Contacts of the strand formed by residues 188 - 197 (chain H) in PDB entry 5D7I
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 188 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H GLY 3.0 23.4 + - - -
150H PHE* 2.7 48.6 + - + -
151H TYR* 3.8 17.6 - + - -
152H PRO* 5.4 0.2 - - + -
153H ASP* 3.5 46.1 + - + +
176H PRO* 3.8 14.6 - - + -
177H LEU 3.3 17.7 - - - +
178H LYS* 3.8 34.6 - - + -
179H GLU* 3.9 3.1 - - - -
184H ASN 5.6 2.1 + - - -
186H SER 3.5 17.1 + - - -
187H ARG* 1.3 76.2 - - - +
189H ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 189 (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* 3.6 31.4 - - + -
147H ALA 3.2 10.3 - - - +
148H THR* 4.1 1.6 - - + -
150H PHE* 3.9 2.5 - - - -
173H ASP* 5.3 0.3 - - - +
176H PRO* 3.2 4.9 - - - +
177H LEU* 2.8 40.7 + - + +
179H GLU* 3.5 22.9 - - + +
188H TYR* 1.3 76.0 - - - +
190H LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G TRP* 5.3 1.3 - - - -
145H CYS 3.9 0.2 - - - +
146H LEU* 3.5 5.2 - - - +
147H ALA* 2.8 38.9 + - + +
150H PHE* 3.8 15.9 - - + -
155H VAL* 3.8 23.8 - - + +
157H LEU* 4.2 20.0 - - + +
172H THR* 3.9 18.6 - - + -
173H ASP* 3.5 37.0 - - + +
174H PRO 5.0 0.7 - - - +
175H GLN 3.9 0.2 - - - -
176H PRO* 3.8 26.5 - - + -
189H ALA* 1.3 75.3 - - - +
191H SER* 1.3 65.2 + - - +
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Residues in contact with SER 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G THR* 3.1 13.5 + - - +
172G VAL* 4.1 11.6 - - - +
174G TRP* 4.5 2.2 - - - -
144H VAL* 4.9 0.4 - - - -
145H CYS 3.3 4.9 - - - -
146H LEU* 3.5 22.2 - - - -
157H LEU* 4.8 1.1 - - - -
172H THR* 3.7 3.6 - - - +
173H ASP* 2.6 58.1 + - - +
190H LEU* 1.3 75.7 - - - +
192H SER* 1.3 62.9 + - - +
193H ARG* 3.6 9.4 + - - -
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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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144H VAL* 3.3 7.2 - - - +
145H CYS* 2.8 32.8 + - - +
157H LEU* 3.5 24.5 - - - -
159H TRP* 2.9 20.5 + - - -
170H VAL* 4.1 0.2 - - - +
171H CYS 3.4 9.0 + - - -
172H THR* 2.6 28.5 + - - -
191H SER* 1.3 76.2 - - - +
193H ARG* 1.3 73.0 + - - +
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Residues in contact with ARG 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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133G LEU* 4.4 12.1 - - - -
154G THR* 4.0 0.8 - - - +
155G ASP 3.7 5.1 + - - -
157G CYS* 2.9 28.4 + - - +
159G LEU* 4.3 15.6 - - + +
170G SER* 2.2 57.4 + - - -
171G ALA* 3.6 5.7 - - - +
172G VAL* 3.5 24.3 - - - +
142H THR* 4.0 13.7 - - + -
143H LEU 3.2 9.9 - - - +
144H VAL* 4.8 2.2 - - + -
159H TRP* 3.8 3.6 - - - -
169H GLY 3.5 1.2 - - - +
170H VAL* 3.2 9.0 - - - +
171H CYS* 2.9 44.2 + - + +
173H ASP* 3.7 8.1 + - - -
191H SER* 3.6 14.5 + - - -
192H SER* 1.3 77.2 + - - +
194H LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 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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142H THR* 4.5 1.3 - - - -
143H LEU* 2.8 40.2 + - + +
159H TRP* 3.5 47.0 - - + -
161H VAL* 3.9 15.5 - - + -
166H VAL* 4.2 7.2 - - + -
168H SER 3.7 22.7 - - - +
169H GLY 3.4 1.8 - - - -
170H VAL* 3.7 9.0 - - + -
193H ARG* 1.3 74.0 - - - +
195H ARG* 1.3 69.8 + - - +
196H VAL* 4.0 13.9 - - + -
208H PHE* 3.9 26.9 - - + -
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Residues in contact with ARG 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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135G THR* 3.9 7.4 + - - +
136G ASP* 2.7 42.4 + - - -
159G LEU* 3.8 30.9 - - + +
161G MET* 3.5 29.5 - - - +
166G PHE* 3.6 7.1 - - - -
168G SER* 2.9 19.0 + - - -
134H GLU* 2.8 27.9 + - - +
138H THR* 3.8 17.4 + - - +
140H LYS* 3.6 15.5 - - + +
141H ALA 3.4 8.1 - - - +
142H THR* 3.1 16.5 + - - +
168H SER 4.7 0.7 - - - +
169H GLY* 2.8 21.6 + - - -
193H ARG 4.2 0.2 - - - -
194H LEU* 1.3 74.8 - - - +
196H VAL* 1.3 70.9 + - - +
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Residues in contact with VAL 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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161G MET* 3.8 9.4 - - - -
140H LYS* 3.5 5.2 - - - +
141H ALA* 2.7 42.5 + - + +
143H LEU* 4.6 4.0 - - + -
161H VAL* 5.8 1.3 - - + -
194H LEU* 4.0 22.9 - - + +
195H ARG* 1.3 78.8 - - - +
197H SER* 1.3 69.2 + - - +
200H PHE* 4.0 24.2 - - + -
201H TRP* 3.9 23.8 - - + +
208H PHE* 4.2 12.6 - - + -
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Residues in contact with SER 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* 4.1 3.8 - - - +
164G MET* 3.6 27.0 - - - +
139H GLN 3.9 7.6 - - - -
140H LYS* 4.4 1.6 - - - +
141H ALA 4.3 0.4 - - - -
196H VAL* 1.3 81.6 - - - +
198H ALA* 1.3 65.8 + - - +
199H THR* 3.3 12.2 + - - -
200H PHE* 3.1 30.8 + - - +
201H TRP* 3.1 10.6 + - - +
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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