Contacts of the strand formed by residues 145 - 155 (chain A) in PDB entry 3IFP
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 MET 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A SER* 1.3 85.9 + - - +
146A VAL* 1.3 60.3 + - - +
147A THR* 5.8 0.2 - - - +
192A THR* 3.8 28.3 - - + +
193A VAL* 2.9 40.4 - - - +
194A PRO* 3.6 11.9 - - + -
195A SER* 4.3 3.1 + - - -
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Residues in contact with VAL 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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136A PRO* 3.9 26.0 - - + -
145A MET* 1.3 76.5 - - - +
147A THR* 1.3 66.1 + - - +
148A LEU* 4.1 5.8 + - + +
191A VAL 4.0 0.3 - - - +
192A THR* 3.4 3.8 - - - +
193A VAL* 3.1 53.0 + - + +
195A SER* 4.3 18.8 - - - +
198A TRP* 4.1 28.9 - - + -
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Residues in contact with THR 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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136A PRO* 4.1 9.4 - - - +
145A MET* 5.7 0.5 - - - +
146A VAL* 1.3 74.6 - - - +
148A LEU* 1.3 69.6 - - - +
190A SER* 3.7 19.1 - - - +
191A VAL 3.4 12.1 - - - +
192A THR* 3.2 20.2 + - - +
119B THR* 5.8 3.6 - - - +
121B SER* 3.9 26.1 + - - +
123B PHE* 3.0 29.7 - - + -
140B PHE* 4.8 0.9 - - + -
142B ASN* 4.8 4.3 + - - +
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Residues in contact with LEU 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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134A LEU 3.9 4.3 - - - +
136A PRO* 3.8 17.0 - - + -
146A VAL* 4.6 6.5 - - + +
147A THR* 1.3 78.5 - - - +
149A GLY* 1.3 59.4 + - - +
164A TRP* 4.6 3.8 - - + -
190A SER* 3.4 2.9 - - - -
191A VAL* 2.8 45.5 + - + +
193A VAL* 5.1 5.2 - - + -
198A TRP* 3.6 57.0 - - + +
203A VAL* 3.7 36.8 - - + -
220A ILE* 3.9 14.8 - - + -
123B PHE* 4.2 2.7 - - - -
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Residues in contact with GLY 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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134A LEU* 2.9 39.0 + - - +
148A LEU* 1.3 76.2 - - - +
150A CYS* 1.3 63.8 + - - +
164A TRP* 4.0 2.9 - - - -
189A SER 3.2 10.8 - - - -
220A ILE* 3.7 9.5 - - - +
123B PHE* 4.1 1.8 - - - -
140B PHE* 3.8 16.2 - - - -
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Residues in contact with CYS 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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131A VAL* 3.8 17.0 - - - -
132A TYR 3.5 10.1 - - - -
133A PRO* 5.4 0.9 - - - -
134A LEU* 3.6 7.3 - - - +
149A GLY* 1.3 76.1 - - - +
151A LEU* 1.3 63.7 + - - +
152A VAL* 4.0 9.7 + - - +
162A VAL* 5.2 1.8 - - - -
164A TRP* 3.8 14.8 - - + -
188A SER* 3.2 5.4 - - - -
189A SER* 2.9 32.7 + - - +
205A CYS* 2.0 46.2 - - + -
220A ILE* 5.0 0.9 - - + -
140B PHE* 4.6 0.4 - - - -
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Residues in contact with LEU 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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130A SER 3.4 4.2 - - - +
131A VAL* 3.5 2.9 - - - +
132A TYR* 2.9 55.8 + - + +
134A LEU* 3.8 16.8 - - + +
150A CYS* 1.3 73.1 - - - +
152A VAL* 1.3 68.7 + - - +
153A LYS* 4.3 9.2 - - + +
186A THR* 3.8 20.4 - - - +
187A LEU 3.9 7.4 - - - +
188A SER* 4.4 6.7 - - - -
129B GLN* 4.9 3.1 - - - +
136B SER* 3.7 31.9 - - - +
138B VAL* 3.8 20.0 - - + -
183B THR* 4.8 8.1 - - + +
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Residues in contact with VAL 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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129A PRO* 3.5 27.6 - - + -
130A SER 3.6 2.9 - - - +
131A VAL* 4.3 1.8 - - + -
150A CYS* 4.4 7.4 - - - +
151A LEU* 1.3 76.6 - - - +
153A LYS* 1.3 57.7 + - - +
155A TYR* 3.8 16.3 - - + -
160A VAL* 4.5 5.4 - - + -
162A VAL* 3.9 15.0 - - + -
186A THR* 2.9 18.9 + - - -
187A LEU* 2.7 35.0 + - + +
207A VAL* 3.3 39.3 - - + -
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Residues in contact with LYS 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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129A PRO* 3.7 0.9 - - - +
130A SER* 2.8 40.6 + - - +
132A TYR* 4.4 13.0 - - + +
151A LEU* 4.3 11.9 - - + +
152A VAL* 1.3 74.9 - - - +
154A GLY* 1.3 74.0 + - - +
155A TYR* 4.0 1.6 - - - -
181A GLN* 2.9 41.8 - - - +
185A TYR 4.0 0.7 - - - -
186A THR* 3.6 8.1 - - - +
129B GLN* 3.9 21.8 - - - +
136B SER* 3.4 9.3 + - - -
183B THR* 6.0 0.8 - - - +
185B THR* 3.4 23.9 + - - +
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Residues in contact with GLY 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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127A THR* 3.8 6.8 - - - +
128A PRO 3.3 14.9 - - - +
130A SER 4.4 0.2 + - - -
153A LYS* 1.3 85.0 - - - +
155A TYR* 1.3 58.9 + - - +
181A GLN* 4.3 3.1 + - - -
184A LEU* 3.5 29.5 - - - +
185A TYR 3.1 13.6 + - - -
186A THR* 4.0 2.0 - - - -
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Residues in contact with TYR 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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127A THR* 3.4 17.7 - - - +
129A PRO* 3.7 20.6 - - + -
152A VAL* 3.8 31.2 - - + -
154A GLY* 1.3 76.0 - - - +
156A PHE* 1.3 65.5 + - - +
157A PRO 3.5 20.9 - - - -
158A GLU* 4.3 11.5 + - + -
160A VAL* 3.6 26.2 + - + +
178A ALA* 3.4 24.6 - - - +
184A LEU* 3.6 6.4 - - - +
185A TYR* 2.9 65.5 + - + +
186A THR* 3.8 6.3 - - - -
187A LEU* 3.6 15.0 - - - +
209A HIS* 3.9 2.2 - - + -
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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