Contacts of the strand formed by residues 145 - 155 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C SER* 1.3 87.1 + - - +
146C VAL* 1.3 61.2 + - - +
147C THR* 5.8 0.4 - - - +
192C THR* 3.8 27.8 - - + +
193C VAL* 2.9 40.6 - - - +
194C PRO* 3.6 11.7 - - + -
195C SER* 4.1 4.4 + - - -
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Residues in contact with VAL 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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136C PRO* 3.9 26.5 - - + -
145C MET* 1.3 76.3 - - - +
147C THR* 1.3 63.5 + - - +
148C LEU* 4.0 6.0 + - + -
191C VAL 4.0 0.5 - - - +
192C THR* 3.4 4.4 - - - +
193C VAL* 3.1 53.6 + - + +
195C SER* 4.4 17.5 - - - -
198C TRP* 4.1 29.2 - - + +
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Residues in contact with THR 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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136C PRO* 4.1 9.2 - - - +
145C MET* 4.4 0.4 - - - +
146C VAL* 1.3 74.5 - - - +
148C LEU* 1.3 68.7 + - - +
190C SER* 3.7 17.0 - - - +
191C VAL 3.3 11.4 - - - +
192C THR* 3.2 25.0 + - - +
119D THR* 5.8 3.5 - - - +
121D SER* 3.9 24.9 + - - +
123D PHE* 3.0 29.8 - - + -
140D PHE* 4.7 1.3 - - + -
142D ASN* 4.8 4.7 + - - +
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Residues in contact with LEU 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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134C LEU 3.9 3.6 - - - +
136C PRO* 3.8 17.3 - - + -
146C VAL* 4.0 6.7 + - + +
147C THR* 1.3 78.1 - - - +
149C GLY* 1.3 60.0 + - - +
164C TRP* 4.7 3.6 - - + -
190C SER* 3.4 2.9 - - - -
191C VAL* 2.8 45.9 + - + +
193C VAL* 5.0 5.2 - - + -
198C TRP* 3.7 53.8 - - + +
203C VAL* 3.7 38.1 - - + -
220C ILE* 3.9 15.7 - - + -
123D PHE* 4.2 2.7 - - - -
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Residues in contact with GLY 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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134C LEU* 2.9 38.7 + - - +
148C LEU* 1.3 75.4 - - - +
150C CYS* 1.3 63.4 - - - +
164C TRP* 4.0 2.7 - - - -
189C SER 3.2 10.5 - - - -
220C ILE* 3.7 9.5 - - - +
123D PHE* 4.1 1.4 - - - -
140D PHE* 3.8 16.4 - - - -
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Residues in contact with CYS 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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131C VAL* 3.8 18.6 - - - -
132C TYR 3.5 8.7 - - - -
133C PRO* 5.4 0.4 - - - -
134C LEU* 3.5 6.2 - - - +
149C GLY* 1.3 75.9 - - - +
151C LEU* 1.3 63.9 + - - +
152C VAL* 4.1 9.6 + - - +
162C VAL* 5.3 2.2 - - - -
164C TRP* 3.8 13.9 - - + -
188C SER* 3.2 5.4 - - - -
189C SER* 2.9 33.2 + - - +
205C CYS* 2.1 45.8 - - + -
207C VAL* 4.5 0.2 - - - -
220C ILE* 5.0 1.3 - - + -
140D PHE* 4.6 0.4 - - - -
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Residues in contact with LEU 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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130C SER 3.5 3.8 - - - +
131C VAL* 3.5 2.6 - - - +
132C TYR* 2.9 54.1 + - + +
134C LEU* 3.8 18.1 - - + +
150C CYS* 1.3 72.8 - - - +
152C VAL* 1.3 72.8 + - - +
153C LYS* 4.3 9.9 - - + +
186C THR* 3.7 20.9 - - - +
187C LEU 3.9 8.3 - - - +
188C SER* 4.3 6.5 - - - -
129D GLN* 4.9 2.7 - - - +
136D SER* 3.7 32.5 - - - +
138D VAL* 3.8 18.8 - - + -
183D THR* 4.7 8.1 - - + +
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Residues in contact with VAL 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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129C PRO* 3.5 28.3 - - + -
130C SER 3.6 2.7 - - - -
131C VAL* 4.3 2.2 - - + -
150C CYS* 4.4 7.2 - - - +
151C LEU* 1.3 75.2 - - - +
153C LYS* 1.3 57.5 + - - +
155C TYR* 3.8 16.1 - - + -
160C VAL* 4.5 5.4 - - + -
162C VAL* 4.0 6.5 - - + -
186C THR* 2.9 19.3 + - - -
187C LEU* 2.7 45.0 + - + +
207C VAL* 3.4 38.4 - - + -
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Residues in contact with LYS 153 (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 PRO* 3.7 0.9 - - - +
130C SER* 2.9 38.5 + - - +
132C TYR* 4.4 13.5 - - + +
151C LEU* 4.3 13.0 - - + +
152C VAL* 1.3 73.6 - - - +
154C GLY* 1.3 72.4 + - - +
155C TYR* 4.0 2.0 - - - -
181C GLN* 2.8 41.0 - - - +
185C TYR 4.0 0.4 - - - -
186C THR* 3.5 7.0 - - - +
129D GLN* 3.9 23.1 - - - +
136D SER* 3.4 9.7 + - - +
183D THR* 5.9 0.6 - - - +
185D THR* 3.3 25.1 + - - +
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Residues in contact with GLY 154 (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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127C THR* 3.8 6.4 - - - +
128C PRO 3.4 12.5 - - - +
153C LYS* 1.3 85.5 - - - +
155C TYR* 1.3 59.3 + - - +
181C GLN* 4.2 3.3 + - - -
184C LEU* 3.6 28.4 - - - +
185C TYR 3.1 14.0 + - - -
186C THR* 4.0 1.8 - - - -
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Residues in contact with TYR 155 (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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127C THR* 3.4 18.2 - - - +
129C PRO* 3.7 16.6 - - + -
152C VAL* 3.8 30.7 - - + -
154C GLY* 1.3 78.3 - - - +
156C PHE* 1.3 64.1 + - - +
157C PRO 3.4 20.9 - - - -
158C GLU* 4.3 8.4 + - - -
160C VAL* 3.6 31.3 + - + +
178C ALA* 3.4 24.6 - - - +
184C LEU* 3.6 6.2 - - - +
185C TYR* 2.9 65.5 + - + +
186C THR* 3.8 7.9 - - - -
187C LEU* 3.5 14.9 - - - +
209C HIS* 4.0 2.5 - - + -
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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