Contacts of the strand formed by residues 193 - 198 (chain A) in PDB entry 4IXU
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 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ILE* 6.3 0.2 - - + -
139A VAL* 3.3 32.3 - - + +
141A TRP* 4.1 15.0 - - + -
164A VAL* 4.1 15.3 - - + -
168A LEU* 4.1 22.2 - - + -
188A ILE* 4.3 7.2 - - + -
189A SER 4.4 0.7 - - - +
190A SER 3.9 18.2 - - - +
191A ALA 3.5 1.9 - - - +
192A SER* 1.3 81.4 - - - +
194A VAL* 1.3 78.7 + - - +
195A TYR* 4.0 25.1 - - + +
214A ILE* 4.1 16.6 - - + +
215A GLN* 3.9 10.0 + - - +
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Residues in contact with VAL 194 (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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139A VAL 3.0 6.1 + - - -
140A VAL* 3.5 5.0 - - - +
141A TRP 2.9 24.4 + - - -
191A ALA 5.6 0.7 - - - +
193A ILE* 1.3 81.1 - - - +
195A TYR* 1.3 75.4 + - - +
196A ILE* 4.6 1.3 - - + -
215A GLN* 3.5 12.8 - - + +
217A PHE* 3.7 15.7 - - + -
234A THR* 3.6 33.4 - - + +
237A LEU* 4.2 21.3 - - + -
238A LEU* 3.7 28.3 - - + -
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Residues in contact with TYR 195 (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 TRP* 3.2 40.8 - + + -
146A ALA* 2.7 35.1 + - + -
148A ILE* 3.7 7.6 - - + +
164A VAL* 3.5 24.8 - - - +
193A ILE* 4.0 12.3 - - + -
194A VAL* 1.3 81.5 - - - +
196A ILE* 1.3 60.8 + - - +
198A LEU* 3.9 23.6 - - + -
209A LEU* 3.7 24.7 - - + -
214A ILE* 3.8 22.4 - - + -
215A GLN 3.3 8.3 + - - -
216A TYR* 3.4 15.1 - - + -
217A PHE 2.8 29.3 + - - -
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Residues in contact with ILE 196 (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 VAL* 3.9 26.5 - - + -
141A TRP 2.9 7.1 + - - -
142A VAL* 3.3 17.1 - - + +
143A ASP 3.1 23.9 + - - -
194A VAL* 4.6 1.8 - - + -
195A TYR* 1.3 80.1 - - - +
197A GLY* 1.3 63.9 + - - +
198A LEU 3.6 1.3 - - - -
217A PHE* 3.5 5.2 - - + +
222A ILE* 3.9 20.4 - - + -
227A ILE* 4.5 0.4 - - + -
230A VAL* 4.1 15.3 - - + -
231A MET* 3.6 30.1 - - + -
234A THR* 3.9 19.5 - - + +
271A LEU* 5.0 0.4 - - + -
279A ILE* 4.0 20.4 - - + -
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Residues in contact with GLY 197 (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 ASP 3.1 10.3 - - - +
144A ALA* 3.7 0.2 - - - -
196A ILE* 1.3 80.3 - - - +
198A LEU* 1.3 66.5 + - - +
199A ARG* 3.3 24.9 + - - -
217A PHE 2.9 10.4 + - - -
219A MET* 3.4 25.0 - - - +
222A ILE* 4.2 2.2 - - - +
254A ALA* 5.3 0.7 - - - -
271A LEU* 4.7 7.6 - - - -
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Residues in contact with LEU 198 (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 ASP* 3.3 7.3 + - + +
144A ALA 3.5 3.4 - - - +
145A HIS 3.4 36.1 - - - +
146A ALA* 3.7 6.1 - - + +
195A TYR* 3.9 25.8 - - + -
197A GLY* 1.3 76.6 - - - +
199A ARG* 1.3 59.0 + - - +
201A VAL* 4.2 14.6 - - + -
209A LEU* 4.1 17.7 - - + -
216A TYR* 3.7 37.0 - - + -
217A PHE 3.7 3.4 + - - +
218A SER* 3.1 30.8 - - - -
219A MET 3.1 6.8 + - - -
327C ARG 3.2 3.9 - - - +
328C GLU* 5.8 0.4 - - - -
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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