Contacts of the strand formed by residues 201 - 210 (chain H) in PDB entry 4OZF
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 TYR 201 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H GLY 3.0 23.4 + - - -
163H PHE* 2.7 50.1 + - + +
164H TYR* 3.6 21.5 - + - -
166H ASP* 3.8 42.2 + - + -
189H PRO* 4.2 14.6 - - + -
190H LEU 3.4 15.7 - - - -
191H LYS* 3.7 34.5 + - + +
192H GLU* 4.1 2.2 - - - -
199H SER 3.4 18.8 - - - -
200H ARG* 1.3 72.8 - - - +
202H ALA* 1.4 59.8 + - - +
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Residues in contact with ALA 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193G TRP* 3.7 30.1 - - + -
160H ALA 3.3 10.8 - - - +
161H THR* 3.9 3.4 - - + -
163H PHE* 3.8 2.0 - - - -
189H PRO* 3.3 3.4 - - - +
190H LEU* 2.8 47.1 + - + +
192H GLU* 3.8 16.1 - - + +
201H TYR* 1.4 73.4 - - - +
203H LEU* 1.3 60.1 + - - +
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Residues in contact with LEU 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173G THR* 6.3 0.2 - - - -
193G TRP* 5.6 0.9 - - - -
158H CYS 4.1 0.2 - - - +
159H LEU* 3.6 5.7 - - - +
160H ALA* 2.8 44.5 + - + +
163H PHE* 3.8 15.0 - - + -
168H VAL* 3.8 24.5 - - + +
170H LEU* 4.0 33.0 - - + +
185H THR* 4.3 4.3 - - + -
186H ASP* 3.5 35.2 - - + +
188H GLN* 4.0 0.7 - - - -
189H PRO* 3.8 26.2 - - + -
202H ALA* 1.3 75.1 - - - +
204H SER* 1.3 63.2 + - - +
225H VAL* 6.1 0.4 - - + -
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Residues in contact with SER 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G THR* 3.8 13.1 - - - +
191G VAL* 3.7 16.9 - - - +
157H VAL* 4.9 0.2 - - - -
158H CYS 3.2 11.9 - - - -
159H LEU* 3.8 15.3 - - - -
170H LEU* 4.5 2.0 - - - -
185H THR* 3.7 4.3 - - - +
186H ASP* 2.9 44.8 + - - +
203H LEU* 1.3 74.9 - - - +
205H SER* 1.3 64.0 + - - +
206H ARG* 3.3 15.6 + - - -
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Residues in contact with SER 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H LEU 4.0 0.2 - - - +
157H VAL* 3.4 5.7 - - - +
158H CYS* 2.9 31.7 + - - +
170H LEU* 3.4 30.9 - - - +
172H TRP* 3.5 16.6 + - - -
183H VAL* 4.5 0.2 - - - +
184H CYS 3.1 12.8 + - - -
185H THR* 2.8 24.7 + - - -
204H SER* 1.3 75.7 + - - +
206H ARG* 1.3 65.2 + - - +
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Residues in contact with ARG 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152G LEU* 5.2 0.9 - - + -
173G THR* 2.8 28.9 + - - -
174G ASP 3.8 4.6 + - - -
176G CYS* 3.6 10.4 - - - -
178G LEU* 4.2 5.1 - - + +
189G SER* 3.4 45.0 + - - +
191G VAL* 3.7 23.5 - - + +
155H THR* 3.8 20.9 - - + -
156H LEU 3.6 4.9 - - - +
157H VAL* 4.5 6.5 - - + -
172H TRP* 3.8 7.0 + - - -
182H GLY 3.7 0.4 - - - +
183H VAL* 3.3 5.9 - - - -
184H CYS* 2.9 60.1 + - + -
186H ASP* 3.1 17.2 + - - +
204H SER* 3.3 24.8 + - - -
205H SER* 1.3 78.4 + - - +
207H LEU* 1.3 60.3 + - - +
208H ARG 4.2 0.2 - - - -
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Residues in contact with LEU 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H ALA 3.4 2.8 - - - +
155H THR* 3.3 2.4 - - - -
156H LEU* 2.9 38.8 + - + +
172H TRP* 3.6 44.4 - - + +
174H VAL* 3.7 26.0 - - + -
179H VAL* 4.2 7.9 - - + -
181H SER 4.1 9.4 - - - +
182H GLY 3.3 13.5 - - - +
183H VAL* 3.6 16.8 - - + -
206H ARG* 1.3 73.6 - - - +
208H ARG* 1.3 65.4 + - - +
209H VAL* 4.4 12.3 - - + -
221H PHE* 4.0 13.5 - - + -
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Residues in contact with ARG 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G TYR* 5.5 0.2 - - - -
154G THR* 3.9 14.8 + - - +
155G ASP* 2.8 32.7 + - - -
178G LEU* 3.7 28.9 - - + +
180G MET* 3.6 30.5 - - + +
185G PHE* 3.4 13.9 - - - -
187G SER* 3.2 15.7 + - - -
147H GLU* 3.2 18.2 + - - +
151H THR* 3.6 22.8 - - - +
153H LYS* 3.7 11.0 - - + +
154H ALA 3.4 5.4 - - - +
155H THR* 2.8 26.1 + - + +
181H SER 4.6 1.4 - - - +
182H GLY* 2.7 20.2 + - - +
206H ARG 4.2 0.4 - - - -
207H LEU* 1.3 75.7 - - - +
209H VAL* 1.3 73.6 + - - +
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Residues in contact with VAL 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G MET* 4.6 8.5 - - - -
153H LYS* 3.5 7.8 - - - +
154H ALA* 2.8 42.8 + - + +
156H LEU* 4.3 8.1 - - + -
174H VAL* 5.6 1.6 - - + -
207H LEU* 4.4 15.3 - - + -
208H ARG* 1.3 79.3 - - - +
210H SER* 1.3 68.6 + - - +
213H PHE* 3.9 26.2 - - + -
214H TRP* 4.3 8.1 - - + -
221H PHE* 4.2 23.3 - - + -
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Residues in contact with SER 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G MET* 5.3 0.4 - - - -
183G MET* 6.0 8.7 - - - -
152H GLN 4.1 5.4 - - - -
153H LYS* 4.6 3.6 - - - +
154H ALA* 4.0 2.5 - - - +
209H VAL* 1.3 79.5 - - - +
211H ALA* 1.4 64.6 + - - +
212H THR* 3.4 10.5 + - - -
213H PHE* 3.2 24.7 + - - +
214H TRP* 3.4 19.8 + - - +
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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