Contacts of the strand formed by residues 206 - 210 (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 206 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ARG* 5.0 0.2 - - - +
129E ILE* 3.3 49.8 - - + -
130E THR* 3.4 33.0 + - + -
154E LEU* 5.6 0.2 - - - +
155E ASP 3.6 7.4 + - - -
156E LEU* 4.3 2.4 - - - +
160E GLU* 2.7 30.2 + - - -
200E TYR* 4.5 6.7 + + - -
201E MET* 3.4 2.9 - - - +
202E THR* 3.2 39.1 + - + +
204E ARG* 3.9 10.1 - - + -
205E GLY* 1.3 78.8 - - - +
207E GLY* 1.3 67.4 + - - +
208E VAL* 4.0 21.1 - - + -
241E VAL* 4.6 5.4 - - + -
242E ILE 3.2 14.6 - - - +
243E ASP* 4.6 1.8 - - - -
250E VAL* 3.8 7.8 - - - +
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Residues in contact with GLY 207 (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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199E PHE* 4.0 6.3 - - - -
200E TYR 3.2 11.9 - - - -
201E MET* 4.0 0.9 - - - -
206E TYR* 1.3 75.6 - - - +
208E VAL* 1.3 64.5 + - - +
241E VAL* 3.4 5.9 - - - +
242E ILE* 2.6 44.4 + - - +
250E VAL* 3.7 17.2 - - - +
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Residues in contact with VAL 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E LEU* 4.2 17.7 - - + -
198E PRO 3.8 1.0 - - - +
199E PHE* 3.3 7.1 - - - -
200E TYR* 2.9 81.3 + - + +
206E TYR* 4.0 13.5 - - + -
207E GLY* 1.3 79.7 - - - +
209E LEU* 1.3 66.8 + - - +
210E VAL* 4.4 10.3 - - + -
230E PHE* 4.5 4.9 - - + -
239E TYR* 4.9 3.6 - - + -
240E PHE 3.0 12.6 - - - +
241E VAL* 4.5 5.4 - - + -
242E ILE* 4.9 0.2 - - - -
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Residues in contact with LEU 209 (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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82E TYR* 4.8 3.8 - - + -
84E LEU* 4.6 10.8 - - + -
198E PRO* 3.5 24.7 - - + +
199E PHE* 3.9 19.2 - - + -
208E VAL* 1.3 72.3 - - - +
210E VAL* 1.3 71.5 + - - +
211E ASN* 3.4 5.2 + - - +
239E TYR* 3.3 2.5 - - - -
240E PHE* 2.8 43.1 + - + +
242E ILE* 4.4 8.0 - - + +
254E TYR* 4.3 6.5 - - + -
257E PHE* 3.7 28.5 - - + -
258E THR* 4.0 19.5 - - + -
470E VAL* 4.3 13.2 - - + -
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Residues in contact with VAL 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E TYR* 4.0 0.3 - - - -
198E PRO* 2.8 38.1 + - + +
208E VAL* 4.4 6.1 - - + -
209E LEU* 1.3 73.1 - - - +
211E ASN* 1.3 60.7 + - - +
212E HIS* 2.9 31.8 + - + -
216E VAL* 4.1 15.0 - - + -
218E PHE* 3.6 26.5 - - + -
230E PHE* 3.6 41.1 - - + -
232E VAL* 5.7 0.2 - - + -
237E LEU* 4.1 4.3 - - + -
238E GLU 3.9 5.8 - - - +
239E TYR* 4.1 2.5 - - + -
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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