Contacts of the strand formed by residues 152 - 163 (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 SER 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A GLU* 3.6 3.6 - - - +
149A GLU* 2.7 49.2 + - - +
150A GLY 3.4 2.7 + - - -
151A ASP* 1.3 87.3 + - - +
153A TRP* 1.3 61.8 + - - +
223A ARG* 4.6 12.4 - - - -
224A ILE 3.0 23.3 - - - -
225A PRO* 4.2 0.9 - - - -
226A LYS* 3.5 7.8 - - - +
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Residues in contact with TRP 153 (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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146A ALA* 4.3 7.0 - - + -
147A ARG 3.2 7.6 - - - -
148A GLU* 3.6 48.0 - - + -
152A SER* 1.3 74.3 - - - +
154A VAL* 1.3 64.1 + - - +
155A LEU* 4.0 9.9 - - + -
177A THR* 4.1 21.8 - - + -
189A PHE* 3.5 34.2 - + + -
222A CYS 3.6 0.9 - - - +
223A ARG* 3.2 6.6 - - - +
224A ILE* 2.8 40.1 + - + +
225A PRO 3.6 8.7 - - - -
226A LYS* 3.0 50.9 + - + +
229A LEU* 3.9 21.9 - - + +
233A PRO* 5.0 12.8 - - + -
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Residues in contact with VAL 154 (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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145A THR 3.6 1.4 - - - +
146A ALA* 3.3 2.8 - - - -
147A ARG* 2.7 54.1 + - - +
149A GLU* 3.3 40.6 - - + +
152A SER* 5.0 0.7 - - - +
153A TRP* 1.3 76.9 - - - +
155A LEU* 1.3 64.5 + - - +
156A ASN* 3.7 13.9 + - - +
221A ASP* 3.7 36.8 - - + +
222A CYS 3.4 2.5 - - - -
223A ARG* 3.7 16.4 - - + +
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Residues in contact with LEU 155 (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* 5.1 2.2 - - + -
145A THR 3.2 8.7 - - - +
146A ALA* 4.3 10.5 - - + -
153A TRP* 4.0 13.5 - - + -
154A VAL* 1.3 77.2 - - - +
156A ASN* 1.3 61.3 + - - +
173A VAL* 3.9 30.3 - - + -
175A ALA* 5.1 4.3 - - + -
189A PHE* 4.8 5.2 - - + -
191A VAL* 4.0 15.3 - - + -
219A PHE* 3.7 31.2 - - + +
221A ASP* 3.2 7.8 + - - -
222A CYS* 2.8 42.5 + - - +
224A ILE* 3.9 25.1 - - + -
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Residues in contact with ASN 156 (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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143A SER 4.5 0.5 - - - +
144A THR* 3.3 5.2 - - - -
145A THR* 2.8 47.6 + - - +
147A ARG* 3.7 22.0 - - - +
154A VAL* 3.7 9.9 + - - +
155A LEU* 1.3 78.6 + - - +
157A GLY* 1.3 58.8 + - - +
219A PHE* 3.5 4.4 - - - +
220A GLU* 3.6 5.4 - - - -
221A ASP* 2.7 41.9 + - - +
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Residues in contact with GLY 157 (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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143A SER 5.4 0.9 - - - -
144A THR* 3.6 13.9 - - - -
156A ASN* 1.3 75.2 - - - +
158A THR* 1.3 63.9 + - - -
218A ILE* 4.7 0.6 - - - +
219A PHE* 2.8 40.8 + - - +
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Residues in contact with THR 158 (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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132A GLU* 3.3 22.3 - - - +
133A PRO* 3.6 28.9 - - + +
144A THR* 3.5 7.5 + - - -
157A GLY* 1.3 74.9 + - - -
159A LYS* 1.3 74.0 + - - +
216A ASN* 4.1 15.7 - - + +
217A LEU 3.5 6.5 - - - +
218A ILE* 4.3 19.0 - - + +
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Residues in contact with LYS 159 (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* 3.1 43.7 - - + +
130A LEU* 3.2 22.1 + - - +
131A SER 3.5 9.4 - - - +
132A GLU* 2.6 26.9 + - + -
142A ALA* 4.5 4.6 - - - +
144A THR* 3.7 14.4 + - + +
157A GLY 4.3 0.2 + - - -
158A THR* 1.3 74.4 - - - +
160A ALA* 1.3 59.4 + - - +
162A ILE* 4.2 5.6 - - + -
173A VAL* 4.1 9.6 - - + -
174A PHE* 2.8 26.4 + - - +
216A ASN* 3.1 9.5 - - - +
217A LEU* 2.9 48.5 + - + +
219A PHE* 4.6 4.2 - - + -
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Residues in contact with ALA 160 (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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131A SER* 2.8 22.5 + - - +
132A GLU* 3.5 6.2 - - - +
133A PRO* 3.5 33.0 - - + -
159A LYS* 1.3 74.2 - - - +
161A TRP* 1.3 89.2 + - + +
162A ILE* 3.1 12.8 - - - +
216A ASN* 3.2 13.7 - - - +
399A FAD 4.1 0.3 + - - -
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Residues in contact with TRP 161 (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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131A SER* 4.2 6.3 - - - -
132A GLU 4.7 5.9 + - - -
133A PRO* 5.4 3.8 + - - +
160A ALA* 1.3 89.5 - - + +
162A ILE* 1.3 54.9 + - - +
204A GLU* 3.4 27.1 + - + -
214A THR* 3.7 24.5 - - + -
215A ALA* 3.8 3.9 + - - +
216A ASN* 3.5 9.0 + - - -
399A FAD 2.5 99.9 + + + +
673B ARG* 6.1 0.4 - - - +
745B GLY* 3.5 33.7 - - - -
746B MET* 3.7 29.4 - - + -
749B VAL* 3.7 22.4 - - + -
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Residues in contact with ILE 162 (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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127A CYS* 3.7 32.1 - - + -
128A PHE 3.7 14.8 - - - +
129A ALA* 3.7 25.4 - - + -
131A SER 4.6 0.7 - - - +
159A LYS* 4.2 4.7 - - + -
160A ALA 3.1 26.7 - - - +
161A TRP* 1.3 71.7 - - - +
163A THR* 1.3 59.8 + - - +
165A SER* 2.9 34.6 + - - -
213A SER 3.4 2.7 - - - +
214A THR* 4.2 0.7 - - - -
215A ALA 2.7 30.2 + - - +
217A LEU* 3.6 25.8 - - + +
399A FAD 3.9 5.6 - - + +
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Residues in contact with THR 163 (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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90A VAL* 4.5 11.9 - - + -
94A VAL* 4.1 17.2 - - + +
127A CYS* 3.2 20.1 - - - +
161A TRP 3.4 0.4 + - - -
162A ILE* 1.3 67.6 - - - +
164A ASN* 1.3 86.3 + - - +
165A SER 3.1 4.4 + - - -
209A ILE* 5.9 1.9 - - + +
212A SER* 4.4 16.2 - - - +
213A SER 3.2 11.7 + - - +
214A THR* 4.6 1.4 + - - +
367A TYR* 5.2 1.4 - - - -
399A FAD 2.9 48.1 + - - +
400A CAA 4.0 9.4 - - - +
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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