Contacts of the strand formed by residues 141 - 152 (chain C) in PDB entry 1D5Z
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 LYS 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C PHE* 3.1 3.2 - - - -
138C GLU* 2.8 37.1 + - - +
139C ASP* 3.8 10.5 - - + +
140C GLY* 1.3 83.7 - - - +
142C ASN* 1.3 59.2 + - - +
143C LEU* 3.2 28.5 + - + +
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Residues in contact with ASN 142 (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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135C ARG* 3.4 29.4 + - - +
136C VAL 2.9 12.9 + - - +
137C PHE* 3.8 19.1 - - + -
140C GLY 4.0 0.8 + - - -
141C LYS* 1.3 68.4 - - - +
143C LEU* 1.3 62.8 + - - +
144C LEU 2.8 30.3 + - - -
145C SER* 3.0 19.3 + - - -
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Residues in contact with LEU 143 (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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136C VAL 3.6 1.4 + - - -
138C GLU* 4.1 35.4 - - + +
141C LYS* 3.2 30.5 + - + +
142C ASN* 1.3 77.5 - - - +
144C LEU* 1.3 60.2 + - - +
172C LYS* 4.2 15.4 + - - +
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Residues in contact with LEU 144 (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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136C VAL* 2.7 42.1 + - + +
142C ASN* 2.8 8.5 + - - -
143C LEU* 1.3 81.8 - - - +
145C SER* 1.3 72.4 + - - +
146C PHE* 3.9 19.3 - - + -
167C TYR* 4.4 17.7 - - + +
168C LEU* 3.9 26.5 - - + -
171C ASN* 5.0 5.8 - - + -
172C LYS* 3.8 33.0 - - + -
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Residues in contact with SER 145 (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 THR* 6.5 0.9 - - - -
134C VAL 3.1 11.2 - - - -
135C ARG* 3.6 16.4 - - - +
142C ASN* 3.0 31.2 + - - -
144C LEU* 1.3 76.9 + - - +
146C PHE* 1.3 64.7 + - - +
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Residues in contact with PHE 146 (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 THR* 5.4 0.2 - - - -
134C VAL* 2.7 60.0 + - + +
136C VAL* 3.7 24.7 - - + -
144C LEU* 3.9 10.3 - - + -
145C SER* 1.3 78.9 - - - +
147C ASP* 1.3 73.0 + - - +
148C VAL* 3.7 22.9 - - + -
164C THR* 3.9 20.4 - - + -
167C TYR* 3.5 58.1 - + + +
168C LEU* 4.0 7.2 - - + -
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Residues in contact with ASP 147 (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 SER* 3.6 21.6 + - - -
132C ILE 3.1 4.7 - - - +
133C THR* 3.0 33.8 - - - +
146C PHE* 1.3 85.3 - - - +
148C VAL* 1.3 62.9 + - - +
149C GLN* 3.3 26.1 + - - +
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Residues in contact with VAL 148 (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 ARG 3.6 0.9 - - - +
131C SER* 3.4 0.2 - - - -
132C ILE* 2.8 50.5 + - + +
134C VAL* 4.0 10.5 - - + -
146C PHE* 3.7 28.7 - - + -
147C ASP* 1.3 71.0 - - - +
149C GLN* 1.3 68.0 + - - +
160C LEU* 4.3 11.9 - - + +
163C LEU* 4.0 27.1 - - + +
164C THR* 3.9 14.1 - - - +
230C ILE* 4.1 10.5 - - + -
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Residues in contact with GLN 149 (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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129C TYR* 4.1 27.6 - - + -
130C ARG 3.2 6.1 - - - +
131C SER* 2.8 28.1 + - - +
147C ASP* 3.3 26.8 + - - +
148C VAL* 1.3 89.9 - - - +
150C THR* 1.3 64.4 + - - +
159C GLU* 4.7 1.6 - - - +
160C LEU* 5.5 0.4 - - - -
163C LEU* 3.5 22.5 - - - +
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Residues in contact with THR 150 (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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126C LEU* 3.8 0.2 - - - +
129C TYR* 3.8 7.9 - - - -
130C ARG* 2.8 32.7 + - + +
132C ILE* 3.9 17.9 - - + -
149C GLN* 1.3 77.4 - - - +
151C ASN* 1.3 63.3 + - - +
152C LYS* 3.0 10.4 + - - +
155C VAL* 2.7 32.2 - - + +
159C GLU* 4.4 8.1 + - - -
160C LEU* 4.6 4.9 - - + -
225C SER* 3.6 30.3 - - - -
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Residues in contact with ASN 151 (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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36C ILE* 6.0 4.2 - - - +
125C GLN* 3.4 22.6 + - - +
126C LEU* 2.7 52.3 + - - +
128C LYS 4.3 6.1 - - - +
129C TYR* 3.7 35.9 + - + -
150C THR* 1.3 73.0 + - - +
152C LYS* 1.3 71.3 + - - +
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Residues in contact with LYS 152 (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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36C ILE* 5.0 8.5 - - - +
83C ASP* 3.6 30.9 - - - +
84C VAL 5.6 0.6 + - - -
85C PHE* 4.5 10.7 - - - +
117C GLY 6.1 0.2 - - - -
119C THR* 3.5 27.4 - - + +
124C ASN* 3.1 17.3 - - - +
125C GLN* 5.2 1.6 - - - +
126C LEU* 3.9 4.1 - - - +
150C THR* 3.0 7.5 + - - +
151C ASN* 1.3 93.3 + - - +
153C LYS* 1.3 56.0 + - - +
154C LYS 3.5 3.8 - - - +
155C VAL* 3.3 25.8 - - + +
159C GLU* 2.9 32.0 + - - +
225C SER* 2.7 30.7 + - - -
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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