Contacts of the strand formed by residues 143 - 153 (chain A) in PDB entry 3OF6
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 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A GLU* 3.5 18.9 - - - +
138A ILE* 3.8 5.1 + - - -
141A THR* 3.0 16.6 + - - +
142A GLN* 1.3 85.0 - - - +
144A ALA* 1.3 60.9 + - - +
198A ARG* 3.3 48.1 + - + +
199A VAL 3.6 11.9 + - - +
200A SER* 4.5 15.1 - - - +
201A ALA* 3.7 6.4 - - - +
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Residues in contact with ALA 144 (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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133A PRO* 3.5 26.7 - - + -
137A GLU* 4.5 0.4 - - - -
138A ILE* 4.4 4.7 - - + -
143A LYS* 1.3 74.8 - - - +
145A THR* 1.3 63.8 + - - +
197A LEU 3.6 0.5 - - - +
198A ARG* 3.3 4.0 - - - +
199A VAL* 2.7 44.1 + - + +
200A SER 4.4 2.2 - - - +
201A ALA* 4.0 2.6 - - - +
204A TRP* 3.5 29.2 - - + -
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Residues in contact with THR 145 (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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132A GLU 4.5 0.9 - - - -
133A PRO* 3.6 20.1 - - - +
137A GLU* 2.7 32.1 + - - +
144A ALA* 1.3 73.8 + - - +
146A LEU* 1.3 74.4 + - - +
147A VAL* 4.1 4.7 + - - +
196A ARG* 4.0 18.8 - - + -
197A LEU 3.3 9.2 - - - +
198A ARG* 3.0 25.4 + - + +
32D LEU* 3.8 23.6 - - + +
34D LEU* 5.3 1.9 - - + +
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Residues in contact with LEU 146 (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 VAL* 4.6 9.6 - - + -
131A PHE 3.8 13.2 - - - +
133A PRO* 3.7 24.9 - - + -
145A THR* 1.3 77.3 - - - +
147A VAL* 1.3 63.4 + - - +
162A TRP* 3.8 22.6 - - + -
195A SER 3.6 0.2 - - - +
196A ARG* 3.3 8.3 - - - -
197A LEU* 2.9 41.2 + - + +
199A VAL* 4.6 14.6 - - + -
204A TRP* 4.2 15.3 - - + -
211A PHE* 3.5 42.8 - - + -
242A ALA* 5.7 2.0 - - + -
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Residues in contact with VAL 147 (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 ALA 3.6 1.4 - - - +
130A VAL* 3.2 5.4 - - - +
131A PHE* 2.9 49.7 + - + -
145A THR 4.6 3.8 - - - +
146A LEU* 1.3 80.2 - - - +
148A CYS* 1.3 63.4 + - - +
149A LEU* 4.0 17.0 - - + -
162A TRP* 4.1 2.9 - - - -
195A SER 3.5 8.5 - - - +
196A ARG* 4.6 5.8 - - + -
30D VAL* 4.9 9.2 - - + -
32D LEU* 4.4 24.2 - - + -
73D LEU* 3.6 35.9 - - + -
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Residues in contact with CYS 148 (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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128A VAL* 3.5 22.0 - - - -
129A ALA 3.4 4.3 - - - -
130A VAL* 4.3 1.1 - - + -
147A VAL* 1.3 75.4 - - - +
149A LEU* 1.3 70.3 + - - +
160A LEU* 4.1 8.9 - - - +
162A TRP* 3.6 10.4 - - + -
193A LEU 3.7 0.2 - - - +
194A SER* 3.2 8.0 - - - -
195A SER* 3.1 31.1 + - - -
213A CYS* 2.0 53.4 - - + -
215A VAL* 4.4 2.0 - - - -
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Residues in contact with LEU 149 (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 GLU 2.7 24.5 - - - +
128A VAL* 3.0 12.1 - - - -
129A ALA* 2.9 17.5 + - + +
131A PHE* 3.4 31.4 - - + -
147A VAL* 4.0 12.8 - - + -
148A CYS* 1.3 86.2 - - - +
150A ALA* 1.3 53.8 + - - +
151A THR* 4.0 6.1 - - + -
193A LEU 3.4 0.7 - - - -
194A SER* 3.6 21.1 - - - -
28D VAL* 5.4 1.8 - - + -
30D VAL* 4.9 3.1 - - + -
60D TYR* 3.6 28.9 - - + +
73D LEU* 4.0 2.5 - - + -
75D HIS* 4.0 27.8 - - + -
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Residues in contact with ALA 150 (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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126A PRO* 4.0 20.2 - - + -
127A GLU 3.8 5.2 - - - -
128A VAL* 4.2 1.1 - - + +
148A CYS* 4.3 0.8 - - - -
149A LEU* 1.3 70.8 - - - +
151A THR* 1.3 60.9 + - - +
153A PHE* 3.1 12.4 - - + -
160A LEU* 5.1 1.8 - - + +
192A CYS* 3.2 0.3 - - - -
193A LEU* 2.8 52.2 + - + -
215A VAL* 4.1 26.5 - - + -
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Residues in contact with THR 151 (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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126A PRO* 3.4 2.6 - - - +
127A GLU* 2.8 48.5 + - - +
149A LEU* 4.6 7.9 - - + -
150A ALA* 1.3 80.8 - - - +
152A GLY* 1.3 67.9 + - - +
153A PHE* 3.2 4.0 + - - -
182A GLU* 3.6 8.5 - - - +
191A TYR 3.6 5.4 - - - -
192A CYS* 4.3 6.5 - - + -
60D TYR* 3.5 24.0 - - - +
75D HIS* 5.0 8.7 - - + +
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Residues in contact with GLY 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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124A PHE* 3.4 13.0 - - - +
125A PRO 2.9 15.8 - - - +
127A GLU* 3.7 10.6 - - - +
151A THR* 1.3 70.4 - - - +
153A PHE* 1.3 57.3 + - - +
182A GLU* 2.7 23.3 + - - -
190A ARG* 3.5 31.6 + - - -
191A TYR 3.2 2.4 + - - -
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Residues in contact with PHE 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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124A PHE* 3.1 13.7 - - - +
126A PRO* 3.6 23.8 - - + -
150A ALA* 3.1 34.3 - - + -
151A THR 3.8 5.6 - - - -
152A GLY* 1.3 77.9 - - - +
154A TYR* 1.3 60.2 + - - +
155A PRO 3.2 12.8 - - - -
156A ASP* 3.7 17.0 - - - -
158A VAL* 3.6 34.3 - - + -
179A PRO* 3.8 14.4 - - + -
190A ARG* 4.1 1.7 - - - +
191A TYR* 3.0 69.0 + - + +
192A CYS* 3.6 5.4 - - - -
193A LEU* 4.1 1.8 - - + -
217A PHE* 4.4 1.8 - + + -
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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