Contacts of the strand formed by residues 129 - 139 (chain C) in PDB entry 2RFQ
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 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C VAL* 3.7 2.3 - - - +
126C VAL* 2.9 28.0 + - - +
127C ASP 3.3 1.6 + - - -
128C GLY* 1.3 79.9 - - - +
130C TYR* 1.3 76.8 + - - -
198C PHE* 3.9 1.6 - - - -
199C VAL 3.3 12.1 - - - -
201C THR* 3.5 13.9 + - - -
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Residues in contact with TYR 130 (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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123C GLY* 4.2 6.3 - - - -
124C GLN 3.1 8.5 - - - +
125C VAL* 3.9 18.4 - - + -
126C VAL* 3.7 7.4 - - - +
129C GLY* 1.3 87.5 - - - -
131C THR* 1.3 59.5 + - - +
132C VAL* 3.9 4.2 + - + -
154C VAL* 3.5 40.3 - - + +
166C PHE* 3.9 18.4 - + + -
197C VAL 3.4 0.9 - - - +
198C PHE* 3.4 6.1 - - - -
199C VAL 2.9 36.1 + - - +
201C THR* 4.1 19.1 + - - +
204C VAL* 3.5 45.0 - - + +
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Residues in contact with THR 131 (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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122C ALA 3.8 0.9 - - - +
123C GLY* 3.3 1.0 - - - -
124C GLN* 2.7 46.7 + - + +
126C VAL* 3.2 25.8 - - - +
130C TYR* 1.3 70.8 - - - +
132C VAL* 1.3 62.2 + - - +
133C ASN* 4.1 11.5 + - - +
196C ASP* 3.4 37.7 - - - +
197C VAL 3.4 4.7 - - - +
198C PHE* 5.3 1.7 - - - +
393C 1PS 5.1 5.2 - - - -
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ALA 3.4 7.6 - - - +
123C GLY* 4.0 2.2 - - - -
130C TYR* 4.2 2.7 - - + -
131C THR* 1.3 76.9 - - - +
133C ASN* 1.3 65.3 + - - +
136C TRP* 3.6 31.6 - - + -
166C PHE* 3.7 33.0 - - + -
168C ILE* 4.1 7.9 - - + -
194C VAL* 3.6 16.2 - - + +
196C ASP 3.3 6.2 + - - -
197C VAL 2.7 34.9 + - - +
199C VAL* 3.6 29.6 - - + -
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Residues in contact with ASN 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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121C GLY* 3.1 1.9 - - - -
122C ALA 2.9 31.3 + - - +
131C THR* 4.1 13.9 + - - +
132C VAL* 1.3 79.8 + - - +
134C GLY* 1.3 59.8 + - - +
136C TRP* 4.1 5.2 - - - -
194C VAL 3.4 4.3 - - - +
195C GLU* 3.6 7.1 - - - +
196C ASP* 2.9 30.6 + - - +
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Residues in contact with GLY 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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120C MSE 3.4 12.6 - - - -
121C GLY* 3.7 0.7 - - - -
133C ASN* 1.3 75.6 - - - +
135C ALA* 1.3 59.8 + - - +
136C TRP* 3.6 17.2 - - - -
193C VAL* 3.6 3.8 - - - +
194C VAL 2.9 33.7 + - - +
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Residues in contact with ALA 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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120C MSE 3.1 22.3 + - - +
134C GLY* 1.3 73.9 - - - +
136C TRP* 1.3 60.7 + - - +
137C ALA* 3.4 7.5 + - - +
191C THR* 3.9 15.2 - - + +
192C VAL 3.6 4.9 - - - -
193C VAL* 4.4 11.4 - - + +
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Residues in contact with TRP 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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116C SER* 3.3 30.9 + - - +
118C ALA 3.1 18.7 + - - -
120C MSE 3.5 10.8 - - + +
121C GLY* 3.5 30.3 - - - -
122C ALA 3.9 0.4 - - - -
132C VAL* 3.6 25.4 - - + -
133C ASN 4.0 0.2 - - - -
134C GLY* 3.6 26.7 - - - -
135C ALA* 1.3 70.9 - - - +
137C ALA* 1.3 64.8 + - - +
139C SER* 4.6 0.5 - - - -
150C LEU* 3.7 39.7 - - + -
151C GLY 2.8 33.7 + - - +
166C PHE* 4.7 4.7 - + - -
190C ASN 4.0 1.4 - - - +
191C THR* 3.3 1.8 - - - -
192C VAL* 2.8 39.2 + - + +
194C VAL* 3.9 18.6 - - + -
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Residues in contact with ALA 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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116C SER* 2.7 26.9 + - - -
120C MSE 3.3 17.0 - - - +
135C ALA 3.4 5.5 + - - +
136C TRP* 1.3 73.6 - - - +
138C TRP* 1.3 91.7 + - + +
139C SER 3.4 0.4 + - - -
178C VAL* 6.0 0.7 - - + -
190C ASN 4.0 0.2 - - - -
191C THR* 3.5 20.8 - - + +
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Residues in contact with TRP 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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115C SER 4.2 3.7 - - - +
116C SER* 5.0 1.9 + - - -
120C MSE 4.1 13.6 - - + -
137C ALA* 1.3 101.2 - - + +
139C SER* 1.3 59.5 + - - +
140C SER* 3.1 12.2 + - - -
179C TRP* 3.5 37.7 - + - -
181C VAL* 5.1 2.9 - - + -
189C SER* 3.5 24.8 + - - -
190C ASN 3.6 1.4 + - - -
191C THR* 4.5 0.2 + - - -
364C VAL* 4.6 6.7 - - + -
343D ALA* 3.5 48.0 - - + -
344D THR* 5.7 0.4 - - - -
346D LEU* 4.2 17.3 - - + -
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Residues in contact with SER 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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114C SER* 3.0 26.3 + - - -
115C SER* 2.8 25.2 + - - -
116C SER* 4.6 5.2 - - - -
136C TRP 4.6 0.9 - - - -
137C ALA 3.4 0.6 - - - -
138C TRP* 1.3 72.8 - - - +
140C SER* 1.3 65.5 + - - +
141C GLY 3.3 0.3 + - - -
142C CYS* 3.1 27.5 + - - +
148C ALA* 5.4 0.2 - - - +
188C GLY 3.5 4.0 - - - +
189C SER* 3.6 3.2 - - - -
190C ASN 3.0 17.1 + - - -
192C VAL* 3.9 14.9 - - - +
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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