Contacts of the strand formed by residues 153 - 163 (chain F) in PDB entry 4OZH
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 LYS 153 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180E MET* 3.8 15.9 - - + -
183E MET* 3.8 35.2 - - + -
185E PHE* 3.4 41.0 - - - +
147F GLU* 3.2 31.2 - - - +
148F ILE* 3.7 4.4 + - - -
151F THR* 3.1 28.5 + - + +
152F GLN* 1.3 81.8 - - - +
154F ALA* 1.3 60.8 - - - +
208F ARG* 3.8 22.7 - - + +
209F VAL 3.5 8.5 - - - +
210F SER* 4.7 0.2 - - - -
211F ALA 4.0 2.5 - - - +
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Residues in contact with ALA 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F PRO* 3.7 26.5 - - + -
147F GLU* 4.0 0.7 - - - -
148F ILE* 4.1 10.1 - - + -
153F LYS* 1.3 73.4 - - - +
155F THR* 1.3 60.8 + - - +
156F LEU* 4.0 1.0 + - - +
207F LEU 3.7 1.6 - - - +
208F ARG* 3.5 2.0 - - - -
209F VAL* 2.7 45.4 + - + +
211F ALA* 4.3 4.0 - - - +
214F TRP* 3.8 25.1 - - + -
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Residues in contact with THR 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E LEU* 3.4 17.0 - - - +
152E LEU* 4.2 20.7 - - + +
154E THR* 5.4 0.6 + - - +
178E LEU* 6.0 0.7 - - + -
189E SER* 6.2 1.6 - - - -
143F PRO* 3.3 18.5 - - - +
147F GLU* 2.6 35.6 + - - +
154F ALA* 1.3 71.2 - - - +
156F LEU* 1.3 66.6 + - - +
157F VAL* 4.4 3.6 - - + -
206F ARG* 4.2 24.2 - - + -
207F LEU 3.4 9.6 - - - +
208F ARG* 3.1 23.2 + - + +
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Residues in contact with LEU 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F VAL* 4.0 17.3 - - + -
141F PHE 3.8 9.9 - - - +
142F GLU* 4.4 1.8 - - - -
143F PRO* 3.8 27.4 - - + -
154F ALA 4.3 6.5 - - - +
155F THR* 1.3 71.8 - - - +
157F VAL* 1.3 60.5 + - - +
172F TRP* 3.7 18.3 - - + -
206F ARG* 3.3 5.9 - - - +
207F LEU* 2.6 54.7 + - + +
209F VAL* 4.4 12.3 - - + -
214F TRP* 4.0 27.1 - - + -
221F PHE* 4.6 12.8 - - + -
252F ALA* 4.4 9.0 - - + -
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Residues in contact with VAL 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E LEU* 3.8 22.2 - - + -
150E VAL* 4.2 13.9 - - + -
152E LEU* 4.1 21.3 - - + -
191E VAL* 3.9 30.7 - - + -
140F VAL 3.7 0.2 - - - -
141F PHE* 2.8 45.9 + - + -
155F THR* 3.9 4.0 + - + -
156F LEU* 1.3 75.7 - - - +
158F CYS* 1.3 67.7 + - - +
159F LEU* 5.2 1.6 - - + -
172F TRP* 4.5 2.2 - - - -
204F SER* 5.0 1.3 - - - -
205F SER 3.4 7.9 - - - +
206F ARG* 4.0 16.6 - - + -
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Residues in contact with CYS 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F VAL* 3.7 17.3 - - - -
139F ALA 3.4 8.5 - - - -
140F VAL* 4.4 2.0 - - - +
157F VAL* 1.3 73.6 - - - +
159F LEU* 1.3 68.8 + - - +
170F LEU* 4.7 5.2 - - - -
172F TRP* 3.5 19.8 - - + -
204F SER* 3.3 6.9 - - - -
205F SER* 2.8 34.9 + - - +
223F CYS* 2.0 50.7 - - + -
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Residues in contact with LEU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E VAL* 3.7 25.6 - - + -
191E VAL* 5.1 1.3 - - + -
193E TRP* 3.6 59.0 - - + +
137F GLU 3.1 5.7 - - - +
138F VAL* 3.3 1.3 - - - -
139F ALA* 2.8 39.3 + - + +
141F PHE* 3.9 17.9 - - + -
157F VAL* 5.2 2.2 - - + -
158F CYS* 1.3 79.5 - - - +
160F ALA* 1.3 59.5 + - - +
161F THR* 4.0 14.7 + - + +
203F LEU 3.5 16.8 - - - +
204F SER* 3.9 9.6 - - - -
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Residues in contact with ALA 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F PRO* 4.3 7.4 - - + -
137F GLU 3.6 6.1 - - - -
138F VAL* 4.2 7.4 - - + +
158F CYS* 5.0 0.4 - - - -
159F LEU* 1.3 70.6 - - - +
161F THR* 1.3 58.9 + - - +
163F PHE* 3.3 18.8 - - + -
168F VAL* 6.1 0.2 - - + -
170F LEU* 4.9 4.0 - - + +
202F ALA* 3.4 0.3 - - - -
203F LEU* 2.8 46.9 + - + +
225F VAL* 4.0 29.6 - - + -
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Residues in contact with THR 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E TRP* 4.2 13.7 - - + +
136F PRO* 3.6 0.5 - - - +
137F GLU* 2.8 50.2 + - - +
159F LEU* 4.0 21.7 + - + +
160F ALA* 1.3 78.4 - - - +
162F GLY* 1.3 64.0 - - - +
163F PHE* 3.4 3.4 + - - -
192F GLU* 3.6 8.1 - - - +
201F TYR 3.9 2.9 - - - -
202F ALA* 3.8 17.7 - - + -
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Residues in contact with GLY 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F PHE* 3.4 6.2 - - - +
135F PRO 3.2 13.2 - - - +
137F GLU* 3.9 11.0 - - - +
161F THR* 1.3 72.2 - - - +
163F PHE* 1.3 57.4 + - - +
192F GLU* 2.8 23.6 + - - -
200F ARG* 2.9 40.6 + - - -
201F TYR 3.3 1.4 + - - -
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Residues in contact with PHE 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F PHE 3.4 6.1 - - - +
135F PRO 4.1 0.2 - - - -
136F PRO* 3.7 36.8 - - + -
160F ALA* 3.3 31.6 - - + -
162F GLY* 1.3 76.8 - - - +
164F TYR* 1.3 60.7 + - - +
165F PRO 3.5 13.7 - - - -
166F ASP* 3.8 12.3 - - + -
168F VAL* 3.7 36.8 - - + -
189F PRO* 4.0 12.6 - - + -
200F ARG* 4.5 0.9 - - - -
201F TYR* 2.7 71.7 + - + +
202F ALA* 3.8 1.8 - - - -
203F LEU* 3.8 7.6 - - + -
227F PHE* 4.3 3.6 - + + -
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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
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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