Contacts of the strand formed by residues 158 - 168 (chain E) in PDB entry 6CU0
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 158 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E GLY* 1.3 75.8 - - - -
159E GLY* 1.3 60.4 + - - +
185E LEU* 3.7 20.7 - - - +
187E PRO* 4.1 22.9 - - - -
219E GLU 4.0 1.2 - - - +
220E ALA* 4.9 0.2 - - - -
221E ARG* 3.1 50.9 + - - +
222E ALA 5.1 0.7 + - - -
223E ARG* 6.1 0.2 - - - -
226E TRP* 4.2 1.8 - - - +
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Residues in contact with GLY 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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191C GLU* 6.5 0.4 - - - -
158E SER* 1.3 77.4 + - - +
160E SER* 1.3 63.2 + - - -
184E ASP* 3.7 5.2 - - - +
185E LEU* 2.8 34.5 + - - +
219E GLU* 3.7 9.9 - - - -
221E ARG* 5.2 2.0 - - - -
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Residues in contact with SER 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C ARG* 6.5 0.7 - - - -
159E GLY* 1.3 75.8 - - - -
161E VAL* 1.3 71.2 + - - +
162E SER* 4.0 4.6 + - - -
182E THR* 3.3 23.2 - - - +
183E VAL 3.5 9.2 - - - -
184E ASP* 4.9 6.7 - - - -
185E LEU* 4.2 3.5 - - - +
218E THR* 3.4 3.6 + - - -
219E GLU* 3.0 42.8 + - - +
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Residues in contact with VAL 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LEU* 5.2 8.1 - - + -
147E LEU* 4.0 14.8 - - + +
149E LEU* 3.9 29.8 - - + -
160E SER* 1.3 79.8 + - - +
162E SER* 1.3 66.6 + - - +
182E THR* 3.4 1.6 - - - +
183E VAL* 2.9 32.3 + - - +
185E LEU* 3.8 26.2 - - + -
216E LEU* 3.5 28.3 - - + -
217E HIS 3.5 7.4 - - - +
218E THR* 4.2 11.7 - - + +
226E TRP* 6.1 0.4 - - + -
228E LEU* 5.2 0.2 - - + -
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Residues in contact with SER 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E LEU* 5.0 0.2 - - - -
160E SER* 4.0 4.0 + - - -
161E VAL* 1.3 80.1 + - - +
163E LEU* 1.3 65.8 + - - +
181E LEU 3.2 13.7 - - - -
182E THR* 3.6 17.8 + - - +
215E HIS 3.5 1.2 - - - +
216E LEU* 3.3 7.4 - - - +
217E HIS* 2.7 53.7 + - - +
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Residues in contact with LEU 163 (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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109E TRP* 5.5 2.9 - - + -
145E PHE* 4.5 16.4 - - + -
146E GLN 4.2 18.6 - - - +
147E LEU* 3.9 26.1 - - + +
162E SER* 1.3 75.9 - - - +
164E ALA* 1.3 62.7 + - - +
180E ALA* 3.6 3.4 - - - +
181E LEU* 3.1 42.1 + - + +
214E VAL* 4.2 25.4 - - + -
215E HIS 3.5 1.6 - - - -
216E LEU* 3.5 34.5 - - + -
228E LEU* 5.8 0.4 - - + -
233E THR* 4.2 13.7 - - + -
234E VAL 5.6 0.2 - - - +
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Residues in contact with ALA 164 (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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162E SER* 6.3 0.2 - - - -
163E LEU* 1.3 77.7 - - - +
165E LEU* 1.3 61.7 - - - +
166E HIS* 3.7 22.7 + - + +
177E ALA* 4.2 12.3 - - + -
179E LEU 3.6 6.3 - - - -
180E ALA* 4.5 2.7 - - + +
214E VAL* 3.4 5.1 - - - -
215E HIS* 2.8 39.1 + - + +
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Residues in contact with LEU 165 (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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143E VAL* 4.1 23.6 - - + -
164E ALA* 1.3 70.7 - - - +
166E HIS* 1.3 63.1 + - - +
167E LEU* 4.7 8.5 - - + -
177E ALA* 3.6 4.5 - - - -
178E ALA* 2.9 42.8 + - + +
179E LEU* 2.8 35.4 + - + +
206E LEU* 6.4 0.9 - - + -
212E LEU* 4.0 22.4 - - + -
213E GLY 3.5 7.9 - - - +
214E VAL* 3.7 26.4 - - + +
235E LEU* 4.3 15.0 - - + -
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Residues in contact with HIS 166 (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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164E ALA* 3.9 22.7 - - + +
165E LEU* 1.3 75.5 + - - +
167E LEU* 1.3 65.0 - - - +
168E GLN 4.0 0.3 + - - -
176E ALA 4.4 7.9 + - - -
177E ALA* 3.9 30.5 - - + +
178E ALA 5.0 0.7 - - - +
211E ARG 3.9 1.0 - - - +
212E LEU* 3.7 2.1 - - - +
213E GLY* 2.8 35.3 + - - +
215E HIS* 4.2 17.4 - - + +
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Residues in contact with LEU 167 (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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165E LEU* 4.4 7.6 + - + -
166E HIS* 1.3 78.2 - - - +
168E GLN* 1.3 62.3 + - - +
169E PRO 3.6 13.4 - - - +
178E ALA* 4.0 27.3 - - + +
204E LEU* 5.9 2.5 - - + -
205E HIS 5.2 4.5 - - - +
206E LEU* 4.2 19.5 - - + -
210E GLN* 3.9 36.6 - - + +
211E ARG 3.9 1.1 - - - -
212E LEU* 4.3 15.7 - - + -
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Residues in contact with GLN 168 (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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132E GLU* 3.9 17.9 - - - +
166E HIS 4.0 0.6 + - - +
167E LEU* 1.3 74.7 - - - +
169E PRO* 1.3 75.9 - - + +
210E GLN* 3.3 4.1 - - - +
211E ARG* 2.9 44.4 + - + +
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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