Contacts of the strand formed by residues 302 - 314 (chain E) in PDB entry 5DST
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 302 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227E GLU* 3.7 9.9 - - - +
269E VAL* 3.6 21.8 - - + +
300E ARG* 2.9 46.0 + - + +
301E ASN* 1.3 75.1 - - - +
303E TYR* 1.3 81.3 + - - +
348E VAL* 3.1 22.9 + - - +
319G HIS* 2.9 24.7 + - - -
320G LYS* 2.9 30.4 + - - +
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Residues in contact with TYR 303 (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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227E GLU* 3.2 27.4 + - + +
229E ARG* 6.5 0.4 - - - -
269E VAL* 4.1 0.3 - - - +
302E ASP* 1.3 89.8 + - - +
304E VAL* 1.3 65.5 + - - +
305E HIS* 3.9 21.8 - + + -
345E TYR* 3.7 25.8 - + + -
346E LEU 3.2 6.1 - - - +
347E THR* 3.7 26.9 - - + -
348E VAL* 4.8 0.4 - - - -
105G HIS* 2.7 45.1 + + + +
106G ASN* 3.1 13.7 + - - -
319G HIS* 3.5 11.0 - - - +
320G LYS* 4.0 37.3 + - + +
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Residues in contact with VAL 304 (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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225E ALA* 3.8 22.0 - - + -
226E ILE 3.4 4.9 - - - +
269E VAL* 3.9 28.3 - - + -
298E ILE* 5.2 0.4 - - + -
303E TYR* 1.3 75.6 - - - +
305E HIS* 1.3 63.7 + - - +
306E ALA 3.8 20.6 - - - +
307E LEU* 5.1 1.3 - - + -
342E LEU* 4.2 15.7 - - + +
345E TYR* 3.2 4.2 - - - -
346E LEU* 2.8 55.6 + - + +
348E VAL* 4.1 14.1 - - + -
354E ILE* 4.6 6.3 - - + -
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Residues in contact with HIS 305 (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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226E ILE 2.9 4.8 + - - -
227E GLU* 3.9 8.9 - - + +
228E ASP* 3.3 35.2 + - + +
229E ARG* 3.1 40.1 - - + +
232E LYS* 4.1 23.9 + - + +
303E TYR* 3.9 26.4 + + + -
304E VAL* 1.3 75.2 - - - +
306E ALA* 1.3 59.9 + - + +
341E TYR* 4.0 4.8 - - + -
342E LEU* 3.0 32.7 + - - +
345E TYR* 3.6 35.0 - + + +
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Residues in contact with ALA 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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225E ALA* 3.5 4.3 - - - -
226E ILE* 3.0 37.5 + - + +
228E ASP* 5.3 0.4 - - + -
304E VAL* 3.7 7.3 - - - +
305E HIS* 1.3 80.3 - - + +
307E LEU* 1.3 64.7 + - - +
339E VAL* 3.7 25.1 - - + -
340E PHE 3.1 18.4 - - - +
341E TYR* 4.0 9.9 - - + -
342E LEU* 4.1 4.9 - - - -
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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
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223E VAL* 4.7 15.5 - - + -
224E VAL 3.4 5.8 - - - +
225E ALA* 4.0 18.2 - - + -
294E PHE* 4.0 18.6 - - + -
296E LEU* 4.1 12.3 - - + -
304E VAL* 5.1 4.0 - - + -
306E ALA* 1.3 79.6 - - - +
308E VAL* 1.3 64.0 + - - +
339E VAL* 3.6 0.2 - - - -
340E PHE* 2.8 46.1 + - + +
342E LEU* 4.6 9.0 - - + -
354E ILE* 5.2 2.7 - - + -
358E ILE* 6.4 0.9 - - + -
374E VAL* 3.8 33.2 - - + -
376E LEU* 4.3 20.2 - - + -
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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
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222E TYR 4.0 0.2 - - - +
223E VAL* 3.4 3.5 - - - -
224E VAL* 2.8 40.6 + - + +
226E ILE* 3.5 44.6 - - + -
263E VAL* 4.2 7.2 - - + -
307E LEU* 1.3 80.3 - - - +
309E THR* 1.3 67.1 + - - +
310E TYR* 4.2 2.4 + - + -
328E PRO* 4.8 9.4 - - + -
337E GLN* 3.7 30.5 - - + -
338E THR 3.2 11.7 - - - +
339E VAL* 4.2 10.1 - - + -
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Residues in contact with THR 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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190E CYS* 3.1 30.9 - - - -
221E LEU* 4.1 7.2 - - + -
222E TYR 3.1 15.5 - - - +
223E VAL* 3.6 20.9 - - + -
275E ILE* 4.7 8.7 - - + -
308E VAL* 1.3 75.6 - - - +
310E TYR* 1.3 61.6 + - - +
337E GLN* 3.9 5.0 - - - -
338E THR* 2.9 37.7 + - - -
340E PHE* 3.9 18.8 - - + -
358E ILE* 5.0 4.9 - - + -
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Residues in contact with TYR 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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221E LEU* 3.5 5.9 - - - +
222E TYR* 2.8 64.0 + + + -
224E VAL* 4.2 21.8 - - + -
272E ALA* 3.3 21.3 - - - +
308E VAL* 4.9 5.8 - - + -
309E THR* 1.3 75.7 - - - +
311E PHE* 1.3 66.0 + - - +
312E ASN* 3.8 18.8 - - - -
326E THR* 3.5 24.7 - - - +
327E ALA* 3.5 26.0 - - + -
328E PRO* 3.7 20.0 - - + -
329E ASP* 5.6 1.9 + - - -
336E LYS 5.5 0.4 - - - -
337E GLN* 4.5 2.9 - - + -
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Residues in contact with PHE 311 (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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187E MET* 4.1 7.9 - - + -
188E GLY 3.6 19.3 - - - -
190E CYS* 4.4 7.0 - - - -
191E LEU* 3.5 34.5 - - + -
220E ALA 3.0 16.6 - - - +
221E LEU* 4.1 8.3 - - + -
310E TYR* 1.3 78.5 - - - +
312E ASN* 1.3 64.4 + - - +
313E ILE* 3.7 32.8 - - + -
324E PHE* 4.6 2.0 - + - -
326E THR* 3.0 50.6 + - + +
335E TRP* 3.5 44.0 - + + -
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Residues in contact with ASN 312 (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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218E ARG* 4.8 3.7 + - - +
219E ALA* 3.3 4.7 - - - -
220E ALA* 2.9 34.5 + - + +
222E TYR* 3.3 27.2 + - + -
310E TYR* 3.8 12.1 - - - -
311E PHE* 1.3 76.2 + - - +
313E ILE* 1.3 68.7 + - - +
324E PHE 3.4 8.5 - - - +
325E SER* 2.9 34.5 + - - -
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Residues in contact with ILE 313 (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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186E TRP* 4.9 1.1 - - + -
187E MET* 3.7 29.6 - - + -
216E PRO* 3.4 31.9 - - + -
218E ARG* 3.7 3.1 - - - +
219E ALA* 3.7 26.9 - - + -
311E PHE* 3.7 23.1 - - + -
312E ASN* 1.3 79.1 - - - +
314E GLU* 1.3 65.0 + - - +
315E PHE* 4.2 4.9 - - + -
321E LYS* 4.7 2.4 + - - -
323E GLY* 3.1 21.4 - - - -
324E PHE* 3.0 43.2 + - + +
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Residues in contact with GLU 314 (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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216E PRO* 3.3 2.7 - - - +
217E ASP* 3.3 22.2 + - - +
218E ARG* 2.9 51.6 + - + +
313E ILE* 1.3 76.2 - - - +
315E PHE* 1.3 75.0 + - - +
316E THR* 3.7 16.4 - - + +
321E LYS* 4.0 29.7 + - + +
322E MET 3.4 11.9 - - - +
323E GLY* 4.2 0.2 - - - -
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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