Contacts of the strand formed by residues 153 - 164 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23H LEU* 5.9 0.2 - - - -
143H ALA 3.6 1.6 - - - +
144H VAL* 3.4 6.0 - - - -
145H GLY 2.8 31.1 + - - -
147H PRO* 3.7 30.0 - - + +
150H LEU* 4.6 1.4 - - - +
151H GLY 3.2 3.6 + - - -
152H GLN* 1.3 71.5 - - - +
154H ALA* 1.3 60.4 + - - +
155H THR* 4.0 17.5 - - + -
186H ASN* 5.1 1.1 - - - +
160I SER* 3.6 14.6 - - - -
164I ARG* 2.8 25.1 + - - -
177I GLN* 3.1 25.3 + - - +
214I GLY 5.8 0.2 - - - +
215I ILE* 4.5 2.2 - - + -
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Residues in contact with ALA 154 (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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19H LEU* 4.4 6.5 - - + -
23H LEU* 4.6 4.7 - - + -
142H VAL* 4.3 10.8 - - + -
143H ALA 3.2 7.4 - - - +
144H VAL* 4.3 9.6 - - + -
153H THR* 1.3 73.0 - - - +
155H THR* 1.3 60.2 + - - +
137I VAL* 3.8 25.8 - - + +
158I ILE* 3.3 16.1 - - + +
160I SER* 2.8 32.3 + - - -
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Residues in contact with THR 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H VAL* 3.3 4.7 - - - +
143H ALA* 2.7 46.2 + - - +
147H PRO* 6.1 0.7 - - + -
153H THR* 4.0 15.7 - - + -
154H ALA* 1.3 78.9 - - - +
156H SER* 1.3 59.2 + - - +
180H ALA* 4.1 1.5 - - - +
181H SER* 2.6 43.2 + - - +
186H ASN* 5.4 0.5 + - - -
158I ILE* 3.9 3.4 - - - -
160I SER* 4.0 3.8 - - - +
179I ASP* 3.6 27.1 - - + -
214I GLY 4.5 4.3 - - - +
215I ILE* 5.4 2.9 - - + -
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Residues in contact with SER 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H LEU* 3.8 16.7 - - - +
140H PHE* 5.7 2.9 - - - +
141H ALA 3.6 9.2 + - - -
142H VAL* 4.5 1.6 - - - +
155H THR* 1.3 74.1 - - - +
157H GLY* 1.3 61.7 + - - +
179H ASP 4.6 1.6 - - - +
180H ALA* 3.7 11.6 - - - -
181H SER 4.7 0.3 + - - -
140I PHE* 5.1 3.1 - - - -
157I GLY* 5.9 1.1 - - - -
158I ILE* 3.9 29.7 - - - +
179I ASP* 3.0 17.4 + - - +
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Residues in contact with GLY 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156G SER* 5.9 1.8 - - - -
140H PHE* 3.6 10.3 - - - +
141H ALA 2.9 28.4 + - - +
156H SER* 1.3 76.6 + - - +
158H ILE* 1.3 65.5 + - - +
178H THR* 4.6 0.4 - - - -
179H ASP* 3.3 12.8 - - - -
180H ALA* 3.8 11.1 - - - +
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Residues in contact with ILE 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LEU* 4.0 9.9 - - + -
19G LEU* 5.1 0.4 - - + -
142G VAL* 4.8 2.5 - - + -
154G ALA* 3.4 39.5 - - + +
155G THR* 4.0 1.6 - - - -
156G SER* 4.0 25.6 - - - +
138H GLY* 3.9 18.6 - - - +
139H ASP 3.3 7.9 - - - +
140H PHE* 3.7 32.5 - - + -
141H ALA* 4.2 3.1 - - - +
157H GLY* 1.3 72.4 - - - -
159H VAL* 1.3 72.1 + - - +
160H SER 3.3 0.9 + - - -
178H THR* 2.9 27.6 + - - -
179H ASP* 2.7 24.7 + - - +
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Residues in contact with VAL 159 (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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135H LEU* 4.6 6.7 - - + -
136H ARG 3.7 18.8 - - - +
137H VAL* 3.4 9.0 - - - +
138H GLY* 2.9 24.8 + - - -
139H ASP* 2.7 29.2 + - + +
141H ALA* 4.5 6.1 - - + -
158H ILE* 1.3 73.3 - - - +
160H SER* 1.3 58.5 + - - +
161H ALA 3.7 18.8 - - - +
162H LEU* 3.8 22.9 - - + -
176H ILE* 3.9 12.8 - - + -
177H GLN 3.7 3.1 - - - -
178H THR* 4.8 0.9 - - - +
191H LEU* 5.4 0.2 - - + -
199H ILE* 4.2 24.5 - - + -
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Residues in contact with SER 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152G GLN 4.2 1.4 - - - +
153G THR* 3.7 17.9 - - - -
154G ALA 2.7 43.8 + - - +
155G THR* 4.0 1.9 - - - +
137H VAL* 3.5 12.7 - - - +
158H ILE* 3.3 2.5 + - - +
159H VAL* 1.3 71.9 - - - +
161H ALA* 1.4 60.0 + - - +
177H GLN* 2.7 27.4 + - - -
178H THR* 3.8 0.8 - - - -
179H ASP* 3.5 26.9 + - - +
214H GLY 4.9 0.5 + - - -
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Residues in contact with ALA 161 (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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152G GLN 4.0 3.1 - - - +
137H VAL* 3.8 9.9 - - - -
159H VAL* 3.6 4.6 - - - +
160H SER* 1.4 79.1 - - - +
162H LEU* 1.3 69.1 + - - +
164H ARG* 3.4 43.1 - - + +
175H PHE 4.8 0.7 - - - -
176H ILE* 3.7 0.5 - - - -
177H GLN* 2.9 38.0 + - + +
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Residues in contact with LEU 162 (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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132H SER 4.9 3.4 - - - +
135H LEU* 3.4 44.2 - - + +
136H ARG* 3.8 12.3 - - - -
137H VAL* 4.0 13.4 - - + +
159H VAL* 3.8 17.9 - - + -
161H ALA* 1.3 79.2 - - - +
163H GLY* 1.3 68.0 + - - +
164H ARG* 3.3 9.5 + - - +
175H PHE 3.9 3.1 - - - -
176H ILE* 3.9 22.9 - - + -
293H LYS* 6.3 1.1 - - - +
296H ASN* 3.5 12.1 + - - -
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Residues in contact with GLY 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162H LEU* 1.3 74.9 - - - +
164H ARG* 1.3 62.0 + - - +
165H SER* 3.7 5.9 + - - -
174H ASN* 3.1 32.9 + - - -
175H PHE 3.1 8.5 + - - -
176H ILE* 5.8 0.2 - - - +
296H ASN* 3.0 29.6 + - - +
297H SER* 4.9 0.2 + - - -
300H GLU* 4.8 2.1 - - - +
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Residues in contact with ARG 164 (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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150G LEU* 3.4 30.9 + - - +
151G GLY* 2.9 18.6 + - - -
152G GLN 3.0 12.9 + - - +
153G THR* 2.7 29.9 + - - -
161H ALA* 3.4 26.9 - - + +
162H LEU 4.5 5.7 + - - +
163H GLY* 1.3 74.5 - - - +
165H SER* 1.3 63.7 + - - +
167H LEU* 4.4 18.2 - - + -
173H GLU 3.8 0.2 - - - -
174H ASN 3.7 3.5 + - - -
175H PHE* 2.9 50.1 + - + +
177H GLN* 2.9 27.5 + - + +
217H PHE* 4.4 2.2 - - + -
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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