Contacts of the strand formed by residues 252 - 257 (chain E) in PDB entry 1TYE
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 GLU 252 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241E VAL* 3.5 7.4 - - - +
242E GLY 3.1 31.3 + - - +
243E GLU* 2.8 9.5 - - - +
244E PHE* 3.1 30.7 - - + +
245E ASP* 2.7 26.6 - - - +
250E THR* 3.0 4.9 + - - +
251E THR* 1.3 85.0 - - - +
253E TYR* 1.3 63.8 + - - +
254E VAL* 4.8 1.4 - - - +
269E ILE* 4.2 14.6 - - + -
270E LEU 3.2 13.7 - - - +
271E ASP* 4.3 6.2 - - - +
277E LEU* 4.2 7.6 - - + +
1418E CA 2.0 31.9 - - - -
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Residues in contact with TYR 253 (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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176E THR* 5.0 7.1 - - + +
180E GLU* 5.7 1.9 + - - -
182E VAL* 3.6 30.1 - - + -
195E LEU* 4.1 16.4 - - + -
197E GLN* 3.5 28.0 + - + +
240E ALA 3.9 3.1 - - - +
241E VAL* 3.9 18.6 - - + -
251E THR* 5.0 8.3 - - + -
252E GLU* 1.3 75.2 - - - +
254E VAL* 1.3 62.5 + - - +
255E VAL* 4.0 3.1 - - + -
268E GLU 3.5 0.9 - - - +
269E ILE* 3.1 6.4 - - - +
270E LEU* 2.7 45.0 + - + +
271E ASP 3.6 25.4 - - - -
272E SER* 3.9 20.9 + - - -
274E TYR* 3.7 30.5 - + - -
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Residues in contact with VAL 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E VAL* 3.1 7.4 - - - +
240E ALA* 2.8 49.2 + - + +
241E VAL* 4.9 0.4 - - - -
244E PHE* 3.8 23.6 - - + -
252E GLU 4.8 2.0 - - - +
253E TYR* 1.3 74.7 - - - +
255E VAL* 1.3 61.4 + - - +
256E GLY 4.3 0.2 + - - -
267E VAL* 4.1 12.6 - - + -
268E GLU 3.4 3.4 - - - -
269E ILE* 3.5 21.1 - - + -
293E VAL* 4.0 18.6 - - + +
295E VAL* 3.9 11.4 - - + -
306E LEU* 3.8 24.2 - - + -
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Residues in contact with VAL 255 (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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195E LEU* 3.6 33.2 - - + -
235E TRP* 3.6 32.4 + - + +
236E GLY* 3.5 31.9 - - - +
238E SER 3.6 3.8 - - - +
239E VAL* 4.4 2.0 - - + -
253E TYR* 4.5 0.4 - - + -
254E VAL* 1.3 79.5 - - - +
256E GLY* 1.3 62.9 + - - +
257E ALA* 3.9 1.4 + - - +
267E VAL* 3.3 6.9 - - - -
268E GLU* 3.0 33.3 + - - +
270E LEU* 3.9 19.7 - - + -
293E VAL* 5.0 0.9 - - - -
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Residues in contact with GLY 256 (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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236E GLY 3.1 20.8 + - - -
237E TYR 3.2 6.2 + - - -
238E SER* 2.7 20.0 + - - -
255E VAL* 1.3 73.4 - - - +
257E ALA* 1.3 58.3 + - - -
258E PRO* 3.2 13.8 - - - +
266E ALA 3.9 4.0 - - - -
267E VAL* 4.0 8.1 - - - -
290E GLY 3.4 18.2 - - - -
293E VAL* 4.5 2.1 - - - +
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Residues in contact with ALA 257 (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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233E GLY 3.5 9.6 - - - +
235E TRP* 3.7 36.3 - - + +
255E VAL 3.9 0.8 + - - +
256E GLY* 1.3 71.4 - - - -
258E PRO* 1.3 54.2 - - - +
259E THR 2.8 16.2 + - - -
260E TRP* 2.9 26.6 + - + -
266E ALA* 2.8 30.2 + - + +
268E GLU* 6.1 1.1 - - + -
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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