Contacts of the strand formed by residues 166 - 175 (chain C) in PDB entry 3T0E
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 PHE 166 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111C ILE* 5.1 1.1 - - + -
112C GLN* 4.1 14.1 - - + -
113C ASN* 3.1 41.3 - - + -
136C ASP* 3.5 27.8 - - - -
159C LEU* 3.9 0.9 - - - +
160C ASP* 3.4 4.9 + - - +
161C MET* 2.9 50.2 + - + +
164C MET* 4.2 17.3 - - + +
165C ASP* 1.3 77.2 - - - +
167C LYS* 1.3 72.0 + - - +
168C SER* 4.2 12.1 - - - -
140D LYS* 3.3 42.6 - - + -
195D ARG* 4.3 3.6 - - - -
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Residues in contact with LYS 167 (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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13C GLU* 2.9 38.6 - - - +
79C LEU* 3.7 26.2 - - - +
109C PRO* 4.9 4.9 - - + -
110C ASN 4.3 11.0 - - - +
111C ILE* 3.4 22.7 - - - +
112C GLN* 4.2 5.0 + - + +
158C VAL* 4.4 11.7 - - + -
159C LEU 3.4 5.8 - - - +
160C ASP* 2.9 41.7 + - + +
162C ARG* 4.0 13.7 - - - +
165C ASP* 5.9 3.8 + - - +
166C PHE* 1.3 81.2 - - - +
168C SER* 1.3 62.5 + - - +
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Residues in contact with SER 168 (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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111C ILE* 3.7 7.0 - - - -
135C THR* 3.9 4.3 + - - -
136C ASP* 2.9 36.4 + - - -
158C VAL* 4.5 2.2 - - - +
159C LEU* 2.8 60.7 + - - +
166C PHE* 4.2 9.3 - - - -
167C LYS* 1.3 75.6 - - - +
169C ASN* 1.3 61.5 + - - +
195D ARG* 4.2 7.4 + - - -
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Residues in contact with ASN 169 (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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109C PRO* 3.5 6.9 - - - +
111C ILE* 3.0 33.1 - - + +
136C ASP 3.2 20.0 + - - -
137C PHE* 3.3 37.2 + - + +
138C ASP 4.1 1.0 + - - -
139C SER* 3.6 17.2 + - - +
156C LYS* 3.3 31.1 + - + +
157C THR 4.0 3.6 - - - -
158C VAL* 3.2 27.7 + - - +
168C SER* 1.3 70.0 - - - +
170C SER* 1.3 59.2 + - - +
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Residues in contact with SER 170 (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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133C LEU* 4.6 0.9 - - - -
134C PHE 3.4 4.7 - - - -
135C THR* 3.6 22.9 - - - -
156C LYS* 4.8 0.2 - - - -
157C THR 3.1 19.4 + - - +
159C LEU* 3.0 24.4 - - - +
168C SER 3.4 0.2 + - - -
169C ASN* 1.3 73.5 - - - +
171C ALA* 1.3 60.8 + - - +
142D THR* 6.1 1.1 - - - -
171D SER* 4.0 0.7 + - - -
193D ARG* 2.9 53.8 + - - -
195D ARG* 5.4 0.7 - - - -
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Residues in contact with ALA 171 (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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133C LEU* 3.2 16.3 - - - +
134C PHE* 2.9 36.0 + - + +
137C PHE* 4.3 3.1 - - + -
143C VAL* 3.7 35.0 - - + -
153C ILE* 5.4 0.9 - - + -
154C THR* 3.9 13.7 - - - +
155C ASP 4.8 1.1 - - - -
156C LYS* 4.0 8.0 - - + +
169C ASN 4.2 0.8 - - - -
170C SER* 1.3 73.7 - - - +
172C VAL* 1.3 62.8 + - - +
193D ARG* 4.9 1.3 - - - -
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Residues in contact with VAL 172 (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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131C VAL* 3.8 21.3 - - + +
132C CYS 4.3 2.7 - - - +
133C LEU* 4.5 12.8 - - + +
134C PHE* 4.7 1.1 - - - +
152C TYR 4.1 0.5 - - - +
153C ILE* 3.5 5.2 - - - +
154C THR* 3.2 38.5 + - + +
171C ALA* 1.3 79.0 - - - +
173C ALA* 1.3 65.2 + - - +
174C TRP* 4.3 10.1 + - + +
144D VAL* 4.8 18.8 - - + -
146D LEU* 6.3 1.3 - - + -
191D SER* 3.5 24.7 - - - +
193D ARG* 3.9 15.3 - - - +
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Residues in contact with ALA 173 (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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130C SER 3.9 1.6 - - - +
131C VAL 3.2 11.2 - - - -
132C CYS* 2.8 33.3 + - + +
134C PHE* 6.0 1.7 - - + +
145C GLN* 5.3 0.7 - - - +
151C VAL* 5.5 0.2 - - + -
152C TYR 3.3 9.4 - - - +
153C ILE* 3.9 17.7 - - + -
172C VAL* 1.3 75.0 - - - +
174C TRP* 1.3 59.8 + - - +
180C PHE* 4.0 16.1 - - + -
188C ASN* 5.0 13.5 - - - +
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Residues in contact with TRP 174 (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 ASP* 4.7 11.5 + - + -
130C SER* 3.8 25.8 - - - -
131C VAL* 4.2 8.7 - - + +
152C TYR* 2.9 80.4 + + + +
154C THR* 5.0 10.5 - - + -
172C VAL* 5.2 11.0 - - + -
173C ALA* 1.3 74.4 - - - +
175C SER* 1.3 69.8 + - - +
176C ASN 5.3 0.4 - - - +
180C PHE* 4.2 3.1 - - - -
146D LEU* 3.3 39.5 - - + +
148D THR* 3.8 12.8 - - + +
177D LEU* 4.3 7.9 - - + -
189D SER* 3.5 35.0 - - - -
190D LEU* 6.1 0.2 - - - -
191D SER* 4.6 13.2 - - - -
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Residues in contact with SER 175 (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 ASP* 5.4 0.7 - - - -
129C LYS 3.3 9.4 - - - +
130C SER* 3.3 21.2 - - - -
150C ASP 2.9 20.9 + - - -
151C VAL* 3.5 26.6 - - - +
152C TYR* 5.3 1.6 - - - -
174C TRP* 1.3 88.9 - - - +
176C ASN* 1.3 77.4 + - - +
177C LYS* 3.7 7.3 + - - +
180C PHE* 3.6 19.9 - - - -
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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