Contacts of the strand formed by residues 214 - 225 (chain A) in PDB entry 1JQI
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 THR 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A TRP* 3.7 33.7 - - + -
162A ILE 3.5 3.8 - - - +
163A THR* 4.8 1.4 + - - +
203A LYS* 3.7 3.1 - - - +
204A GLU* 2.9 48.2 + - + +
206A LYS* 2.9 34.5 + - + +
212A SER* 4.0 2.3 + - - -
213A SER* 1.3 76.9 + - - +
215A ALA* 1.3 64.0 + - - +
399A FAD 3.9 25.3 - - + +
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A TRP 4.2 1.1 - - - -
162A ILE* 2.7 38.9 + - - +
165A SER* 3.4 9.7 + - - +
166A TRP* 3.4 29.6 - - + +
200A LEU* 5.4 0.2 - - + -
201A GLY 3.4 12.6 - - - +
202A LYS 3.6 9.9 - - - +
204A GLU* 4.5 5.2 - - - -
214A THR* 1.3 77.5 - - - +
216A ASN* 1.3 68.1 + - - +
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Residues in contact with ASN 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PRO* 4.8 6.7 - - - +
158A THR* 4.1 13.1 - - + +
159A LYS 3.1 13.2 - - - +
160A ALA* 3.2 23.8 - - - +
161A TRP* 3.5 4.3 + - - -
200A LEU* 3.6 1.0 - - - +
201A GLY* 2.8 30.7 + - - +
202A LYS 4.9 0.4 + - - -
204A GLU* 5.1 8.0 - - - +
215A ALA* 1.3 78.6 - - - +
217A LEU* 1.3 68.4 - - - +
218A ILE* 4.0 14.5 - - + +
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 4.0 18.8 - - + -
157A GLY 3.9 0.5 - - - +
158A THR* 3.5 2.4 - - - -
159A LYS* 2.9 38.6 + - + +
162A ILE* 3.6 25.1 - - + -
165A SER* 4.0 11.2 - - - -
171A THR* 4.2 23.6 - - + +
193A MET* 3.9 12.8 - - + -
198A LEU* 4.2 7.0 - - + -
199A THR 3.5 2.0 - - - -
200A LEU* 3.3 32.1 - - + -
216A ASN* 1.3 76.1 - - - +
218A ILE* 1.3 64.4 + - - +
219A PHE* 3.8 19.1 + - + -
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Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLY 3.9 2.7 - - - +
158A THR* 4.3 20.9 - - + +
197A GLY 3.4 5.7 - - - +
198A LEU* 3.5 2.4 - - - -
199A THR* 2.8 62.1 + - + +
200A LEU 4.0 1.3 - - - -
201A GLY* 3.7 25.6 - - - +
216A ASN* 3.9 12.1 - - + +
217A LEU* 1.3 74.4 - - - +
219A PHE* 1.3 69.1 + - - +
220A GLU* 5.0 8.2 - - + +
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Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A THR* 4.7 9.2 - - + -
155A LEU* 3.7 33.7 - - + +
156A ASN* 3.5 3.3 - - - +
157A GLY* 2.8 45.5 + - - +
159A LYS* 4.6 6.5 - - + -
171A THR* 4.9 4.0 - - + -
173A VAL* 4.1 32.3 - - + -
191A VAL* 4.4 9.0 - - + -
197A GLY 3.6 1.6 - - - -
198A LEU* 3.7 26.5 - - + -
217A LEU* 3.9 33.4 - - + -
218A ILE* 1.3 75.5 - - - +
220A GLU* 1.3 60.7 + - - +
222A CYS* 3.8 26.0 - - + -
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Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU 4.1 0.2 + - - -
156A ASN* 3.6 3.8 - - - -
197A GLY* 3.0 29.4 + - - +
199A THR* 4.6 11.7 + - - +
218A ILE* 5.1 8.5 - - + +
219A PHE* 1.3 73.4 - - - +
221A ASP* 1.3 72.8 - - - +
222A CYS 3.1 0.9 + - - +
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Residues in contact with ASP 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ARG* 4.7 8.3 + - - -
154A VAL* 3.7 16.6 - - - +
155A LEU 3.2 4.3 + - - -
156A ASN* 2.7 32.6 + - - +
196A PRO 5.0 0.7 - - - +
197A GLY* 4.8 1.7 - - - -
220A GLU* 1.3 74.6 - - - +
222A CYS* 1.3 62.7 + - - +
223A ARG* 3.4 42.9 + - - +
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Residues in contact with CYS 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A TRP 3.6 1.4 - - - +
154A VAL* 3.4 0.7 - - - -
155A LEU* 2.8 41.4 + - + +
191A VAL* 4.5 1.3 - - - -
195A THR* 3.7 22.0 - - - -
196A PRO 3.6 21.1 - - - -
197A GLY 3.9 13.2 - - - +
198A LEU 4.4 0.2 - - - -
219A PHE* 3.8 35.4 - - + -
220A GLU 3.1 1.7 + - - -
221A ASP* 1.3 73.9 - - - +
223A ARG* 1.3 62.7 + - - +
224A ILE* 4.5 13.5 - - - -
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Residues in contact with ARG 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ARG* 5.4 1.4 - - - +
149A GLU* 3.3 28.3 + - - -
152A SER* 4.6 11.2 - - - +
153A TRP 3.2 5.2 - - - +
154A VAL* 3.7 17.3 - - + +
195A THR* 4.6 7.8 + - - -
196A PRO 4.4 4.2 + - - +
221A ASP* 3.4 39.7 + - - +
222A CYS* 1.3 74.2 - - - +
224A ILE* 1.3 68.9 + - - +
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Residues in contact with ILE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A SER* 3.0 7.0 - - - -
153A TRP* 2.8 41.0 + - + +
155A LEU* 3.9 19.3 - - + -
189A PHE* 3.9 32.3 - - + -
190A LEU 4.2 2.9 - - - +
191A VAL* 4.2 27.8 - - + -
192A PRO* 4.8 5.2 - - + -
195A THR* 5.4 2.0 - - - +
222A CYS* 4.5 9.4 - - - +
223A ARG* 1.3 81.9 - - - +
225A PRO* 1.3 74.6 - - + +
228A ASN* 3.8 22.4 - - + +
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Residues in contact with PRO 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ASP 3.8 6.7 - - - +
152A SER* 4.2 1.8 - - - -
153A TRP* 3.6 4.7 - - - -
192A PRO* 6.1 1.6 - - + -
224A ILE* 1.3 90.9 - - + +
226A LYS* 1.3 64.0 + - - +
227A GLU* 3.3 22.2 - - + +
228A ASN* 2.9 48.2 + - - +
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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