Contacts of the strand formed by residues 153 - 164 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160D SER* 3.7 9.6 - - - -
164D ARG* 2.8 25.3 + - - -
177D GLN* 3.1 25.1 + - - +
215D ILE* 4.5 3.1 - - + -
143F ALA 3.6 1.6 - - - +
144F VAL* 3.3 6.6 - - - +
145F GLY 2.9 29.1 + - - -
147F PRO* 3.6 28.8 - - + +
150F LEU* 4.6 1.6 - - - +
151F GLY 3.6 2.9 + - - -
152F GLN* 1.4 71.8 - - - +
154F ALA* 1.3 62.3 + - - +
155F THR* 4.0 22.0 - - + -
186F ASN* 4.8 2.5 - - - +
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Residues in contact with ALA 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D VAL* 3.8 26.4 - - + +
158D ILE* 3.3 16.2 - - + +
160D SER* 2.6 39.7 + - - -
19F LEU* 4.3 11.9 - - + -
23F LEU* 4.6 4.3 - - + -
142F VAL* 4.3 5.4 - - + -
143F ALA 3.2 7.2 - - - +
144F VAL* 4.4 8.7 - - + +
153F THR* 1.3 71.9 - - - +
155F THR* 1.3 57.5 + - - +
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Residues in contact with THR 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D ILE* 3.9 3.6 - - - -
160D SER* 3.9 3.6 - - - +
179D ASP* 3.5 28.0 - - + -
214D GLY 4.3 4.7 - - - +
215D ILE* 5.3 2.5 - - + -
142F VAL* 3.3 5.4 - - - +
143F ALA* 2.8 46.4 + - - +
147F PRO* 6.3 0.2 - - + -
153F THR* 4.0 15.0 - - + -
154F ALA* 1.3 80.0 - - - +
156F SER* 1.3 60.3 + - - +
180F ALA* 4.1 1.5 - - - +
181F SER* 2.7 42.4 + - - +
186F ASN* 5.3 1.4 + - - +
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Residues in contact with SER 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D PHE* 5.1 3.1 - - - -
157D GLY* 5.9 1.1 - - - -
158D ILE* 3.9 30.4 - - - +
179D ASP* 2.9 16.5 + - - +
15F LEU* 3.9 16.0 - - - +
140F PHE* 5.6 4.7 - - - +
141F ALA 3.6 9.0 + - - -
142F VAL* 4.4 1.7 - - - +
155F THR* 1.3 73.3 - - - +
157F GLY* 1.3 62.0 + - - +
179F ASP 4.6 1.6 - - - +
180F ALA* 3.7 11.9 - - - -
181F SER 4.8 0.3 + - - -
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Residues in contact with GLY 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E SER* 5.9 1.3 - - - -
140F PHE* 3.6 11.1 - - - +
141F ALA* 2.9 29.4 + - - +
156F SER* 1.3 78.3 + - - +
158F ILE* 1.3 65.4 + - - +
178F THR* 4.6 0.9 - - - -
179F ASP* 3.3 13.7 - - - -
180F ALA* 3.8 9.5 - - - +
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Residues in contact with ILE 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E LEU* 4.0 9.2 - - + -
19E LEU* 5.0 0.2 - - + -
142E VAL* 4.8 2.7 - - + -
154E ALA* 3.3 40.6 - - + +
155E THR* 3.9 10.1 - - - -
156E SER* 3.9 17.5 - - - +
138F GLY* 3.8 18.6 - - - +
139F ASP 3.3 7.4 - - - +
140F PHE* 3.7 29.4 - - + -
141F ALA* 4.3 2.5 - - - +
157F GLY* 1.3 75.9 - - - -
159F VAL* 1.4 71.7 + - - +
160F SER 3.3 3.6 + - - -
178F THR* 2.9 24.8 + - - -
179F ASP* 2.7 27.6 + - - +
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Residues in contact with VAL 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F LEU* 4.5 7.0 - - + -
136F ARG 3.7 18.4 - - - +
137F VAL* 3.4 9.2 - - - +
138F GLY* 2.9 24.6 + - - -
139F ASP* 2.7 29.0 + - + +
141F ALA* 4.5 5.4 - - + -
158F ILE* 1.4 73.0 - - - +
160F SER* 1.3 58.1 + - - +
161F ALA 3.7 10.1 - - - +
162F LEU* 3.7 18.4 - - + -
176F ILE* 3.7 30.7 - - + -
177F GLN 3.7 3.1 - - - -
178F THR* 4.8 0.9 - - - +
191F LEU* 5.5 0.4 - - + -
199F ILE* 4.2 21.1 - - + -
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Residues in contact with SER 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E GLN 4.1 1.4 - - - +
153E THR* 3.7 18.0 - - - -
154E ALA 2.7 41.1 + - - -
155E THR* 4.0 2.3 - - - +
137F VAL* 3.5 12.6 - - - +
158F ILE* 3.3 2.5 + - - +
159F VAL* 1.3 72.9 - - - +
161F ALA* 1.4 59.1 + - - +
177F GLN* 2.7 27.0 + - - -
178F THR 3.8 1.0 - - - -
179F ASP* 3.5 26.5 + - - +
214F GLY 4.9 0.4 + - - -
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Residues in contact with ALA 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E GLN 3.9 3.6 - - - +
137F VAL* 3.8 9.8 - - - +
159F VAL* 3.6 3.8 - - - +
160F SER* 1.4 78.7 - - - +
162F LEU* 1.3 68.5 + - - +
164F ARG* 3.4 42.8 - - + +
175F PHE 4.8 0.2 - - - -
176F ILE* 3.7 1.9 - - - -
177F GLN* 2.9 36.8 + - + +
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Residues in contact with LEU 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F SER 5.0 3.4 - - - +
135F LEU* 3.5 44.4 - - + +
136F ARG* 3.8 11.2 - - - -
137F VAL* 4.0 14.3 - - + +
159F VAL* 3.7 18.8 - - + -
161F ALA* 1.3 77.5 - - - +
163F GLY* 1.3 65.3 + - - +
164F ARG* 3.3 9.9 + - - +
175F PHE 3.8 3.8 - - - -
176F ILE* 3.9 22.4 - - + -
293F LYS* 6.3 0.4 - - - +
296F ASN* 3.5 13.5 + - - +
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Residues in contact with GLY 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F LEU* 1.3 75.7 - - - +
164F ARG* 1.4 62.4 + - - +
165F SER* 3.5 8.5 + - - -
174F ASN* 3.1 31.9 + - - +
175F PHE 3.2 7.2 + - - -
296F ASN* 3.1 28.9 - - - +
297F SER* 4.7 0.2 + - - -
300F GLU* 4.8 1.7 - - - +
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Residues in contact with ARG 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E LEU* 3.3 30.8 + - - +
151E GLY* 3.1 13.9 + - - -
152E GLN 2.9 18.0 + - - +
153E THR* 2.8 28.5 + - - -
161F ALA* 3.4 26.1 - - + +
162F LEU 4.5 5.6 + - - +
163F GLY* 1.4 74.2 - - - +
165F SER* 1.3 62.0 + - - +
167F LEU* 4.4 19.1 - - + -
173F GLU* 3.7 0.2 - - - +
174F ASN 3.7 4.7 + - - -
175F PHE* 2.9 50.7 + - + +
177F GLN* 2.9 27.5 + - + +
217F PHE* 4.5 2.7 - - + -
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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