Contacts of the strand formed by residues 218 - 226 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349F ARG* 5.4 2.6 - - - +
216K PRO* 3.9 1.8 - - - +
217K ASP* 1.3 80.8 + - - +
219K ALA* 1.3 63.0 + - - +
220K ALA* 3.8 25.9 - - - +
222K TYR* 5.1 3.4 + - - -
277K GLU* 3.3 32.9 + - - +
278K VAL 3.4 10.1 - - - +
279K ASP* 5.0 6.7 - - + +
280K ILE* 4.6 3.1 - - - +
312K ASN* 5.6 4.2 + - - +
313K ILE* 3.7 5.8 - - - +
314K GLU* 2.8 69.4 + - + +
316K THR* 4.1 20.2 - - + -
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Residues in contact with ALA 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K TRP* 4.3 12.6 - - + -
191K LEU* 4.2 20.6 - - + -
218K ARG* 1.3 79.4 + - - +
220K ALA* 1.3 63.7 + - - +
276K LYS 4.0 0.2 - - - +
277K GLU* 3.7 2.6 - - - +
278K VAL* 2.9 42.8 + - + +
280K ILE* 4.9 0.9 - - + +
312K ASN 3.3 7.0 - - - -
313K ILE* 3.7 20.6 - - + -
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Residues in contact with ALA 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191K LEU* 4.6 2.2 - - - +
218K ARG* 3.8 20.4 - - - +
219K ALA* 1.3 78.9 - - - +
221K LEU* 1.3 60.3 + - - +
222K TYR* 3.7 23.0 - - + +
274K LEU* 3.9 13.0 - - + -
276K LYS 3.3 5.4 - - - +
277K GLU* 4.8 1.6 - - - -
311K PHE* 3.0 7.0 - - - +
312K ASN* 2.8 43.1 + - + +
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Residues in contact with LEU 221 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K CYS* 4.1 31.9 - - - +
191K LEU* 4.2 10.7 - - + +
192K PHE* 4.2 19.3 - - + -
220K ALA* 1.3 73.5 - - - +
222K TYR* 1.3 63.2 + - - +
274K LEU* 3.7 4.2 - - - +
275K ILE* 2.9 50.1 + - + +
276K LYS* 2.9 23.5 + - + +
290K PHE* 5.0 2.0 - - + -
309K THR* 4.2 14.4 - - - -
310K TYR 3.5 18.2 - - - +
311K PHE* 4.0 11.4 - - + -
358K ILE* 5.9 1.1 - - + -
360K MET* 4.9 7.4 - - - -
372K PHE* 6.0 0.4 - - + -
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Residues in contact with TYR 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351F GLY* 6.4 1.1 - - - -
218K ARG* 5.1 3.5 + - - -
220K ALA* 3.7 31.5 - - + +
221K LEU* 1.3 75.2 - - - +
223K VAL* 1.3 61.6 + - - +
272K ALA* 4.3 9.0 - - + -
273K CYS 3.2 21.5 - - - +
274K LEU* 3.7 25.6 - - + +
275K ILE* 4.3 3.6 - - - -
308K VAL 4.6 0.2 - - - -
309K THR* 3.1 29.6 - - - +
310K TYR* 2.8 56.3 + + + +
312K ASN* 3.3 23.3 + - - -
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Residues in contact with VAL 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222K TYR* 1.3 73.4 - - - +
224K VAL* 1.3 69.8 + - - +
272K ALA* 3.3 2.1 - - - +
273K CYS* 2.9 34.8 + - + +
275K ILE* 3.5 31.6 - - + -
294K PHE* 4.0 24.0 - - + -
296K LEU* 3.5 8.5 - - + +
307K LEU* 4.7 20.0 - - + -
308K VAL 3.4 5.6 - - - +
309K THR* 3.6 24.2 - - + -
310K TYR* 5.2 0.4 - - - -
358K ILE* 4.9 9.9 - - + -
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Residues in contact with VAL 224 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223K VAL* 1.3 82.0 - - - +
225K ALA* 1.3 62.4 + - - +
226K ILE* 4.0 7.0 - - + -
268K VAL* 3.5 38.1 - - + -
270K THR* 3.6 5.4 - - - +
271K ASN 3.3 18.8 - - - +
272K ALA* 3.7 14.6 - - + -
296K LEU* 3.9 6.9 - - - +
307K LEU* 3.4 5.2 - - - +
308K VAL* 2.7 42.1 + - + +
310K TYR* 4.3 14.6 - - + -
328K PRO* 5.6 2.9 - - + -
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Residues in contact with ALA 225 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224K VAL* 1.3 73.6 - - - +
226K ILE* 1.3 66.9 + - - +
268K VAL* 3.8 1.2 - - - -
269K VAL* 3.1 23.9 + - - +
270K THR* 3.0 29.3 + - + -
296K LEU* 3.7 11.8 - - + +
304K VAL* 3.9 19.3 - - + -
306K ALA 3.4 9.9 - - - +
307K LEU* 4.0 6.5 - - + -
354K ILE* 4.1 5.8 - - + -
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Residues in contact with ILE 226 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224K VAL* 4.0 4.0 - - + -
225K ALA* 1.3 81.3 - - - +
227K GLU* 1.3 62.3 + - - +
228K ASP* 3.9 27.6 - - + +
263K VAL* 4.0 22.9 - - + -
267K GLN* 3.3 15.0 - - + +
268K VAL* 3.9 20.0 - - + -
269K VAL* 4.1 6.7 - - - -
304K VAL* 3.3 5.0 - - - -
305K HIS 2.9 23.4 + - - -
306K ALA* 2.9 25.5 + - + +
308K VAL* 3.5 35.2 - - + -
339K 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