Contacts of the strand formed by residues 327 - 331 (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 ARG 327 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E GLU* 2.7 34.4 + - - -
310E ALA* 2.9 34.0 + - - +
313E TYR* 3.3 44.8 + - + +
315E GLU* 5.0 7.1 + - - +
326E GLY* 1.3 74.8 - - - +
328E VAL* 1.3 75.2 + - - +
329E TYR* 3.6 20.8 - - + -
346E LEU* 3.2 29.5 - - - +
347E LEU 3.4 12.6 - - - +
348E THR* 3.4 29.5 + - - +
356E PHE* 3.7 3.7 + - - +
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Residues in contact with VAL 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E LEU* 3.8 27.4 - - + -
308E VAL 3.3 7.4 - - - +
309E GLY* 4.4 0.2 - - - -
327E ARG* 1.3 77.0 - - - +
329E TYR* 1.3 67.5 + - - +
330E LEU* 5.9 0.4 - - + -
345E LEU 4.1 0.2 - - - +
346E LEU* 3.6 2.4 - - - -
347E LEU* 2.6 53.3 + - + +
356E PHE* 3.7 13.7 - - + -
357E GLY* 3.6 30.5 - - - -
360E ILE* 4.0 15.3 - - + -
376E VAL* 3.9 13.9 - - + -
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Residues in contact with TYR 329 (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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282E ALA* 6.0 0.2 - - - -
283E GLU* 2.9 52.1 + - + +
287E SER* 4.9 1.6 + - - -
289E PHE* 3.6 34.7 - + - -
306E LEU 3.8 0.3 - - - +
307E LEU* 3.3 9.5 - - - +
308E VAL* 2.8 41.3 + - + +
310E ALA* 3.9 16.3 - - + +
313E TYR* 3.8 8.3 - - - -
327E ARG* 3.6 22.8 - - + -
328E VAL* 1.3 79.2 - - - +
330E LEU* 1.3 60.7 + - - +
331E PHE* 3.6 23.1 - + + -
343E PRO* 4.5 14.6 - - + -
345E LEU 3.9 3.6 - - - -
346E LEU* 4.4 13.2 - - + -
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Residues in contact with LEU 330 (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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298E VAL* 4.3 7.4 - - + -
305E ASP* 4.7 2.2 - - + -
306E LEU 3.6 14.4 - - - +
307E LEU* 3.7 24.9 - - + -
328E VAL* 5.9 0.2 - - + -
329E TYR* 1.3 76.2 - - - +
331E PHE* 1.3 63.8 + - - +
332E LEU* 3.8 30.5 - - + -
343E PRO* 3.5 4.9 - - - +
344E SER* 2.8 31.6 + - - -
345E LEU* 3.2 31.2 + - + +
347E LEU* 6.2 1.1 - - + -
398E GLY* 4.2 3.8 - - - -
399E LEU* 3.7 42.4 - - + +
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Residues in contact with PHE 331 (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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280E LEU* 4.0 28.9 - - + -
281E ARG 5.6 2.0 - - - -
289E PHE* 4.5 7.9 - + - -
305E ASP* 3.4 4.3 - - - +
306E LEU* 2.7 62.1 + - + +
308E VAL* 4.2 20.9 - - + -
329E TYR* 3.6 28.9 - + + -
330E LEU* 1.3 75.8 - - - +
332E LEU* 1.3 63.4 + - - +
333E GLN 3.8 0.3 + - - -
340E LEU* 4.0 16.2 - - + +
341E GLY 3.7 25.8 - - - -
342E ALA 4.1 2.7 - - - -
343E PRO* 3.7 32.1 - - + -
344E SER* 4.7 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