Contacts of the strand formed by residues 132 - 141 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C THR* 1.3 78.4 - - - +
133C PHE* 1.3 65.4 + - - -
134C TYR* 3.3 11.0 - - - -
181C GLN* 3.5 4.5 - - - -
182C ILE 2.8 36.9 + - - -
212C LYS* 4.2 0.9 - - - -
214C ALA 3.5 10.5 - - - -
215C PHE 4.2 11.7 - - - -
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Residues in contact with PHE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B SER* 3.5 26.7 - - - -
113B GLN 3.8 15.3 - - - -
114B PHE* 4.0 35.9 - + + -
132C GLY* 1.3 74.3 - - - -
134C TYR* 1.3 60.1 + - - +
179C ILE* 4.3 4.9 - - + -
180C THR 3.5 2.2 - - - -
181C GLN* 3.6 40.6 - - + -
212C LYS* 3.6 4.5 - - - +
213C VAL* 2.9 29.8 + - + -
214C ALA* 2.8 26.6 + - + +
215C PHE 3.9 22.9 - - - -
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Residues in contact with TYR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ALA* 3.7 9.8 - - + +
118C ILE* 3.8 27.1 - - + -
128C ILE* 3.3 26.1 - - + +
130C GLU 2.7 28.7 + - - -
132C GLY* 3.3 29.4 - - - -
133C PHE* 1.3 74.3 - - - +
135C LYS* 1.3 62.1 + - - +
136C ILE* 3.9 2.8 + - + +
178C ALA 3.8 0.5 - - - +
179C ILE* 3.2 4.2 - - - +
180C THR* 2.8 51.4 + - + +
182C ILE* 3.5 19.1 - - + -
210C ILE* 4.1 8.5 - - + -
211C GLU 3.3 5.6 - - - +
212C LYS* 3.6 40.7 - - + +
213C VAL* 4.4 2.7 - - - -
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Residues in contact with LYS 135 (chain C).
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* 3.0 24.1 - - - +
135B LYS* 3.6 17.0 - - - +
137B THR* 4.7 8.9 + - - +
209B ILE* 4.1 25.1 - - + +
211B GLU* 3.5 32.7 + - - +
134C TYR* 1.3 73.0 - - - +
136C ILE* 1.3 64.0 + - - +
137C THR* 4.1 15.4 + - - +
177C GLN* 5.1 1.1 - - - -
178C ALA 3.4 9.9 - - - +
179C ILE* 4.4 6.5 - - + +
209C ILE* 3.5 1.8 - - - +
210C ILE* 3.4 5.2 - - - -
211C GLU* 2.9 48.1 + - + +
213C VAL* 4.1 18.0 - - + +
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Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ILE* 5.7 0.7 - - + -
134C TYR* 4.3 7.9 - - + +
135C LYS* 1.3 79.6 - - - +
137C THR* 1.3 64.8 - - - +
138C VAL* 4.3 1.1 - - + -
153C ILE* 3.9 35.5 - - + +
155C VAL* 5.0 1.6 - - + -
160C VAL* 5.4 1.3 - - + -
176C ILE 3.7 1.2 - - - +
177C GLN* 3.4 2.9 - - - -
178C ALA* 2.8 40.0 + - + +
180C THR* 3.9 24.9 - - + -
189C VAL* 4.2 26.5 - - + -
208C ILE* 4.2 23.6 - - + -
209C ILE 3.4 7.9 - - - +
210C ILE* 4.2 16.4 - - + -
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Residues in contact with THR 137 (chain C).
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* 5.1 4.9 + - - -
177A GLN* 2.9 39.8 + - - +
135C LYS* 4.1 22.2 + - - +
136C ILE* 1.3 74.5 + - - +
138C VAL* 1.3 69.8 + - - +
139C ILE* 4.9 5.6 - - + -
175C VAL* 5.0 7.6 - - + -
176C ILE 3.2 10.8 - - - +
177C GLN* 4.3 10.2 - - + +
208C ILE* 3.4 2.4 - - - +
209C ILE* 3.1 24.7 + - - -
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Residues in contact with VAL 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C PHE* 5.1 5.2 - - + -
136C ILE* 4.3 1.1 - - + -
137C THR* 1.3 78.6 - - - +
139C ILE* 1.3 75.1 + - - +
140C ALA* 4.7 2.0 - - + +
151C LEU* 4.8 6.7 - - + -
153C ILE* 3.9 24.7 - - + -
174C ILE 3.6 1.1 - - - +
175C VAL* 3.4 5.9 - - - +
176C ILE* 2.8 49.4 + - + +
191C VAL* 4.0 36.3 - - + -
206C ALA* 5.6 1.1 - - + -
207C SER 3.5 9.4 - - - +
208C ILE* 4.1 14.4 - - + -
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Residues in contact with ILE 139 (chain C).
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* 6.2 0.2 - - + -
175A VAL* 3.5 49.4 - - + +
177A GLN* 3.7 42.1 - - + +
137C THR* 4.9 3.4 - - + -
138C VAL* 1.3 79.4 - - - +
140C ALA* 1.3 64.6 + - - +
141C ASN* 3.9 22.8 + - - +
173C PRO* 4.8 2.9 - - + -
174C ILE 3.5 5.2 - - - +
175C VAL* 4.6 14.6 - - + -
206C ALA* 3.2 5.2 - - - +
207C SER* 2.8 41.3 + - - +
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Residues in contact with ALA 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C VAL* 6.2 0.2 - - + -
138C VAL* 4.9 1.8 - - + -
139C ILE* 1.3 76.5 - - - +
141C ASN* 1.3 63.2 + - - +
142C THR* 3.5 3.0 + - - +
151C LEU* 3.5 32.1 - - + -
173C PRO* 3.4 3.6 - - - +
174C ILE* 2.8 44.0 + - + +
200C LEU* 4.3 12.8 - - + -
205C SER 3.5 8.3 - - - +
206C ALA* 4.3 6.7 - - + +
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Residues in contact with ASN 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A SER* 3.9 22.9 + - - +
166A SER 6.0 1.8 - - - +
168A ILE* 6.2 0.9 - - + -
175A VAL 4.7 3.9 + - - +
139C ILE* 3.9 22.7 + - - +
140C ALA* 1.3 69.7 - - - +
142C THR* 1.3 61.9 + - - +
172C ALA 5.5 0.2 - - - -
173C PRO* 4.1 13.1 - - - +
200C LEU* 3.5 7.4 - - - +
201C ALA* 2.8 32.5 + - + +
204C THR* 2.9 38.2 + - - +
205C SER 3.0 10.9 + - - +
206C ALA* 4.9 0.8 - - - +
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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