Contacts of the strand formed by residues 236 - 243 (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 TYR 236 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68E ARG* 3.6 43.0 + - + +
69E ILE 3.2 7.0 - - - +
70E GLU* 3.5 24.5 - - + +
72E PHE 5.6 0.9 - - - +
77E ASN* 3.5 39.1 - - - +
81E HIS* 4.7 9.7 + - - -
150E MET* 3.4 6.4 - - - +
211E ASN 4.9 3.6 + - - -
212E HIS* 3.3 33.9 + + - -
232E VAL* 4.4 0.2 - - - +
234E SER* 2.9 31.1 + - - -
235E GLU* 1.3 84.8 - - + +
237E LEU* 1.3 66.5 + - - +
238E GLU* 4.1 7.2 - - + -
435E LYS* 4.5 14.8 + - - -
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Residues in contact with LEU 237 (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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67E VAL 3.5 1.4 - - - +
68E ARG* 3.3 1.9 - - - -
69E ILE* 2.6 50.9 + - + +
150E MET* 3.7 17.8 - - + +
151E PHE* 3.6 38.1 - - - +
152E GLU* 3.6 17.9 - - + +
210E VAL* 4.1 14.1 - - + -
212E HIS* 3.3 25.6 - - + +
230E PHE* 4.0 11.4 - - + +
231E SER* 5.8 0.4 - - - -
232E VAL* 4.0 11.4 - - + -
236E TYR* 1.3 76.1 - - - +
238E GLU* 1.3 63.6 + - - +
239E TYR* 4.4 10.8 - - + -
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Residues in contact with GLU 238 (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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58E PHE* 3.5 25.5 - - + -
67E VAL 3.1 11.0 - - - +
68E ARG* 2.9 37.6 + - + +
210E VAL* 3.7 1.6 - - - +
211E ASN* 2.6 60.3 + - + +
212E HIS* 3.1 13.6 + - - +
236E TYR* 4.1 16.3 - - + -
237E LEU* 1.3 76.1 - - - +
239E TYR* 1.3 64.4 + - - +
240E PHE* 4.0 7.7 - - + -
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Residues in contact with TYR 239 (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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65E VAL 3.9 0.3 - - - +
66E GLY* 3.5 2.4 - - - -
67E VAL* 2.8 57.6 + - + +
69E ILE* 4.3 9.6 - - + -
120E LEU* 3.5 20.1 - - - +
122E PHE* 3.5 25.3 - + - -
152E GLU* 2.7 38.1 + - + -
154E LEU* 4.2 11.4 - - + +
208E VAL* 4.9 3.6 - - + -
209E LEU 3.3 12.1 - - - +
210E VAL* 4.1 8.1 - - + -
211E ASN 4.2 0.7 - - - +
230E PHE* 3.9 26.9 - + + -
237E LEU* 4.4 8.1 - - + -
238E GLU* 1.3 77.3 - - - +
240E PHE* 1.3 67.6 + - - +
241E VAL* 4.0 15.3 - - + -
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Residues in contact with PHE 240 (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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58E PHE* 3.7 26.0 - + - -
60E PRO* 3.7 20.2 - - + -
64E ILE* 3.8 22.4 - - + -
65E VAL 3.4 1.3 - - - -
66E GLY* 3.2 32.3 - - - -
84E LEU* 4.0 6.1 - - + -
86E ILE* 5.4 3.4 - - + -
207E GLY 3.7 0.2 - - - +
208E VAL* 3.0 8.0 - - - +
209E LEU* 2.8 48.5 + - + +
211E ASN* 3.8 30.3 - - + -
238E GLU* 4.0 7.6 - - + -
239E TYR* 1.3 76.0 - - - +
241E VAL* 1.3 62.7 + - - +
242E ILE* 3.7 3.0 + - + +
257E PHE* 3.8 30.3 - + + -
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Residues in contact with VAL 241 (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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64E ILE* 3.5 2.1 - - - +
65E VAL* 3.0 31.9 + - + +
108E LEU* 3.2 32.4 - - + +
122E PHE* 3.8 44.6 - - + -
129E ILE* 4.6 11.0 - - + -
130E THR* 5.1 3.1 - - + -
154E LEU* 4.9 4.7 - - + -
206E TYR* 4.6 10.3 - - + -
207E GLY 3.4 7.2 - - - +
208E VAL* 4.8 6.5 - - + -
239E TYR* 4.0 14.6 - - + -
240E PHE* 1.3 73.7 - - - +
242E ILE* 1.3 62.8 + - - +
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Residues in contact with ILE 242 (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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63E GLY 3.9 2.0 - - - -
64E ILE* 3.9 21.1 - - + -
108E LEU* 4.6 0.7 - - - -
199E PHE* 3.8 27.8 - - + -
206E TYR* 3.2 6.1 - - - +
207E GLY 2.6 43.3 + - - +
209E LEU* 4.4 12.1 - - + +
240E PHE* 3.9 6.1 - - + +
241E VAL* 1.3 75.7 - - - +
243E ASP* 1.3 64.6 + - - +
250E VAL* 4.0 13.4 - - + +
253E ARG* 3.5 32.1 - - + -
254E TYR* 3.8 22.7 - - + +
257E PHE* 4.8 8.5 - - + -
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Residues in contact with ASP 243 (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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63E GLY* 3.1 23.4 + - - +
107E ASN* 4.2 19.2 + - - +
108E LEU* 3.9 25.6 + - + +
124E ARG* 2.5 47.2 + - - +
129E ILE* 4.9 0.7 - - - +
205E GLY 3.9 1.1 - - - -
206E TYR* 4.6 3.6 - - - +
241E VAL 4.0 1.0 + - - -
242E ILE* 1.3 75.5 - - - +
244E GLY* 1.3 69.0 + - - +
245E PRO* 4.6 2.1 - - - +
250E VAL* 3.8 9.6 - - - -
253E ARG* 2.8 33.0 + - - +
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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