Contacts of the strand formed by residues 153 - 164 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160J SER* 3.6 14.8 - - - -
164J ARG* 2.8 24.8 + - - -
177J GLN* 3.2 26.4 + - - +
215J ILE* 4.3 2.2 - - + -
143L ALA 3.7 1.4 - - - +
144L VAL* 3.5 6.5 - - - +
145L GLY 2.8 27.7 + - - -
147L PRO* 3.7 29.1 - - + +
150L LEU* 4.6 1.6 - - - +
151L GLY 3.2 4.3 + - - -
152L GLN* 1.3 70.8 - - - +
154L ALA* 1.3 62.3 - - - +
155L THR* 4.0 17.0 - - + +
186L ASN* 5.1 0.7 - - - +
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Residues in contact with ALA 154 (chain L).
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* 3.9 25.6 - - + -
158J ILE* 3.3 14.8 - - + +
160J SER* 2.6 39.0 + - - -
19L LEU* 4.1 12.8 - - + -
23L LEU* 4.7 4.9 - - + -
142L VAL* 4.2 6.5 - - + -
143L ALA 3.4 6.5 - - - +
144L VAL* 4.5 7.9 - - + +
153L THR* 1.3 73.3 - - - +
155L THR* 1.3 58.8 + - - +
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Residues in contact with THR 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J ILE* 4.0 3.4 - - - -
160J SER* 4.0 3.1 - - - +
179J ASP* 3.5 26.7 - - + -
214J GLY 4.4 4.5 - - - +
215J ILE* 5.0 2.9 - - + -
142L VAL* 3.3 5.0 - - - +
143L ALA* 2.8 45.2 + - - +
147L PRO* 6.1 0.7 - - + -
153L THR* 4.0 14.8 - - + -
154L ALA* 1.3 79.1 - - - +
156L SER* 1.3 59.2 + - - +
180L ALA* 4.1 1.3 - - - +
181L SER* 2.7 43.9 + - - +
186L ASN* 5.3 0.5 + - - -
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Residues in contact with SER 156 (chain L).
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* 5.1 3.3 - - - -
157J GLY* 5.8 1.3 - - - -
158J ILE* 3.9 30.5 - - - +
179J ASP* 3.0 16.9 + - - +
15L LEU* 3.9 15.8 - - - +
140L PHE* 5.7 3.6 - - - +
141L ALA 3.6 9.3 + - - -
142L VAL* 4.5 2.0 - - - +
155L THR* 1.3 73.5 - - - +
157L GLY* 1.3 62.6 + - - +
179L ASP 4.6 1.4 - - - +
180L ALA* 3.7 12.5 - - - -
181L SER 4.7 0.3 + - - -
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Residues in contact with GLY 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K SER* 5.9 1.3 - - - -
140L PHE* 3.6 11.4 - - - +
141L ALA 2.9 28.9 + - - +
156L SER* 1.3 78.3 + - - +
158L ILE* 1.4 64.6 + - - +
178L THR* 4.6 0.7 - - - -
179L ASP* 3.3 13.5 - - - -
180L ALA* 3.8 9.1 - - - +
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Residues in contact with ILE 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K LEU* 4.0 13.9 - - + -
19K LEU* 5.0 0.4 - - + -
142K VAL* 4.8 2.7 - - + -
154K ALA* 3.4 37.9 - - + +
155K THR 4.0 1.6 - - - +
156K SER* 4.0 21.1 - - - +
138L GLY* 3.8 19.3 - - - +
139L ASP 3.3 8.3 - - - +
140L PHE* 3.7 29.6 - - + -
141L ALA* 4.2 2.5 - - - +
157L GLY* 1.4 75.1 - - - -
159L VAL* 1.4 72.2 + - - +
160L SER 3.4 0.7 + - - -
178L THR* 2.8 28.8 + - - -
179L ASP* 2.7 27.5 + - - +
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Residues in contact with VAL 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135L LEU* 4.5 6.3 - - + -
136L ARG 3.7 17.9 - - - +
137L VAL* 3.4 8.0 - - - +
138L GLY* 2.9 24.8 + - - -
139L ASP* 2.7 29.0 + - + +
140L PHE 5.2 0.2 - - - +
141L ALA* 4.5 5.8 - - + -
158L ILE* 1.4 73.3 - - - +
160L SER* 1.3 59.9 + - - +
161L ALA 3.7 19.5 - - - +
162L LEU* 3.7 24.9 - - + -
176L ILE* 4.0 15.5 - - + -
177L GLN 3.7 3.1 - - - -
178L THR* 4.8 0.9 - - - +
191L LEU* 5.4 0.7 - - + -
199L ILE* 4.3 20.4 - - + -
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Residues in contact with SER 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152K GLN 4.3 1.2 - - - +
153K THR* 3.7 17.9 - - - -
154K ALA 2.7 44.2 + - - -
155K THR* 4.0 2.4 - - - +
137L VAL* 3.6 12.9 - - - +
158L ILE* 3.4 2.3 + - - +
159L VAL* 1.3 71.9 - - - +
161L ALA* 1.3 60.0 + - - +
177L GLN* 2.7 27.0 + - - -
178L THR* 3.8 1.0 - - - -
179L ASP* 3.5 26.0 + - - +
214L GLY 4.9 0.2 + - - -
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Residues in contact with ALA 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152K GLN 4.0 3.1 - - - +
137L VAL* 3.8 9.2 - - - -
159L VAL* 3.6 3.8 - - - +
160L SER* 1.3 79.6 - - - +
162L LEU* 1.3 69.3 + - - +
164L ARG* 3.4 42.8 - - + +
175L PHE 4.8 0.4 - - - -
176L ILE* 3.7 1.6 - - - -
177L GLN* 2.8 37.6 + - + +
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Residues in contact with LEU 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132L SER 4.9 3.4 - - - +
135L LEU* 3.4 44.0 - - + +
136L ARG* 3.8 11.0 - - - -
137L VAL* 4.0 14.6 - - + +
159L VAL* 3.7 19.5 - - + -
161L ALA* 1.3 78.1 - - - +
163L GLY* 1.3 65.7 + - - +
164L ARG* 3.3 8.8 + - - +
175L PHE 3.9 3.4 - - - -
176L ILE* 3.9 23.3 - - + -
296L ASN* 3.6 13.1 + - - +
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Residues in contact with GLY 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162L LEU* 1.3 75.2 - - - +
164L ARG* 1.3 61.8 + - - +
165L SER* 3.5 9.8 + - - -
174L ASN* 3.2 31.5 + - - +
175L PHE 3.2 7.2 + - - -
296L ASN* 3.2 27.2 - - - +
297L SER* 4.9 0.2 + - - -
300L GLU* 4.9 1.5 - - - +
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Residues in contact with ARG 164 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K LEU* 3.5 30.9 + - - +
151K GLY* 3.1 13.1 + - - -
152K GLN 2.9 18.0 + - - +
153K THR* 2.8 29.5 + - - -
161L ALA* 3.4 27.7 - - + +
162L LEU 4.5 6.1 + - - +
163L GLY* 1.3 75.4 - - - +
165L SER* 1.3 62.8 + - - +
167L LEU* 4.4 19.1 - - + -
173L GLU* 3.8 0.2 - - - +
174L ASN 3.7 4.5 + - - -
175L PHE* 2.9 52.0 + - + +
177L GLN* 2.9 25.9 + - + +
217L PHE* 4.4 2.4 - - + -
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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