Contacts of the strand formed by residues 153 - 164 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ALA 3.6 1.4 - - - +
144A VAL* 3.4 6.7 - - - +
145A GLY 2.9 34.6 + - - -
147A PRO* 3.7 24.2 - - + +
150A LEU* 4.6 1.4 - - - +
151A GLY 3.3 3.1 + - - -
152A GLN* 1.3 72.0 - - - +
154A ALA* 1.3 61.0 + - - +
155A THR* 4.0 21.9 - - + +
186A ASN* 5.1 0.9 - - - +
160B SER* 3.6 9.4 - - - -
164B ARG* 2.8 25.6 + - - -
177B GLN* 3.2 25.2 + - - +
215B ILE* 4.5 2.2 - - + -
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Residues in contact with ALA 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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19A LEU* 4.4 5.6 - - + -
23A LEU* 4.7 5.2 - - + -
142A VAL* 4.3 13.2 - - + -
143A ALA 3.4 5.2 - - - -
144A VAL* 4.5 7.4 - - + -
153A THR* 1.3 72.5 - - - +
155A THR* 1.3 58.9 + - - +
137B VAL* 3.7 27.6 - - + +
158B ILE* 3.4 15.1 - - + +
160B SER* 2.7 38.7 + - - +
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Residues in contact with THR 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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142A VAL* 3.3 6.4 - - - +
143A ALA* 2.8 47.5 + - - +
153A THR* 4.0 15.3 - - + -
154A ALA* 1.3 78.3 - - - +
156A SER* 1.3 60.7 + - - +
180A ALA* 4.3 1.1 - - - -
181A SER* 2.6 42.5 + - - +
186A ASN* 5.4 0.7 + - - -
158B ILE* 4.0 3.6 - - - -
160B SER* 4.0 3.8 - - - +
179B ASP* 3.6 28.3 - - + -
214B GLY 4.4 4.5 - - - +
215B ILE* 5.4 2.5 - - + -
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Residues in contact with SER 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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15A LEU* 3.7 19.7 - - - +
140A PHE* 6.0 2.4 - - - +
141A ALA 3.6 7.7 + - - -
142A VAL* 4.3 0.9 - - - +
155A THR* 1.3 73.2 - - - +
157A GLY* 1.3 60.2 + - - +
179A ASP* 4.5 2.3 - - - +
180A ALA* 3.8 11.7 - - - -
181A SER 4.8 0.3 + - - -
140B PHE* 5.2 2.6 - - - -
157B GLY* 5.8 1.8 - - - -
158B ILE* 4.0 27.2 - - - +
179B ASP* 2.9 19.5 + - - +
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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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140A PHE* 3.6 9.1 - - - +
141A ALA* 2.7 38.3 + - - +
156A SER* 1.3 76.8 + - - +
158A ILE* 1.3 59.5 + - - +
179A ASP* 3.3 14.6 - - - -
180A ALA* 3.8 9.3 - - - +
156C SER* 6.2 1.1 - - - -
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Residues in contact with ILE 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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138A GLY* 3.9 12.3 - - - +
139A ASP 3.0 10.1 - - - +
140A PHE* 3.7 31.9 - - + -
141A ALA* 4.5 2.2 - - - -
157A GLY* 1.3 74.6 - - - -
159A VAL* 1.4 70.8 - - - +
160A SER* 3.5 3.2 + - - +
178A THR* 3.0 20.4 + - - -
179A ASP* 2.7 26.9 + - - +
15C LEU* 3.8 19.1 - - + -
19C LEU* 5.0 0.2 - - + -
142C VAL* 4.8 2.5 - - + -
154C ALA* 3.4 39.7 - - + +
155C THR 4.0 1.6 - - - +
156C SER* 4.0 21.3 - - - +
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Residues in contact with VAL 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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135A LEU* 4.5 6.7 - - + -
136A ARG 3.8 19.5 - - - +
137A VAL* 3.5 5.4 - - - +
138A GLY* 2.8 26.5 + - - -
139A ASP* 2.7 29.2 + - + +
140A PHE 5.1 0.2 - - - +
141A ALA* 4.4 6.3 - - + -
158A ILE* 1.4 73.1 - - - +
160A SER* 1.4 57.2 + - - +
161A ALA 3.7 19.3 - - - +
162A LEU* 3.8 23.1 - - + -
176A ILE* 3.8 11.7 - - + -
177A GLN 3.7 2.9 - - - -
178A THR* 4.8 1.3 - - - +
191A LEU* 5.4 0.2 - - + -
199A ILE* 4.1 26.2 - - + -
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Residues in contact with SER 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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137A VAL* 3.5 13.1 - - - +
158A ILE 3.5 1.6 + - - -
159A VAL* 1.4 71.9 - - - +
161A ALA* 1.3 60.0 + - - +
177A GLN* 2.7 26.5 + - - -
178A THR* 3.8 1.0 - - - -
179A ASP* 3.5 26.5 + - - +
214A GLY 4.9 0.5 + - - -
152C GLN 4.2 1.2 - - - +
153C THR* 3.6 18.1 - - - -
154C ALA 2.7 43.2 + - - -
155C THR* 4.0 2.1 - - - +
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Residues in contact with ALA 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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137A VAL* 3.9 9.6 - - - -
159A VAL* 3.7 4.7 - - - +
160A SER* 1.3 79.6 - - - +
162A LEU* 1.3 69.9 + - - +
164A ARG* 3.4 41.1 - - + +
175A PHE 4.8 0.2 - - - -
176A ILE* 3.7 2.1 - - - -
177A GLN* 2.8 38.2 + - + +
152C GLN 3.9 4.0 - - - +
153C THR* 4.7 0.2 - - - +
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Residues in contact with LEU 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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132A SER 5.0 3.1 - - - +
135A LEU* 3.5 43.3 - - + +
136A ARG* 3.9 11.7 - - - -
137A VAL* 4.0 13.0 - - + +
159A VAL* 3.8 15.9 - - + -
161A ALA* 1.3 81.9 - - - +
163A GLY* 1.3 65.4 + - - +
164A ARG* 3.3 10.2 + - - +
175A PHE 3.9 3.1 - - - -
176A ILE* 3.9 22.2 - - + -
293A LYS* 6.2 1.6 - - - +
296A ASN* 3.5 13.8 + - - +
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Residues in contact with GLY 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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162A LEU* 1.3 75.1 - - - +
164A ARG* 1.3 62.0 - - - +
165A SER* 3.5 8.5 + - - -
174A ASN* 3.1 29.9 + - - +
175A PHE 3.2 7.5 + - - -
176A ILE* 5.9 0.2 - - - +
296A ASN* 3.1 29.3 - - - +
297A SER* 4.8 0.3 + - - -
300A GLU* 4.8 2.1 - - - +
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Residues in contact with ARG 164 (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 ALA* 3.4 24.6 - - + +
162A LEU 4.4 5.9 + - - +
163A GLY* 1.3 74.2 - - - +
165A SER* 1.4 63.4 + - - +
167A LEU* 4.4 11.0 - - + -
173A GLU* 3.8 0.2 - - - +
174A ASN 3.7 2.4 + - - -
175A PHE* 3.0 53.6 + - + +
177A GLN* 2.9 28.3 + - + +
217A PHE* 4.4 9.9 - - + -
150C LEU* 3.5 31.5 + - - +
151C GLY* 2.9 14.8 + - - -
152C GLN 2.9 17.2 + - - +
153C THR* 2.7 29.5 + - - -
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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