Contacts of the strand formed by residues 218 - 226 (chain G) 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 ARG 218 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ARG* 5.2 3.4 - - - +
216G PRO* 4.5 1.7 - - - +
217G ASP* 1.3 85.2 + - - +
219G ALA* 1.3 64.6 + - - +
220G ALA* 3.8 24.8 - - - +
222G TYR* 5.1 3.8 + - - -
274G LEU* 5.9 0.2 - - - +
277G GLU* 3.3 32.7 + - - +
278G VAL 3.4 8.5 - - - +
279G ASP* 5.1 6.3 - - + +
280G ILE* 4.5 3.4 - - - +
312G ASN* 5.8 3.6 + - - +
313G ILE* 3.7 6.8 - - - +
314G GLU* 2.8 73.3 + - + +
316G THR* 4.1 16.4 - - + -
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Residues in contact with ALA 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G TRP* 4.2 15.9 - - + -
191G LEU* 4.1 19.3 - - + -
218G ARG* 1.3 80.2 + - - +
220G ALA* 1.3 63.5 + - - +
276G LYS 4.6 0.4 - - - -
277G GLU* 3.7 3.3 - - - +
278G VAL* 2.9 40.5 + - + +
280G ILE* 4.8 0.6 - - + +
312G ASN 3.4 6.7 - - - -
313G ILE* 3.7 20.0 - - + -
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Residues in contact with ALA 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191G LEU* 4.5 2.4 - - - +
218G ARG* 3.8 20.6 - - - +
219G ALA* 1.3 77.6 - - - +
221G LEU* 1.3 60.2 + - - +
222G TYR* 3.7 23.2 - - + +
274G LEU* 3.8 13.0 - - + -
276G LYS 3.3 6.5 - - - +
277G GLU* 4.8 1.1 - - - -
311G PHE* 3.0 8.4 - - - -
312G ASN* 2.8 40.6 + - + +
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Residues in contact with LEU 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G CYS* 4.1 22.2 - - - +
191G LEU* 4.1 19.5 - - + +
192G PHE* 4.2 19.7 - - + -
220G ALA* 1.3 74.7 - - - +
222G TYR* 1.3 60.1 + - - +
274G LEU* 3.7 4.0 - - - +
275G ILE* 2.9 50.6 + - + +
276G LYS* 2.8 24.6 + - + +
290G PHE* 4.7 6.3 - - + -
309G THR* 4.2 14.4 - - + -
310G TYR 3.5 17.5 - - - +
311G PHE* 4.1 11.0 - - + -
358G ILE* 5.9 0.9 - - + -
360G MET* 5.0 4.0 - - - -
372G PHE* 6.1 0.2 - - + -
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Residues in contact with TYR 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B GLY* 6.0 3.5 - - - -
218G ARG* 5.1 3.6 + - - -
220G ALA* 3.7 27.5 - - + +
221G LEU* 1.3 75.1 - - - +
223G VAL* 1.3 62.4 + - - +
272G ALA* 4.4 3.8 - - + -
273G CYS 3.3 22.4 - - - +
274G LEU* 3.5 36.9 - - + +
275G ILE* 4.3 3.4 - - - -
309G THR* 3.0 32.0 - - - +
310G TYR* 2.8 56.2 + + + +
312G ASN* 3.2 22.3 + - - -
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Residues in contact with VAL 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222G TYR* 1.3 72.1 - - - +
224G VAL* 1.3 70.7 + - - +
272G ALA* 3.4 1.9 - - - +
273G CYS* 3.0 40.1 + - + +
275G ILE* 3.6 31.2 - - + -
294G PHE* 4.1 17.9 - - + -
296G LEU* 3.5 9.3 - - + +
307G LEU* 4.5 20.6 - - + -
308G VAL 3.3 6.3 - - - +
309G THR* 3.6 24.9 - - + -
310G TYR* 5.2 0.4 - - - -
340G PHE* 6.1 0.2 - - + -
358G ILE* 4.8 9.2 - - + -
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Residues in contact with VAL 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223G VAL* 1.3 81.7 - - - +
225G ALA* 1.3 64.3 + - - +
226G ILE* 4.0 7.6 - - + -
268G VAL* 3.5 39.5 - - + -
270G THR* 3.7 4.3 - - - -
271G ASN 3.4 18.2 - - - +
272G ALA* 3.7 15.5 - - + -
296G LEU* 3.8 6.5 - - - -
307G LEU* 3.4 6.1 - - - +
308G VAL* 2.9 37.9 + - + +
310G TYR* 4.3 13.7 - - + -
328G PRO* 5.5 4.0 - - + -
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Residues in contact with ALA 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G VAL* 1.3 74.4 - - - +
226G ILE* 1.3 65.9 + - - +
268G VAL* 3.7 1.6 - - - -
269G VAL* 2.9 25.7 + - - +
270G THR* 3.1 27.6 + - + -
296G LEU* 3.8 5.6 - - + +
304G VAL* 3.8 19.1 - - + -
306G ALA 3.4 11.0 - - - +
307G LEU* 3.9 12.3 - - + -
354G ILE* 4.1 6.1 - - + -
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Residues in contact with ILE 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G VAL* 4.0 8.3 - - + -
225G ALA* 1.3 79.9 - - - +
227G GLU* 1.3 60.3 + - - +
228G ASP* 3.8 29.2 - - + +
263G VAL* 4.1 20.6 - - + -
267G GLN* 3.2 19.3 - - - +
268G VAL* 3.9 14.6 - - + -
269G VAL* 4.1 4.0 - - - -
303G TYR 4.1 3.1 - - - -
304G VAL* 3.3 4.1 - - - -
305G HIS 2.8 25.1 + - - -
306G ALA* 2.9 26.5 + - + +
308G VAL* 3.6 34.5 - - + -
339G VAL* 4.6 4.7 - - + -
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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