Contacts of the strand formed by residues 305 - 310 (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 ASP 305 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E PHE* 4.8 2.2 - - - -
294E ALA 3.8 0.5 - - - +
295E VAL* 3.6 5.1 - - - -
296E THR* 3.1 38.5 + - - +
297E ASP* 3.0 2.1 - - - +
298E VAL* 2.9 29.8 + - + +
299E ASN* 3.0 3.8 + - - +
303E ARG 3.5 0.9 - - - +
304E HIS* 1.3 73.9 - - - +
306E LEU* 1.3 61.1 + - - +
307E LEU* 4.9 0.8 - - - +
330E LEU* 4.7 3.4 - - + -
331E PHE 3.4 10.1 - - - +
332E LEU* 3.4 22.9 - - + +
333E GLN 3.1 22.2 + - - +
1419E CA 2.1 31.3 - - - -
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Residues in contact with LEU 306 (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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244E PHE* 4.5 11.0 - - + -
254E VAL* 3.8 27.6 - - + -
267E VAL* 4.3 3.1 - - + -
269E ILE* 4.0 11.9 - - + -
280E LEU* 3.7 30.1 - - + -
293E VAL* 4.7 0.7 - - + -
294E ALA 3.6 12.3 - - - +
295E VAL* 4.7 3.6 - - + -
304E HIS 4.4 0.2 + - - -
305E ASP* 1.3 72.3 - - - +
307E LEU* 1.3 76.0 + - - +
308E VAL* 4.0 18.8 - - + -
329E TYR 3.8 0.3 - - - +
330E LEU* 3.6 5.2 - - - +
331E PHE* 2.7 51.5 + - + +
333E GLN 5.3 0.2 - - - +
340E LEU* 3.8 17.3 - - + -
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Residues in contact with LEU 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293E VAL* 3.2 6.4 - - - -
294E ALA* 2.9 45.1 + - + +
296E THR* 3.9 28.0 - - + -
298E VAL* 4.6 2.0 - - + -
305E ASP 4.9 1.6 - - - +
306E LEU* 1.3 78.6 - - - +
308E VAL* 1.3 65.2 + - - +
328E VAL* 3.8 17.0 - - + -
329E TYR 3.3 14.6 - - - +
330E LEU* 3.7 22.9 - - + -
347E LEU* 5.5 0.2 - - + -
360E ILE* 4.2 14.0 - - + +
374E ILE* 3.6 37.5 - - + -
399E LEU* 4.2 4.5 - - + -
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Residues in contact with VAL 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267E VAL* 3.9 22.0 - - + -
280E LEU* 5.7 0.2 - - + -
289E PHE* 3.5 35.4 - - + -
290E GLY 3.7 19.3 - - - +
292E SER 3.7 5.2 - - - +
293E VAL* 4.6 1.3 - - + -
306E LEU* 4.0 22.4 - - + -
307E LEU* 1.3 80.3 - - - +
309E GLY* 1.3 62.5 + - - +
328E VAL* 3.3 5.2 - - - +
329E TYR* 2.8 41.2 + - + -
331E PHE* 4.2 15.0 - - + -
360E ILE* 3.9 4.0 - - - -
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Residues in contact with GLY 309 (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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288E TYR 3.2 3.6 - - - +
290E GLY 3.0 24.9 + - - -
291E HIS 3.4 5.7 + - - -
292E SER* 3.2 11.7 + - - -
308E VAL* 1.3 78.1 - - - +
310E ALA* 1.3 59.3 + - - -
311E PRO* 3.5 6.5 - - - -
327E ARG 3.9 4.0 - - - -
328E VAL* 4.4 0.9 - - - -
357E GLY 3.3 19.1 - - - -
360E ILE* 3.8 8.9 - - - +
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Residues in contact with ALA 310 (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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287E SER* 3.1 25.6 - - - +
288E TYR 3.6 1.6 - - - -
289E PHE* 3.7 15.0 - - + -
309E GLY* 1.3 72.6 - - - +
311E PRO* 1.3 56.1 - - - +
312E LEU 2.8 16.8 + - - -
313E TYR* 2.9 15.7 + - + -
327E ARG 2.9 27.5 + - - +
329E TYR* 3.9 17.9 - - + +
357E GLY 4.1 0.4 + - - -
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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