Contacts of the strand formed by residues 189 - 198 (chain H) in PDB entry 5U2V
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 189 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150H GLY 3.1 23.7 + - - -
151H PHE* 2.8 48.0 + - + -
152H TYR* 3.8 14.0 - + - -
153H PRO* 5.4 0.2 - - + -
154H ASP* 3.8 39.0 - - + +
177H PRO* 3.8 19.1 - - + -
178H LEU 3.3 18.4 - - - +
179H LYS* 4.0 30.7 - - + -
180H GLU* 4.0 3.4 - - - -
185H ASN 5.8 0.3 + - - -
187H SER 3.6 16.4 + - - -
188H ARG* 1.3 78.4 - - - +
190H ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 190 (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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174G TRP* 3.5 30.5 - - + -
148H ALA 3.2 9.9 - - - +
149H THR* 4.0 2.0 - - + -
151H PHE* 4.0 2.5 - - - -
174H ASP* 5.4 0.2 - - - +
177H PRO* 3.2 5.7 - - - +
178H LEU* 2.9 46.0 + - + +
180H GLU* 3.6 17.7 - - + +
189H TYR* 1.3 75.3 - - - +
191H LEU* 1.3 61.8 + - - +
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Residues in contact with LEU 191 (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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154G THR* 6.2 0.2 - - - -
174G TRP* 5.1 2.4 - - - -
146H CYS 3.7 0.7 - - - +
147H LEU* 3.5 5.2 - - - +
148H ALA* 2.8 39.0 + - + +
151H PHE* 4.1 14.6 - - + -
156H VAL* 4.2 19.7 - - + -
158H LEU* 4.0 30.9 - - + +
173H THR* 4.0 12.1 - - + -
174H ASP* 3.6 34.3 - - + +
176H GLN 4.0 0.2 - - - -
177H PRO* 3.8 28.9 - - + -
190H ALA* 1.3 74.8 - - - +
192H SER* 1.3 64.7 + - - +
213H VAL* 6.2 0.2 - - + -
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Residues in contact with SER 192 (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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154G THR* 3.3 19.3 - - - +
172G VAL* 4.4 11.0 - - - -
174G TRP* 4.5 2.5 - - - -
146H CYS 3.2 5.4 - - - -
147H LEU* 3.8 20.0 - - - -
158H LEU* 4.9 0.4 - - - -
173H THR* 3.9 4.0 - - - +
174H ASP* 2.5 55.0 + - - -
191H LEU* 1.3 76.5 - - - +
193H SER* 1.3 63.2 + - - +
194H ARG* 3.8 8.1 + - - -
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Residues in contact with SER 193 (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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145H VAL* 3.2 10.3 - - - +
146H CYS* 2.7 33.2 + - - -
158H LEU* 3.5 25.1 - - - +
160H TRP* 2.9 23.6 + - - -
171H VAL* 4.1 0.2 - - - +
172H CYS 3.3 9.9 + - - -
173H THR* 2.5 28.9 + - - -
192H SER* 1.3 74.4 - - - +
194H ARG* 1.3 67.1 + - - +
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Residues in contact with ARG 194 (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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133G LEU* 4.6 1.0 - - - +
154G THR* 3.4 11.7 + - - -
157G CYS* 3.2 20.4 - - - +
159G LEU* 4.5 12.1 - - + -
170G SER* 2.6 26.4 + - - -
171G ALA* 3.7 5.9 - - - +
172G VAL* 3.1 45.8 - - - +
143H THR* 4.1 17.3 - - + -
144H LEU 3.1 8.3 - - - +
145H VAL* 4.6 3.4 - - + -
160H TRP* 3.8 6.5 + - - -
170H GLY 3.6 1.1 - - - +
171H VAL* 3.2 6.2 - - - -
172H CYS* 2.9 60.3 + - + +
174H ASP* 3.1 22.0 + - - -
192H SER* 3.8 7.2 + - - -
193H SER* 1.3 77.7 + - - +
195H LEU* 1.3 59.9 + - - +
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Residues in contact with LEU 195 (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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143H THR* 4.4 1.6 - - - -
144H LEU* 2.7 45.3 + - + +
160H TRP* 3.6 43.0 - - + -
162H VAL* 3.8 15.5 - - + -
167H VAL* 4.2 8.5 - - + -
169H SER 3.6 23.1 - - - +
170H GLY 3.3 1.8 - - - +
171H VAL* 3.7 11.4 - - + -
194H ARG* 1.3 73.6 - - - +
196H ARG* 1.3 66.8 + - - +
197H VAL* 4.1 11.0 - - + -
209H PHE* 3.8 29.6 - - + -
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Residues in contact with ARG 196 (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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135G THR* 4.2 9.0 + - - +
136G ASP* 2.7 43.6 + - - -
159G LEU* 3.9 31.2 - - + +
161G MET* 3.2 29.4 - - - +
166G PHE* 3.5 12.9 - - - -
168G SER* 2.9 16.4 + - - -
135H GLU* 2.8 28.4 + - - +
139H THR* 3.8 15.2 + - - +
141H LYS* 3.7 12.0 - - + +
142H ALA 3.1 12.1 - - - +
143H THR* 3.0 16.2 + - - +
169H SER 4.8 0.3 - - - +
170H GLY* 2.8 21.7 + - - -
194H ARG 4.2 0.4 - - - -
195H LEU* 1.3 75.5 - - - +
197H VAL* 1.3 67.0 + - - +
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Residues in contact with VAL 197 (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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161G MET* 3.7 9.2 - - - -
141H LYS* 3.6 4.5 - - - +
142H ALA* 2.7 42.3 + - + +
144H LEU* 4.4 7.4 - - + -
162H VAL* 5.8 0.9 - - + -
195H LEU* 4.1 17.5 - - + +
196H ARG* 1.3 78.9 - - - +
198H SER* 1.3 68.7 + - - +
201H PHE* 4.1 16.8 - - + -
202H TRP* 3.9 25.6 - - + +
209H PHE* 3.9 23.1 - - + -
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Residues in contact with SER 198 (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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161G MET* 4.0 6.8 - - - +
164G MET* 4.9 17.7 - - - -
140H GLN 4.2 5.8 - - - -
141H LYS* 4.6 1.1 - - - +
197H VAL* 1.3 78.7 - - - +
199H ALA* 1.3 66.0 + - - +
200H THR* 3.2 20.2 + - - -
201H PHE* 3.0 25.7 + - - +
202H TRP 3.1 10.4 + - - -
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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