Contacts of the strand formed by residues 153 - 164 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143G ALA 3.6 1.6 - - - +
144G VAL* 3.4 5.9 - - - -
145G GLY 2.8 31.7 + - - -
147G PRO* 3.6 30.5 - - + +
150G LEU* 4.6 1.7 - - - +
151G GLY 3.1 4.3 + - - -
152G GLN* 1.3 70.9 - - - +
154G ALA* 1.3 60.2 + - - +
155G THR* 4.1 16.8 - - + -
186G ASN* 5.0 1.3 - - - +
160H SER* 3.7 13.9 - - - -
164H ARG* 2.7 26.3 + - - -
177H GLN* 3.3 24.3 + - - +
215H ILE* 4.5 2.2 - - + -
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Residues in contact with ALA 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G LEU* 4.5 5.6 - - + -
23G LEU* 4.6 5.2 - - + -
142G VAL* 4.3 11.4 - - + -
143G ALA 3.2 7.0 - - - +
144G VAL* 4.3 9.2 - - + +
153G THR* 1.3 72.8 - - - +
155G THR* 1.4 58.1 + - - +
137H VAL* 3.9 25.4 - - + -
158H ILE* 3.4 14.3 - - + +
160H SER* 2.7 37.7 + - - -
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Residues in contact with THR 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G VAL* 3.3 4.5 - - - +
143G ALA* 2.7 47.5 + - - +
147G PRO* 6.2 0.2 - - + -
153G THR* 4.1 15.0 - - + -
154G ALA* 1.4 78.7 - - - +
156G SER* 1.3 58.5 + - - +
180G ALA* 4.1 1.2 - - - +
181G SER* 2.7 43.3 + - - +
186G ASN* 5.1 1.2 + - - -
158H ILE* 4.0 4.7 - - - -
160H SER* 4.0 3.6 - - - +
179H ASP* 3.5 27.4 - - + -
214H GLY 4.4 4.7 - - - +
215H ILE* 5.3 2.2 - - + -
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Residues in contact with SER 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LEU* 3.9 17.2 - - - +
140G PHE* 5.6 4.2 - - - +
141G ALA 3.6 8.5 + - - -
142G VAL* 4.5 2.0 - - - +
155G THR* 1.3 73.4 - - - +
157G GLY* 1.3 62.7 + - - +
179G ASP 4.6 1.7 - - - +
180G ALA* 3.7 12.9 - - - -
181G SER 4.7 0.3 + - - -
140H PHE* 5.1 3.7 - - - -
157H GLY* 5.9 0.9 - - - -
158H ILE* 4.0 30.0 - - - +
179H ASP* 3.0 15.8 + - - +
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Residues in contact with GLY 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G PHE* 3.6 10.4 - - - +
141G ALA 2.9 29.3 + - - +
156G SER* 1.3 78.6 + - - +
158G ILE* 1.3 66.4 + - - +
178G THR* 4.6 0.9 - - - -
179G ASP* 3.3 12.6 - - - -
180G ALA* 3.8 9.3 - - - +
156I SER* 6.2 1.1 - - - -
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Residues in contact with ILE 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G GLY* 3.8 19.1 - - - +
139G ASP 3.3 7.4 - - - +
140G PHE* 3.7 29.6 - - + -
141G ALA* 4.3 3.1 - - - +
157G GLY* 1.3 76.5 - - - -
159G VAL* 1.4 70.3 + - - +
160G SER 3.4 0.7 + - - -
178G THR* 2.8 27.6 + - - -
179G ASP* 2.7 25.2 + - - +
15I LEU* 3.9 14.1 - - + -
19I LEU* 5.0 0.4 - - + -
142I VAL* 4.8 2.5 - - + -
154I ALA* 3.4 41.7 - - + +
155I THR* 3.9 9.6 - - - +
156I SER* 4.0 11.9 - - - +
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Residues in contact with VAL 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G LEU* 4.5 7.0 - - + -
136G ARG 3.7 18.8 - - - +
137G VAL* 3.4 8.1 - - - +
138G GLY* 2.9 24.6 + - - -
139G ASP* 2.7 28.0 + - + +
141G ALA* 4.5 5.6 - - + -
158G ILE* 1.4 73.7 - - - +
160G SER* 1.3 58.7 + - - +
161G ALA 3.7 19.5 - - - +
162G LEU* 3.8 23.6 - - + -
176G ILE* 4.0 13.5 - - + -
177G GLN 3.7 3.4 - - - -
178G THR* 4.8 0.7 - - - +
191G LEU* 5.5 0.2 - - + -
199G ILE* 4.2 23.6 - - + -
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Residues in contact with SER 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G VAL* 3.5 12.2 - - - +
158G ILE* 3.4 2.0 + - - +
159G VAL* 1.3 72.8 - - - +
161G ALA* 1.3 60.0 + - - +
177G GLN* 2.7 38.2 + - - -
178G THR* 3.8 1.0 - - - -
179G ASP* 3.5 25.6 + - - +
214G GLY 4.9 0.5 + - - -
152I GLN 4.1 1.7 - - - +
153I THR* 3.7 7.7 - - - -
154I ALA 2.6 44.8 + - - +
155I THR* 3.9 2.1 - - - +
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Residues in contact with ALA 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G VAL* 3.8 9.4 - - - +
159G VAL* 3.6 4.2 - - - +
160G SER* 1.3 79.8 - - - +
162G LEU* 1.3 67.5 + - - +
164G ARG* 3.4 41.5 - - + +
175G PHE 4.8 0.4 - - - -
176G ILE* 3.7 1.2 - - - -
177G GLN* 2.8 39.0 + - + +
152I GLN 3.8 4.5 - - - +
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Residues in contact with LEU 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G SER 5.0 2.9 - - - +
135G LEU* 3.4 42.4 - - + +
136G ARG* 3.8 15.5 - - - -
137G VAL* 4.0 10.5 - - + +
159G VAL* 3.8 17.9 - - + -
161G ALA* 1.3 76.8 - - - +
163G GLY* 1.3 68.0 + - - +
164G ARG* 3.3 9.7 + - - +
175G PHE 3.9 3.4 - - - -
176G ILE* 3.8 24.5 - - + -
293G LYS* 6.3 0.7 - - - +
296G ASN* 3.5 12.5 + - - +
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Residues in contact with GLY 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G LEU* 1.3 74.9 - - - +
164G ARG* 1.3 61.7 + - - +
165G SER* 3.5 8.8 + - - -
174G ASN* 3.1 31.1 + - - +
175G PHE 3.2 7.6 + - - -
176G ILE* 5.9 0.2 - - - +
296G ASN* 3.1 29.1 - - - +
297G SER* 4.8 0.7 + - - -
300G GLU* 4.8 1.5 - - - +
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Residues in contact with ARG 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161G ALA* 3.4 25.3 - - + +
162G LEU 4.5 5.9 + - - +
163G GLY* 1.3 73.2 - - - +
165G SER* 1.3 63.8 + - - +
167G LEU* 4.4 21.8 - - + -
173G GLU* 3.8 0.2 - - - +
174G ASN 3.7 2.3 + - - -
175G PHE* 3.0 53.2 + - + +
177G GLN* 2.9 26.1 + - + +
217G PHE* 4.4 2.7 - - + -
150I LEU* 3.5 29.0 + - - +
151I GLY* 3.1 15.0 + - - -
152I GLN 2.9 17.4 + - - +
153I THR* 2.9 28.5 + - - -
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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