Contacts of the strand formed by residues 227 - 232 (chain E) in PDB entry 1XSK
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 LYS 227 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133E GLN* 3.1 17.1 + - - -
136E ASN* 3.9 30.7 - - - +
153E ARG* 4.2 17.9 - - + -
154E LEU 3.3 8.1 - - - +
155E ASP* 2.6 35.6 + - - +
156E LEU* 4.3 3.8 - - - +
219E GLU 3.5 2.4 - - - +
221E GLY* 2.8 25.1 + - - -
224E LYS* 3.0 32.3 + - + +
225E VAL 3.4 1.2 + - - -
226E SER* 1.3 98.3 + - - +
228E VAL* 1.3 65.4 + - - +
229E GLN* 3.8 1.3 - - + +
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Residues in contact with VAL 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E GLU 3.7 1.2 - - - +
153E ARG* 3.3 2.3 - - - -
154E LEU 2.8 32.5 + - - +
156E LEU* 3.8 28.9 - - + -
162E VAL* 3.9 17.0 - - + -
200E TYR* 3.6 44.4 - - + +
218E PHE* 4.2 19.1 - - + -
219E GLU 3.7 2.2 - - - -
220E VAL* 4.2 17.0 - - + +
227E LYS* 1.3 73.5 - - - +
229E GLN* 1.3 60.4 + - - +
230E PHE* 3.9 7.2 + - + -
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Residues in contact with GLN 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET 2.9 29.5 + - - +
3E ILE* 3.9 12.6 - - + +
151E PHE* 4.7 5.2 - - + -
152E GLU 3.3 6.1 - - - +
153E ARG* 2.6 44.6 + - + +
217E SER 3.6 1.3 + - - +
218E PHE* 3.2 4.3 - - - +
219E GLU* 2.7 57.1 + - + +
223E GLU* 3.0 29.1 + - + +
224E LYS* 5.9 2.2 - - + +
227E LYS* 3.8 1.9 - - + -
228E VAL* 1.3 74.1 - - - +
230E PHE* 1.3 67.4 + - - +
231E SER* 5.0 3.2 + - - -
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Residues in contact with PHE 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E MET 4.2 0.2 - - - +
151E PHE* 3.4 2.2 - - - -
152E GLU* 2.8 64.9 + - + -
154E LEU* 3.9 26.2 - - + -
200E TYR* 4.5 8.3 - + - -
208E VAL* 4.5 1.1 - - + -
210E VAL* 3.6 30.5 - - + -
216E VAL* 4.1 7.0 - - + -
217E SER 3.2 5.6 - - - +
218E PHE* 3.7 29.4 - + + -
228E VAL* 3.9 15.5 - - + -
229E GLN* 1.3 76.4 - - - +
231E SER* 1.3 61.1 + - - +
237E LEU* 4.0 8.2 - - + +
239E TYR* 3.9 31.6 - + + -
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Residues in contact with SER 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.8 41.8 + - - +
3E ILE* 4.9 2.8 - - - +
149E TYR* 4.7 3.5 - - - -
150E MET 3.3 13.7 - - - -
151E PHE* 3.6 14.4 - - - -
215E CYS 4.3 0.3 - - - +
216E VAL* 3.7 3.0 - - - -
217E SER* 2.9 36.0 + - - -
229E GLN* 5.0 3.3 + - - +
230E PHE* 1.3 76.0 - - - +
232E VAL* 1.3 63.8 + - - +
237E LEU* 5.7 0.9 - - - -
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Residues in contact with VAL 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E TYR* 3.4 6.3 - - - -
150E MET* 3.1 24.5 + - + +
212E HIS* 3.6 38.8 - - + +
214E GLN* 2.7 37.7 - - - +
215E CYS 3.8 15.7 - - - +
216E VAL* 4.6 4.9 - - + -
231E SER* 1.3 77.1 - - - +
233E GLU* 1.3 59.7 + - - +
234E SER* 3.0 19.8 + - - -
236E TYR 4.4 1.8 - - - +
237E LEU* 4.0 11.9 - - + -
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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