Contacts of the strand formed by residues 141 - 147 (chain A) in PDB entry 2IPM
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 ILE 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ILE* 3.9 25.1 - - + -
127A TRP* 3.5 36.8 - - + -
140A GLN* 1.3 71.3 - - - +
142A GLN* 1.3 65.9 + - - +
143A PHE* 3.4 11.5 + - + -
166A LEU* 4.1 12.8 - - + -
171A ILE* 3.6 24.0 - - + -
172A LYS 2.9 11.0 + - - +
173A THR* 3.3 8.0 - - + -
174A GLU 2.9 24.5 + - - +
205A GLU* 3.7 3.8 - - - +
206A VAL* 3.5 34.3 - - + -
208A ILE* 5.9 1.1 - - + -
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Residues in contact with GLN 142 (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 ASN* 3.2 10.6 - - - +
138A ASP* 2.9 22.8 + - - -
140A GLN* 4.1 7.2 + - - +
141A ILE* 1.3 69.1 - - - +
143A PHE* 1.3 59.4 + - - +
174A GLU* 2.8 40.8 + - + +
176A LEU* 3.6 18.2 - - + -
203A LYS* 3.2 28.5 - - + +
205A GLU* 2.9 44.2 + - - +
206A VAL 3.2 6.6 + - - -
502A CA 2.3 30.7 - - - -
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Residues in contact with PHE 143 (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 ILE* 3.8 19.1 - - + -
142A GLN* 1.3 74.7 - - - +
144A VAL* 1.3 74.6 + - - +
145A LEU* 3.9 20.2 - - + -
163A ILE* 3.5 34.1 - - + -
173A THR* 3.7 18.4 - - + -
174A GLU 3.0 15.6 + - - -
175A GLN* 3.5 48.2 - - + -
176A LEU* 2.8 30.4 + - - +
177A GLN 3.7 0.2 + - - -
178A LEU* 5.1 1.1 - - + -
204A ILE* 5.2 0.2 - - - -
206A VAL 3.2 12.3 - - - +
208A ILE* 4.0 22.2 - - + -
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Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A PHE* 1.3 81.7 - - - +
145A LEU* 1.3 61.8 + - - +
176A LEU* 4.1 2.5 - - + -
177A GLN* 3.3 32.1 - - + +
192A MET* 4.0 7.9 - - + -
195A TRP* 3.7 27.6 - - + -
204A ILE* 3.9 28.0 - - + -
206A VAL 3.1 4.9 + - - +
207A VAL* 3.9 29.1 - - + +
208A ILE* 2.9 27.7 + - - +
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Residues in contact with LEU 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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143A PHE* 3.9 23.6 - - + -
144A VAL* 1.3 75.7 - - - +
146A LEU* 1.3 77.9 + - - +
147A LYS* 3.7 9.6 - - + +
159A THR* 3.7 34.8 - - + +
162A VAL* 4.0 17.7 - - + -
163A ILE* 4.7 1.6 - - + -
177A GLN 3.0 6.9 + - - -
178A LEU* 3.3 20.5 - - + -
179A ASP 3.2 26.2 + - - +
195A TRP* 3.5 3.8 - - - -
208A ILE* 3.1 29.6 - - + +
210A ASN* 3.9 4.0 - - - +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A LEU* 1.3 73.3 - - - +
147A LYS* 1.3 60.4 - - - +
179A ASP 3.5 3.4 - - - +
181A ALA* 4.2 7.4 - - + -
188A ALA* 4.2 19.1 - - + +
191A LYS* 3.9 20.9 - - + -
192A MET* 4.8 2.2 - - - -
195A TRP* 3.7 30.1 - - + -
207A VAL* 4.2 13.2 - - + -
208A ILE 2.9 10.7 + - - +
209A ALA* 3.5 9.1 - - + -
210A ASN* 2.9 29.6 + - - -
214A MET* 3.4 27.2 - - + +
218A ALA* 3.8 28.7 - - + -
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Residues in contact with LYS 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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145A LEU* 3.7 9.1 - - + +
146A LEU* 1.3 75.3 - - - +
148A GLY* 1.3 74.7 + - - +
150A PRO* 4.7 9.9 - - + +
155A ALA* 4.1 8.7 - - + -
156A GLU* 2.9 42.4 + - - -
159A THR* 3.6 21.0 - - + +
178A LEU* 4.3 18.2 - - + +
179A ASP 2.9 16.7 + - - +
180A THR* 3.1 8.6 + - - +
181A ALA 2.9 25.3 + - - -
210A ASN* 3.3 13.9 - - - +
214A MET* 3.3 6.9 - - - +
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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