Contacts of the strand formed by residues 193 - 198 (chain C) in PDB entry 4I06
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C VAL* 3.2 32.3 - - + +
141C TRP* 4.0 17.7 - - + -
164C VAL* 4.1 14.4 - - + -
168C LEU* 4.2 26.5 - - + -
188C ILE* 5.1 1.3 - - + -
190C SER 3.7 19.7 - - - +
191C ALA 3.5 2.3 - - - -
192C SER* 1.3 81.1 - - - +
194C VAL* 1.3 78.9 + - - +
195C TYR* 4.0 23.3 - - + -
214C ILE* 3.9 16.0 - - + +
215C GLN* 3.8 10.8 + - - +
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Residues in contact with VAL 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C VAL 2.9 6.9 + - - -
140C VAL* 3.5 5.7 - - - +
141C TRP* 2.9 24.2 + - - +
191C ALA 5.6 0.2 - - - +
193C ILE* 1.3 79.7 - - - +
195C TYR* 1.3 76.3 + - - +
196C ILE* 4.5 1.8 - - + -
215C GLN* 3.4 13.2 - - + +
217C PHE* 3.7 14.8 - - + -
234C THR* 3.7 34.3 - - + +
237C LEU* 4.1 23.1 - - + -
238C LEU* 3.8 27.1 - - + -
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Residues in contact with TYR 195 (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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141C TRP* 3.3 40.4 - + + -
146C ALA* 2.7 36.7 + - + -
148C ILE* 3.8 8.2 - - + +
164C VAL* 3.4 23.4 - - - +
193C ILE* 4.0 11.9 - - + -
194C VAL* 1.3 77.7 - - - +
196C ILE* 1.3 66.2 + - - +
197C GLY 4.3 0.2 - - - -
198C LEU* 3.9 24.9 - - + -
209C LEU* 3.7 23.1 - - + -
214C ILE* 3.8 12.8 - - + -
215C GLN 3.2 16.2 + - - -
216C TYR* 3.4 19.3 - - + -
217C PHE 2.8 25.1 + - - -
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Residues in contact with ILE 196 (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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140C VAL* 3.9 25.6 - - + -
141C TRP 2.9 7.5 + - - -
142C VAL* 3.3 16.7 - - + +
143C ASP 3.0 24.5 + - - -
194C VAL* 4.5 2.7 - - + -
195C TYR* 1.3 81.0 - - - +
197C GLY* 1.3 61.8 + - - +
198C LEU 3.7 1.3 - - - -
217C PHE* 3.4 4.0 - - + +
222C ILE* 4.0 19.7 - - + -
227C ILE* 4.4 1.1 - - + -
230C VAL* 4.2 15.9 - - + -
231C MET* 3.5 30.1 - - + -
234C THR* 3.8 19.5 - - + +
271C LEU* 4.9 0.7 - - + -
279C ILE* 4.0 20.6 - - + -
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Residues in contact with GLY 197 (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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143C ASP 3.0 12.1 - - - +
196C ILE* 1.3 76.7 - - - +
198C LEU* 1.3 66.4 + - - +
199C ARG* 3.4 13.5 + - - -
217C PHE 2.9 10.8 + - - -
219C MET* 3.3 32.5 - - - +
222C ILE* 4.3 5.3 - - - +
254C ALA* 5.4 1.1 - - - -
271C LEU* 4.8 6.7 - - - -
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Residues in contact with LEU 198 (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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327B ARG* 3.2 6.0 - - - +
328B GLU* 5.7 0.4 - - - -
143C ASP 3.3 7.6 + - - +
144C ALA 3.5 2.5 - - - -
145C HIS* 3.4 35.7 - - - +
146C ALA* 3.7 6.1 - - + +
195C TYR* 3.9 28.7 - - + -
196C ILE 5.2 0.4 - - - -
197C GLY* 1.3 77.0 - - - +
199C ARG* 1.3 58.3 + - - +
200C ASP 4.0 0.2 - - - -
201C VAL* 4.2 13.5 - - + -
209C LEU* 4.1 17.7 - - + -
216C TYR* 3.7 35.7 - - + -
217C PHE 4.9 0.2 - - - +
218C SER* 3.1 33.9 - - - +
219C MET* 3.2 5.7 + - - +
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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