.0 - - + +
213L TRP* 6.1 3.1 - - + -
214L VAL* 4.2 12.1 - - + -
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Residues in contact with ARG 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ASP* 3.8 16.6 + - - +
21F ASP* 3.9 22.6 + - - +
22F LEU* 3.1 40.5 - - + +
203G PHE* 6.1 0.8 - - - +
42J PRO* 5.8 7.6 - - + -
45J LEU* 3.9 30.7 - - + +
162L HIS* 3.1 14.8 + - - +
163L LEU* 3.8 4.7 + - - +
164L ILE 3.1 0.8 - - - -
165L ALA* 1.3 78.0 - - - +
167L GLN* 1.3 73.3 + - - +
168L ASN 3.7 0.3 + - - -
207L ARG* 4.0 9.2 + - - +
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Residues in contact with GLN 167 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F SER* 5.5 5.9 + - - -
199F VAL* 6.2 1.2 - - - +
163L LEU* 3.4 25.7 - - - +
164L ILE* 3.3 11.3 + - - +
166L ARG* 1.3 88.0 - - - +
168L ASN* 1.3 65.3 + - - +
171L GLY* 3.7 2.8 - - - -
172L VAL* 3.6 19.7 - - - +
174L ARG* 3.4 28.1 - - - +
175L HIS* 3.7 26.6 + - + -
202L TRP* 2.9 23.7 - - - -
207L ARG* 3.5 3.8 + - - -
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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