Contacts of the strand formed by residues 218 - 226 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349H ARG* 5.0 3.9 - - - +
216M PRO* 3.8 1.6 - - - +
217M ASP* 1.3 86.4 + - - +
219M ALA* 1.3 62.9 + - - +
220M ALA* 3.8 25.5 - - - +
222M TYR* 5.0 4.2 + - - -
274M LEU* 5.9 0.2 - - - +
277M GLU* 3.2 33.1 + - - +
278M VAL 3.6 9.4 + - - +
279M ASP* 5.2 6.1 - - + +
280M ILE* 4.7 2.2 - - - +
312M ASN* 5.8 4.2 + - - +
313M ILE* 3.5 6.3 - - - +
314M GLU* 2.9 63.4 + - + +
316M THR* 4.1 19.1 - - + -
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Residues in contact with ALA 219 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186M TRP* 4.2 24.2 - - + -
191M LEU* 4.2 11.4 - - + -
218M ARG* 1.3 78.3 + - - +
220M ALA* 1.3 62.9 + - - +
276M LYS 4.1 0.4 - - - +
277M GLU* 3.7 1.7 - - - +
278M VAL* 2.9 39.4 + - + +
280M ILE* 4.9 1.1 - - + +
312M ASN 3.4 7.2 - - - -
313M ILE* 3.6 21.1 - - + -
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Residues in contact with ALA 220 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191M LEU* 4.5 2.6 - - - +
218M ARG* 3.8 21.5 - - - +
219M ALA* 1.3 76.2 - - - +
221M LEU* 1.3 61.9 + - - +
222M TYR* 3.7 25.9 - - + +
274M LEU* 3.9 11.0 - - + -
276M LYS 3.2 5.8 - - - +
277M GLU* 4.7 1.6 - - - -
311M PHE* 3.1 7.4 - - - +
312M ASN* 2.9 37.0 + - + +
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Residues in contact with LEU 221 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190M CYS* 4.1 29.8 - - - +
191M LEU* 4.1 12.5 - - + +
192M PHE* 4.2 19.3 - - + -
220M ALA* 1.3 74.4 - - - +
222M TYR* 1.3 61.2 + - - +
274M LEU* 3.7 3.5 - - - +
275M ILE* 2.9 50.4 + - + +
276M LYS* 2.7 24.4 + - + +
290M PHE* 4.9 6.3 - - + -
309M THR* 4.2 14.4 - - - +
310M TYR 3.3 20.6 - - - +
311M PHE* 4.1 7.9 - - + -
358M ILE* 5.8 1.3 - - + -
360M MET* 4.9 4.3 - - - -
372M PHE* 6.1 0.4 - - + -
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Residues in contact with TYR 222 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351H GLY* 6.1 2.9 - - - -
218M ARG* 5.0 4.7 + - - -
220M ALA* 3.7 30.8 - - + +
221M LEU* 1.3 76.3 - - - +
223M VAL* 1.3 62.2 + - - +
272M ALA* 4.5 4.7 - - + -
273M CYS 3.4 11.9 - - - +
274M LEU* 3.5 42.8 - - + +
275M ILE* 4.3 2.7 - - - -
308M VAL 4.5 0.2 - - - -
309M THR* 3.0 31.4 - - - +
310M TYR* 2.8 53.7 + + + +
312M ASN* 3.4 24.1 + - - -
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Residues in contact with VAL 223 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222M TYR* 1.3 71.7 - - - +
224M VAL* 1.3 64.7 + - - +
272M ALA* 3.3 8.0 - - - +
273M CYS* 3.0 34.4 + - + +
275M ILE* 3.5 32.3 - - + -
294M PHE* 4.0 23.6 - - + -
296M LEU* 3.4 9.0 - - + +
307M LEU* 4.7 20.0 - - + -
308M VAL 3.4 5.6 - - - +
309M THR* 3.6 24.9 - - + -
358M ILE* 4.8 9.4 - - + -
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Residues in contact with VAL 224 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223M VAL* 1.3 80.7 - - - +
225M ALA* 1.3 65.8 + - - +
226M ILE* 4.0 8.1 - - + -
268M VAL* 3.5 39.5 - - + -
270M THR* 3.7 4.7 - - - +
271M ASN 3.6 17.0 - - - +
272M ALA* 3.8 14.8 - - + -
296M LEU* 3.8 6.7 - - - -
307M LEU* 3.4 6.1 - - - +
308M VAL* 2.8 39.3 + - + +
310M TYR* 4.2 14.6 - - + -
328M PRO* 5.5 2.9 - - + -
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Residues in contact with ALA 225 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224M VAL* 1.3 75.9 - - - +
226M ILE* 1.3 64.5 + - - +
269M VAL* 3.0 25.4 + - - +
270M THR* 3.1 28.9 + - + -
296M LEU* 3.7 5.8 - - + +
304M VAL* 3.8 18.8 - - + -
306M ALA 3.4 11.4 - - - +
307M LEU* 3.8 11.9 - - + -
354M ILE* 4.0 5.8 - - + -
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Residues in contact with ILE 226 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224M VAL* 4.0 8.5 - - + -
225M ALA* 1.3 79.5 - - - +
227M GLU* 1.3 55.3 + - - +
228M ASP* 3.9 26.7 - - + +
263M VAL* 4.0 21.5 - - + -
267M GLN* 3.3 20.9 - - - +
268M VAL* 3.9 15.7 - - + -
269M VAL* 4.2 3.8 - - - -
303M TYR 4.1 3.4 - - - -
304M VAL* 3.3 2.9 - - - -
305M HIS 2.8 29.8 + - - -
306M ALA* 3.0 26.3 + - + +
308M VAL* 3.6 34.3 - - + -
339M VAL* 4.6 4.0 - - + -
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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