Contacts of the strand formed by residues 153 - 164 (chain J) in PDB entry 3STJ
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 153 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143J ALA 3.6 1.2 - - - +
144J VAL* 3.3 7.2 - - - +
145J GLY 2.8 27.6 + - - -
147J PRO* 3.6 30.2 - - + +
150J LEU* 4.6 1.4 - - - +
151J GLY 3.2 4.0 + - - -
152J GLN* 1.3 72.4 - - - +
154J ALA* 1.3 59.3 + - - +
155J THR* 4.0 22.2 - - + -
186J ASN* 5.2 1.4 - - - +
160K SER* 3.6 9.0 - - - -
164K ARG* 2.7 27.0 + - - -
177K GLN* 3.3 24.9 + - - +
215K ILE* 4.6 1.3 - - + -
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Residues in contact with ALA 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J LEU* 4.5 5.6 - - + -
23J LEU* 4.6 4.7 - - + -
142J VAL* 4.2 11.7 - - + -
143J ALA 3.2 7.4 - - - +
144J VAL* 4.4 9.4 - - + +
153J THR* 1.3 73.4 - - - +
155J THR* 1.3 56.9 + - - +
137K VAL* 3.8 25.8 - - + +
158K ILE* 3.4 14.6 - - + +
160K SER* 2.7 39.1 + - - -
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Residues in contact with THR 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J VAL* 3.3 4.7 - - - +
143J ALA* 2.8 45.3 + - - +
147J PRO* 6.1 0.7 - - + -
153J THR* 4.0 15.3 - - + -
154J ALA* 1.3 79.6 - - - +
156J SER* 1.3 61.4 + - - +
180J ALA* 4.1 1.1 - - - +
181J SER* 2.6 43.2 + - - +
186J ASN* 5.3 1.0 + - - -
158K ILE* 3.9 4.0 - - - -
160K SER* 3.9 4.0 - - - +
179K ASP* 3.5 26.9 - - + -
214K GLY 4.3 5.4 - - - +
215K ILE* 5.2 2.7 - - + -
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Residues in contact with SER 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J LEU* 3.9 16.6 - - - +
140J PHE* 5.6 4.2 - - - +
141J ALA 3.6 8.4 + - - -
142J VAL* 4.4 1.5 - - - +
155J THR* 1.3 73.7 - - - +
157J GLY* 1.3 62.5 + - - +
179J ASP 4.6 1.6 - - - +
180J ALA* 3.8 12.2 - - - -
181J SER 4.7 0.3 + - - -
140K PHE* 5.1 3.3 - - - -
157K GLY* 5.9 1.1 - - - -
158K ILE* 3.9 29.7 - - - +
179K ASP* 3.0 17.1 + - - +
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Residues in contact with GLY 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J PHE* 3.6 10.6 - - - +
141J ALA* 2.9 29.6 + - - +
156J SER* 1.3 77.8 + - - +
158J ILE* 1.3 65.2 + - - +
178J THR* 4.6 0.9 - - - -
179J ASP* 3.3 13.2 - - - -
180J ALA* 3.8 9.5 - - - +
156L SER* 5.8 1.1 - - - -
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Residues in contact with ILE 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J GLY* 3.9 14.1 - - - +
139J ASP 3.3 7.9 - - - +
140J PHE* 3.7 32.8 - - + -
141J ALA* 4.6 2.7 - - - -
157J GLY* 1.3 73.0 - - - -
159J VAL* 1.4 69.8 - - - +
160J SER 3.4 0.3 + - - -
178J THR* 2.8 28.8 + - - -
179J ASP* 2.7 23.9 + - - +
15L LEU* 3.9 19.3 - - + -
19L LEU* 4.9 0.2 - - + -
142L VAL* 4.9 2.2 - - + -
154L ALA* 3.3 41.1 - - + +
155L THR 4.0 1.1 - - - +
156L SER* 3.9 21.8 - - - +
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Residues in contact with VAL 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J LEU* 4.5 7.4 - - + -
136J ARG 3.7 19.1 - - - +
137J VAL* 3.4 7.3 - - - +
138J GLY* 2.9 24.4 + - - -
139J ASP* 2.7 29.2 + - + +
141J ALA* 4.5 5.8 - - + -
158J ILE* 1.4 73.5 - - - +
160J SER* 1.4 59.4 + - - +
161J ALA 3.7 19.7 - - - +
162J LEU* 3.8 23.6 - - + -
176J ILE* 4.1 12.6 - - + -
177J GLN 3.7 2.9 - - - -
178J THR* 4.8 0.7 - - - +
191J LEU* 5.5 0.4 - - + -
199J ILE* 4.3 23.8 - - + -
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Residues in contact with SER 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J VAL* 3.5 12.0 - - - +
158J ILE 3.4 2.3 + - - -
159J VAL* 1.4 73.6 - - - +
161J ALA* 1.3 59.1 + - - +
177J GLN* 2.7 26.8 + - - -
178J THR* 3.8 1.9 - - - -
179J ASP* 3.5 25.6 + - - +
214J GLY 4.9 0.4 + - - -
152L GLN 4.0 1.9 - - - +
153L THR* 3.6 19.2 - - - -
154L ALA 2.6 43.4 + - - -
155L THR* 4.0 2.1 - - - +
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Residues in contact with ALA 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J VAL* 3.8 9.8 - - - +
159J VAL* 3.6 5.6 - - - +
160J SER* 1.3 79.3 - - - +
162J LEU* 1.3 68.3 + - - +
164J ARG* 3.4 42.2 - - + +
175J PHE 4.8 0.4 - - - -
176J ILE* 3.8 0.9 - - - -
177J GLN* 2.9 38.3 + - + +
152L GLN 4.1 4.0 - - - +
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Residues in contact with LEU 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J SER 5.0 3.1 - - - +
135J LEU* 3.5 44.2 - - + +
136J ARG* 3.8 12.1 - - - -
137J VAL* 4.0 13.4 - - + +
159J VAL* 3.8 18.4 - - + -
161J ALA* 1.3 78.3 - - - +
163J GLY* 1.3 65.6 - - - +
164J ARG* 3.3 10.2 + - - +
175J PHE 3.9 3.1 - - - -
176J ILE* 4.0 21.1 - - + -
293J LYS* 6.3 0.7 - - - +
296J ASN* 3.6 12.7 + - - +
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Residues in contact with GLY 163 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162J LEU* 1.3 75.6 - - - +
164J ARG* 1.3 61.6 + - - +
165J SER* 3.6 8.5 + - - -
174J ASN* 3.1 31.7 + - - +
175J PHE 3.2 7.2 + - - -
176J ILE* 6.0 0.2 - - - +
296J ASN* 3.1 29.8 - - - +
297J SER* 4.8 0.7 + - - -
300J GLU* 4.9 1.7 - - - +
304J ARG* 5.8 0.7 - - - -
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Residues in contact with ARG 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161J ALA* 3.4 26.2 - - + +
162J LEU 4.5 5.6 + - - +
163J GLY* 1.3 74.6 - - - +
165J SER* 1.3 62.0 + - - +
167J LEU* 4.4 20.0 - - + -
173J GLU* 3.8 0.2 - - - +
174J ASN 3.7 4.0 + - - -
175J PHE* 3.0 50.9 + - + +
177J GLN* 2.9 25.2 + - + +
217J PHE* 4.4 2.2 - - + -
150L LEU* 3.4 31.3 + - - +
151L GLY* 3.0 19.6 + - - -
152L GLN 3.2 12.7 + - - +
153L THR* 2.8 28.7 + - - -
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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