Contacts of the strand formed by residues 151 - 161 (chain A) in PDB entry 3DB3
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 TRP 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ASP* 3.5 25.6 - - + -
143A ALA 3.5 11.9 - - - -
144A ARG* 3.5 49.4 - - + +
149A GLY 4.2 6.8 + - - -
150A ALA* 1.3 73.9 - - - +
152A PHE* 1.3 66.9 + - - +
153A GLU* 5.0 1.0 - - - +
202A ARG 4.0 7.2 - - - -
203A ASP 3.4 34.8 - - - -
204A VAL* 4.0 1.8 - - - -
205A ARG* 3.2 57.5 - - + +
224A MSE 3.8 20.1 - - - +
237A PHE* 5.8 0.3 - - - +
238A TRP* 2.8 36.7 + - - +
240A ASP* 3.5 21.1 + - - +
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Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ASP* 3.3 6.2 - - - -
143A ALA* 2.7 40.0 + - - -
145A ASP* 3.9 9.2 - - + -
148A MSE 3.9 12.1 - - + -
150A ALA* 3.3 30.7 - - + -
151A TRP* 1.3 76.5 - - - +
153A GLU* 1.3 70.5 + - - +
154A ALA* 3.4 1.4 + - - +
188A TYR* 3.7 21.8 - + + -
191A TYR* 4.0 17.7 - + + -
237A PHE* 3.8 33.7 - + + -
9B M3L 3.7 49.4 - - - -
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL 3.6 5.8 - - - -
142A ASP* 3.5 9.4 + - - +
151A TRP 5.0 1.2 - - - +
152A PHE* 1.3 82.8 - - - +
154A ALA* 1.3 60.3 + - - +
188A TYR* 3.8 5.5 - - - +
189A ASP* 3.1 28.3 + - + +
190A ASP* 4.3 17.4 + - - +
207A ARG* 3.4 33.4 - - - +
238A TRP* 6.1 0.7 - - - -
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TYR* 3.4 1.2 - - - -
141A VAL* 2.8 34.5 + - + +
143A ALA* 3.8 18.6 - - + -
152A PHE 4.0 0.7 - - - +
153A GLU* 1.3 77.2 - - - +
155A GLN* 1.3 62.0 + - - +
186A VAL* 3.7 20.4 - - + -
187A LYS 3.2 16.2 - - - +
188A TYR* 4.0 4.7 - - + -
189A ASP* 3.6 7.9 - - - -
207A ARG* 3.1 10.0 + - - +
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Residues in contact with GLN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ASN* 3.0 44.3 + - - +
139A GLU 3.4 14.8 - - - +
140A TYR* 3.7 31.7 + - + -
141A VAL 4.6 0.2 - - - +
154A ALA* 1.3 76.8 - - - +
156A VAL* 1.3 68.5 + - - +
157A VAL* 3.4 3.1 + - - +
186A VAL* 3.4 5.1 - - - -
187A LYS* 2.8 66.7 + - - +
189A ASP* 4.3 4.7 - - - +
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A TYR* 4.5 4.7 - - + -
136A LYS 3.4 24.5 - - - +
137A VAL* 4.0 3.3 - - - +
138A ASN* 2.6 32.4 + - - +
139A GLU 3.1 13.2 + - - +
141A VAL* 4.1 24.7 - - + -
155A GLN* 1.3 72.3 - - - +
157A VAL* 1.3 60.5 + - - +
158A ARG 3.7 20.2 - - - +
159A VAL* 3.7 17.9 - - + -
184A TYR* 4.1 20.2 - - + -
185A HIS 3.7 5.4 - - - +
186A VAL* 4.2 7.2 - - + -
204A VAL* 5.0 0.9 - - + -
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 3.4 18.9 - - - +
138A ASN* 5.7 3.1 - - - +
155A GLN 3.6 13.0 - - - +
156A VAL* 1.3 74.3 - - - +
158A ARG* 1.3 63.9 + - + +
185A HIS 2.7 19.1 + - - +
186A VAL 4.1 1.8 - - - -
187A LYS* 3.7 41.1 - - + +
196A VAL* 4.2 17.7 - - + -
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Residues in contact with ARG 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TRP 3.3 27.1 + - - -
128A ASP* 4.0 12.2 + - - +
130A THR* 2.8 32.5 + - - +
137A VAL* 3.8 9.4 - - + -
156A VAL* 3.7 5.4 - - - +
157A VAL* 1.3 81.9 - - + +
159A VAL* 1.3 64.0 + - - +
160A THR* 3.8 9.7 - - - +
185A HIS* 2.8 54.0 + - + +
196A VAL* 6.0 0.9 - - + -
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A THR* 3.3 9.9 + - - +
131A GLU 3.0 35.7 + - - +
132A LEU* 5.3 0.9 - - - -
133A GLY 4.5 9.9 - - - +
135A TYR 3.8 17.0 - - - +
136A LYS* 4.6 0.4 - - - -
137A VAL* 3.9 20.5 - - + +
156A VAL* 3.7 20.0 - - + -
158A ARG* 1.3 79.6 - - - +
160A THR* 1.3 61.5 - - - +
182A VAL* 3.2 31.4 - - + -
183A ILE 3.6 2.2 - - - -
184A TYR* 3.8 12.3 - - + -
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Residues in contact with THR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TRP* 3.7 23.7 - - - +
129A GLU* 3.4 14.1 - - - +
130A THR 3.6 15.0 - - - +
131A GLU* 4.0 4.3 - - - +
158A ARG* 3.8 10.7 - - - +
159A VAL* 1.3 80.1 - - - +
161A ARG* 1.3 62.8 + - - +
182A VAL* 3.2 9.0 - - - +
183A ILE* 2.9 37.6 + - - +
185A HIS* 2.9 33.3 + - + +
198A GLN* 5.5 0.2 + - - -
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLU* 2.9 31.2 + - + +
131A GLU* 4.0 15.0 - - + -
160A THR* 1.3 75.8 - - - +
162A LYS* 1.3 66.1 + - - +
181A ASP 4.8 0.2 - - - -
182A VAL* 4.8 6.5 - - + +
183A ILE* 5.1 0.2 - - - -
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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