Contacts of the strand formed by residues 132 - 141 (chain B) in PDB entry 3TWI
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 GLY 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B THR* 1.3 80.0 - - - +
133B PHE* 1.3 64.9 + - - -
134B TYR* 3.7 9.7 - - - -
181B GLN* 3.5 5.3 - - - +
182B ILE* 2.7 36.4 + - - +
212B LYS* 4.5 0.7 - - - -
214B ALA 3.5 11.2 - - - -
215B PHE 4.4 10.3 - - - -
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A SER* 3.4 27.4 - - - -
113A GLN 3.6 21.8 - - - -
114A PHE* 3.8 39.9 - + + -
132B GLY* 1.3 75.7 - - - -
134B TYR* 1.3 64.6 + - - +
179B ILE* 4.2 4.9 - - + -
180B THR 3.5 2.0 - - - +
181B GLN* 3.7 39.0 - - + -
212B LYS* 3.7 2.3 - - - +
213B VAL* 2.9 27.2 + - + -
214B ALA* 2.9 25.6 + - + +
215B PHE 4.5 11.2 - - - -
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Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA* 3.5 8.5 - - + +
118B ILE* 4.0 15.0 - - + -
128B ILE* 3.4 26.7 - - + +
130B GLU 2.5 31.4 + - - -
132B GLY* 3.7 20.2 - - - -
133B PHE* 1.3 76.9 - - - +
135B LYS* 1.3 60.5 + - - +
136B ILE* 3.9 3.8 + - + +
178B ALA 3.7 0.7 - - - +
179B ILE* 3.2 6.7 - - - +
180B THR* 2.9 43.3 + - + +
182B ILE* 3.6 17.7 - - + -
210B ILE* 4.1 20.4 - - + -
211B GLU 3.2 7.6 - - - +
212B LYS* 3.5 44.1 - - + +
213B VAL* 4.4 0.4 - - - -
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LYS* 3.6 22.6 - - - +
137A THR* 4.3 10.5 + - - +
209A ILE* 4.3 19.5 - - + +
211A GLU* 3.3 36.1 + - - +
134B TYR* 1.3 73.1 - - - +
136B ILE* 1.3 66.1 + - - +
137B THR* 4.2 17.9 - - - +
177B GLN* 5.5 0.4 - - - -
178B ALA 3.4 9.9 - - - +
179B ILE* 4.4 10.3 - - + +
209B ILE* 3.6 1.4 - - - +
210B ILE* 3.4 5.0 - - - -
211B GLU* 2.8 46.4 + - - +
213B VAL* 3.8 18.4 - - + +
135C LYS* 3.6 16.8 - - - +
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE* 5.8 0.9 - - + -
134B TYR* 4.4 7.0 - - + +
135B LYS* 1.3 79.6 - - - +
137B THR* 1.3 65.8 + - - +
138B VAL* 4.2 2.7 - - + -
153B ILE* 3.8 42.1 - - + +
155B VAL* 4.9 1.8 - - + -
160B VAL* 5.5 1.6 - - + -
176B ILE 3.8 0.7 - - - +
177B GLN* 3.3 4.3 - - - -
178B ALA* 2.8 40.1 + - + +
180B THR* 4.1 24.0 - - + -
189B VAL* 4.4 20.6 - - + -
208B ILE* 4.2 22.4 - - + -
209B ILE 3.4 7.6 - - - +
210B ILE* 4.4 14.6 - - + -
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Residues in contact with THR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A THR* 6.0 2.5 - - + -
135B LYS* 4.2 22.2 - - - +
136B ILE* 1.3 78.9 - - - +
138B VAL* 1.3 64.2 + - - +
139B ILE* 6.0 0.9 - - - -
175B VAL* 6.3 2.9 - - + -
176B ILE 3.3 3.6 - - - +
177B GLN* 4.0 21.3 - - + +
208B ILE* 3.3 2.8 - - - +
209B ILE* 3.0 32.7 + - - +
135C LYS* 4.7 7.5 + - - +
177C GLN* 2.8 40.0 + - - +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B VAL* 6.5 0.4 - - + -
107B PHE* 5.0 4.9 - - + -
136B ILE* 4.2 1.3 - - + -
137B THR* 1.3 78.5 - - - +
139B ILE* 1.3 74.5 + - - +
140B ALA* 4.6 1.1 - - + +
151B LEU* 4.5 12.1 - - + -
153B ILE* 4.2 20.0 - - + -
174B ILE 3.7 1.4 - - - +
175B VAL* 3.4 5.4 - - - +
176B ILE* 2.9 43.4 + - + +
191B VAL* 4.0 35.9 - - + -
206B ALA* 5.7 1.1 - - + -
207B SER 3.4 8.5 - - - +
208B ILE* 3.9 20.6 - - + -
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B THR* 6.0 0.9 - - - -
138B VAL* 1.3 80.6 - - - +
140B ALA* 1.3 62.3 + - - +
141B ASN* 3.9 24.5 + - - +
173B PRO* 4.4 11.0 - - + -
174B ILE 3.5 6.1 - - - +
175B VAL* 4.4 9.0 - - + -
206B ALA* 3.1 5.2 - - - +
207B SER* 2.8 43.9 + - - +
137C THR* 6.0 0.2 - - + -
175C VAL* 3.7 42.6 - - + +
177C GLN* 3.5 46.9 - - + +
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B VAL* 5.9 0.2 - - + -
138B VAL* 4.2 1.3 - - + -
139B ILE* 1.3 71.7 - - - +
141B ASN* 1.3 64.9 + - - +
142B THR* 3.5 3.8 + - - +
151B LEU* 3.5 32.8 - - + -
173B PRO* 3.3 3.7 - - - +
174B ILE* 2.9 42.5 + - + +
200B LEU* 4.2 17.5 - - + -
205B SER 3.5 5.4 - - - +
206B ALA* 4.3 7.0 - - + +
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Residues in contact with ASN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ILE* 3.9 20.7 + - - +
140B ALA* 1.3 70.1 - - - +
142B THR* 1.3 61.0 + - - +
171B GLY 5.7 0.9 - - - +
173B PRO* 4.0 13.2 - - - +
200B LEU* 3.6 5.7 - - - +
201B ALA* 2.9 30.5 + - + -
204B THR* 2.8 38.6 + - - +
205B SER* 2.8 14.7 + - - +
206B ALA* 4.7 0.8 - - - +
165C SER* 4.2 20.9 + - - +
166C SER 6.0 1.3 - - - +
168C ILE* 6.4 0.4 - - + -
175C VAL 4.8 5.2 + - - +
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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