Contacts of the strand formed by residues 153 - 161 (chain E) in PDB entry 3Q2K
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 ILE 153 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145E ILE* 4.4 30.3 - - + -
150E PHE* 3.8 17.7 - - + -
151E GLY 3.3 12.3 + - - +
152E ARG* 1.3 83.2 + - - +
154E TYR* 1.3 68.1 + - - +
156E VAL* 4.1 18.2 - - + -
200E VAL* 4.2 18.4 - - + +
231E HIS* 4.3 15.9 + - + +
233E ALA* 3.6 31.6 + - + +
254E ILE* 4.2 17.5 - - + -
255E LEU 3.9 7.9 - - - +
256E GLY* 4.0 0.7 - - - -
213F LEU* 4.7 0.9 - - - +
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Residues in contact with TYR 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E ARG* 3.4 23.8 - - + +
153E ILE* 1.3 82.7 - - - +
155E MET* 1.3 67.9 + - + +
233E ALA* 3.5 5.8 - - - -
234E MET 3.1 19.6 + - - +
255E LEU* 2.8 11.6 + - + +
256E GLY* 3.6 16.2 - - - -
257E GLU* 3.1 46.9 - - + +
213F LEU* 3.6 48.2 - - + +
214F ALA* 3.7 14.8 - - + +
222F THR* 3.8 5.8 - - - +
240F THR* 4.7 9.0 - - + +
242F LEU* 3.6 35.7 - - + -
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Residues in contact with MET 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E ILE* 4.3 0.2 - - - +
154E TYR* 1.3 83.4 - - + +
156E VAL* 1.3 77.5 + - - +
157E THR* 5.1 0.2 - - - +
234E MET* 3.2 12.8 - - + +
235E GLY* 4.2 3.1 - - - -
253E THR* 3.8 0.8 - - + +
254E ILE* 3.6 0.7 - - - -
255E LEU* 3.0 40.5 + - + +
161F PHE* 3.9 22.0 - - + -
222F THR* 3.4 15.5 - - + -
223F GLY 3.4 16.4 - - - +
224F VAL* 3.7 17.9 - - + -
238F ASN* 4.0 15.3 - - - -
239F VAL 3.4 28.7 - - - +
240F THR* 4.1 14.8 - - + -
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Residues in contact with VAL 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E ILE* 4.1 17.5 - - + -
155E MET* 1.3 85.6 - - - +
157E THR* 1.3 71.2 + - - +
158E VAL* 4.5 6.7 - - + -
196E LEU* 5.0 1.3 - - + -
200E VAL* 4.1 21.8 - - + -
229E TRP* 3.8 35.4 - - + -
233E ALA* 4.7 0.9 - - + -
234E MET 2.9 7.0 + - - +
235E GLY* 2.8 25.3 - - - -
236E SER 3.1 4.1 + - - +
252E ILE* 4.4 9.6 - - + -
253E THR 3.1 11.9 - - - +
254E ILE* 4.3 12.1 - - + -
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Residues in contact with THR 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E MET* 5.1 0.2 - - - +
156E VAL* 1.3 73.9 - - - +
158E VAL* 1.3 66.3 + - - +
159E ASN* 4.3 9.0 - - - +
236E SER* 3.1 28.0 - - - +
238E ASN* 3.8 8.3 - - - +
251E SER* 4.5 0.5 + - - -
252E ILE* 3.3 4.0 - - - +
253E THR* 2.8 40.2 + - - +
157F THR* 5.3 1.6 - - + -
159F ASN* 4.2 6.9 + - - +
161F PHE* 3.4 28.4 - - - -
238F ASN* 3.5 22.5 - - - +
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Residues in contact with VAL 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E VAL* 4.5 3.4 - - + -
157E THR* 1.3 80.5 - - - +
159E ASN* 1.3 67.3 + - - +
160E VAL* 4.3 2.7 - - + -
192E TYR* 3.8 27.6 - - + +
195E LEU* 5.5 0.4 - - + -
196E LEU* 3.9 22.9 - - + -
236E SER 2.9 9.0 + - - +
237E ILE* 3.2 28.3 - - + -
238E ASN* 3.0 24.9 + - - -
251E SER 3.3 13.9 - - - +
252E ILE* 3.6 28.5 - - + -
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Residues in contact with ASN 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E THR* 4.3 9.0 - - - +
158E VAL* 1.3 80.1 - - - +
160E VAL* 1.3 67.4 + - - +
161E PHE* 3.7 29.3 - - + -
238E ASN* 3.4 22.0 + - - +
249E GLU* 3.2 23.8 + - - +
250E GLY* 3.1 4.3 - - - -
251E SER* 2.8 44.6 + - - +
262E ARG* 5.4 2.0 - - - +
157F THR* 4.5 11.2 + - - +
159F ASN* 5.3 6.7 - - - +
262F ARG* 6.1 1.4 - - - +
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Residues in contact with VAL 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E VAL* 4.3 4.5 - - + -
159E ASN* 1.3 79.5 - - - +
161E PHE* 1.3 59.7 + - - +
162E TRP* 3.7 40.8 - - + -
189E ALA* 4.0 17.3 - - + -
192E TYR* 3.2 44.2 - - + -
238E ASN 3.0 7.9 + - - -
239E VAL* 3.4 16.4 - - + +
240E THR 3.0 27.2 + - - +
241E MET* 4.2 5.4 - - + -
249E GLU 3.4 2.5 - - - -
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Residues in contact with PHE 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E ASN* 3.7 33.0 - - + -
160E VAL* 1.3 79.5 - - - +
162E TRP* 1.3 57.5 + - - +
238E ASN* 3.7 15.7 - - + -
239E VAL 4.7 0.2 - - - -
240E THR* 3.8 6.5 - - + -
243E THR* 3.1 15.3 + - - +
248E LEU* 2.9 35.6 + - + -
249E GLU* 2.6 44.2 + - + +
155F MET* 3.6 25.6 - - + -
157F THR* 3.9 19.3 - - - -
253F THR* 4.2 20.9 - - + -
255F LEU* 3.5 22.2 - - + -
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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