Contacts of the strand formed by residues 215 - 218 (chain C) 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 GLN 215 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C SER 4.6 1.9 + - - +
191C ALA* 6.3 3.1 - - - -
193C ILE 3.7 5.6 + - - +
194C VAL* 3.3 17.0 - - + -
195C TYR 3.2 17.7 + - - -
213C ASP* 3.2 44.0 + - - +
214C ILE* 1.3 78.2 + - - +
216C TYR* 1.3 61.3 + - - +
217C PHE* 5.4 1.5 - - + -
237C LEU* 3.7 43.7 - - + +
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Residues in contact with TYR 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU* 3.2 44.6 + - + +
195C TYR* 3.4 28.0 - - + -
198C LEU* 3.7 19.5 - - + -
201C VAL* 6.5 0.2 - - + -
206C HIS* 4.2 5.6 + + - -
209C LEU* 4.1 31.6 - - + -
210C LYS* 3.3 35.3 + - + -
214C ILE 3.5 15.7 - - - -
215C GLN* 1.3 75.7 + - - +
217C PHE* 1.3 71.7 + - - +
218C SER* 3.9 12.3 - - - -
221C ASP* 3.6 9.5 - - - +
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Residues in contact with PHE 217 (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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194C VAL* 3.7 17.9 - - + -
195C TYR 2.8 11.5 + - - +
196C ILE* 3.4 4.3 - - + +
197C GLY 2.9 25.6 + - - -
198C LEU 3.8 1.0 + - - -
215C GLN* 5.4 0.7 - - + -
216C TYR* 1.3 82.3 - - - +
218C SER* 1.3 64.6 + - - +
221C ASP* 3.5 13.2 - - + -
222C ILE* 4.4 1.4 - - + +
225C LEU* 4.0 22.2 - - + -
230C VAL* 3.7 37.2 - - + -
233C ARG* 3.6 32.3 - - + -
234C THR* 3.4 28.9 - - - -
237C LEU* 4.2 15.0 - - + -
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Residues in contact with SER 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ARG 4.3 2.5 - - - -
328B GLU* 2.7 38.4 + - - -
197C GLY 4.5 0.2 - - - -
198C LEU* 3.1 29.2 - - - +
216C TYR* 3.9 7.7 - - - -
217C PHE* 1.3 78.9 - - - +
219C MET* 1.3 64.3 + - - +
220C ARG* 3.2 13.1 + - - +
221C ASP* 2.9 22.5 + - - -
222C ILE* 3.0 10.9 + - - +
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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