Contacts of the strand formed by residues 218 - 226 (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 ARG 218 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216E PRO* 3.9 1.8 - - - +
217E ASP* 1.3 84.9 + - - +
219E ALA* 1.3 63.8 + - - +
220E ALA* 3.8 26.0 - - - +
222E TYR* 5.2 3.2 + - - -
274E LEU* 5.9 0.2 - - - +
277E GLU* 3.2 33.1 + - - +
278E VAL 3.4 9.6 + - - +
279E ASP* 5.0 6.7 - - + +
280E ILE* 4.1 3.4 - - - +
312E ASN* 5.7 4.0 + - - +
313E ILE* 3.7 6.3 - - - +
314E GLU* 2.9 68.8 + - + +
316E THR* 4.1 19.7 - - + -
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Residues in contact with ALA 219 (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* 4.2 18.2 - - + -
191E LEU* 4.1 18.2 - - + -
218E ARG* 1.3 79.0 + - - +
220E ALA* 1.3 63.6 + - - +
276E LYS 4.1 0.2 - - - +
277E GLU* 3.6 2.4 - - - +
278E VAL* 2.8 40.9 + - + +
312E ASN 3.3 7.6 - - - -
313E ILE* 3.7 20.4 - - + -
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Residues in contact with ALA 220 (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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191E LEU* 4.6 2.6 - - - +
218E ARG* 3.8 20.6 - - - +
219E ALA* 1.3 76.7 - - - +
221E LEU* 1.3 61.3 + - - +
222E TYR* 3.7 24.3 - - + +
274E LEU* 3.9 13.0 - - + -
276E LYS 3.2 5.6 - - - +
277E GLU* 4.7 1.8 - - - -
311E PHE* 3.0 7.0 - - - -
312E ASN* 2.9 37.3 + - + +
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Residues in contact with LEU 221 (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* 4.0 29.8 - - - +
191E LEU* 4.2 10.1 - - + -
192E PHE* 4.1 20.9 - - + -
220E ALA* 1.3 73.5 - - - +
222E TYR* 1.3 61.7 + - - +
274E LEU* 3.6 4.5 - - - +
275E ILE* 2.9 50.0 + - + +
276E LYS* 2.8 24.7 + - + +
290E PHE* 4.8 5.4 - - + -
309E THR* 4.1 15.3 - - - -
310E TYR 3.5 20.0 - - - +
311E PHE* 4.1 8.3 - - + -
358E ILE* 5.8 0.9 - - + -
360E MET* 4.9 4.5 - - - -
372E PHE* 6.1 0.4 - - + -
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Residues in contact with TYR 222 (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* 5.2 2.9 + - - -
220E ALA* 3.7 30.0 - - + +
221E LEU* 1.3 75.9 - - - +
223E VAL* 1.3 62.3 + - - +
272E ALA* 4.3 8.7 - - + -
273E CYS* 3.3 17.7 - - - +
274E LEU* 3.7 32.4 - - + +
275E ILE* 4.3 3.4 - - - -
308E VAL 4.5 0.2 - - - -
309E THR* 3.1 30.8 - - - +
310E TYR* 2.8 52.5 + + + +
312E ASN* 3.3 23.8 + - - -
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Residues in contact with VAL 223 (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* 1.3 70.7 - - - +
224E VAL* 1.3 71.0 + - - +
272E ALA* 3.4 2.1 - - - +
273E CYS* 3.0 36.1 + - + +
275E ILE* 3.6 31.6 - - + -
294E PHE* 3.9 24.7 - - + -
296E LEU* 3.5 7.7 - - + +
307E LEU* 4.7 19.5 - - + -
308E VAL 3.4 6.7 - - - +
309E THR* 3.6 24.9 - - + -
310E TYR* 5.3 0.4 - - - -
358E ILE* 5.0 9.6 - - + -
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Residues in contact with VAL 224 (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* 1.3 83.1 - - - +
225E ALA* 1.3 64.5 + - - +
226E ILE* 4.0 8.3 - - + -
268E VAL* 3.5 37.2 - - + -
270E THR* 3.7 6.1 - - - +
271E ASN 3.4 18.4 - - - +
272E ALA* 3.7 14.6 - - + -
296E LEU* 3.8 7.4 - - - -
307E LEU* 3.4 5.0 - - - +
308E VAL* 2.8 41.6 + - + +
310E TYR* 4.2 14.6 - - + -
328E PRO* 5.5 2.9 - - + -
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Residues in contact with ALA 225 (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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224E VAL* 1.3 73.5 - - - +
226E ILE* 1.3 67.0 + - - +
268E VAL* 3.7 1.0 - - - -
269E VAL* 2.9 26.2 + - - +
270E THR* 3.1 28.0 + - + -
296E LEU* 3.7 11.6 - - + +
304E VAL* 3.8 24.5 - - + -
306E ALA 3.5 5.8 - - - +
307E LEU* 4.0 6.3 - - + -
354E ILE* 4.0 6.3 - - + -
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Residues in contact with ILE 226 (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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224E VAL* 4.0 4.0 - - + -
225E ALA* 1.3 79.7 - - - +
227E GLU* 1.3 60.1 + - - +
228E ASP* 3.9 26.5 - - + +
263E VAL* 3.9 22.9 - - + -
267E GLN* 3.3 13.9 - - + +
268E VAL* 3.9 25.1 - - + -
269E VAL* 4.2 6.1 - - - -
304E VAL* 3.4 4.2 - - - -
305E HIS 2.9 23.0 + - - -
306E ALA* 3.0 24.6 + - + +
308E VAL* 3.5 34.3 - - + -
328E PRO* 6.1 0.2 - - + -
339E VAL* 4.6 4.3 - - + -
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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