Contacts of the strand formed by residues 218 - 226 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216J PRO* 3.8 1.4 - - - +
217J ASP* 1.3 84.8 - - - +
219J ALA* 1.3 65.8 + - - +
220J ALA* 3.8 24.8 - - - +
222J TYR* 5.0 4.0 + - - -
274J LEU* 6.0 0.2 - - - +
277J GLU* 3.2 31.9 + - - +
278J VAL 3.5 9.0 - - - +
279J ASP* 5.1 7.6 - - + +
280J ILE* 4.1 2.8 - - - +
312J ASN* 5.8 4.4 + - - +
313J ILE* 3.6 5.6 - - - +
314J GLU* 2.9 70.7 + - + +
316J THR* 4.0 20.6 - - + -
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Residues in contact with ALA 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186J TRP* 4.3 12.1 - - + -
191J LEU* 4.1 20.2 - - + -
218J ARG* 1.3 79.5 + - - +
220J ALA* 1.3 64.2 + - - +
277J GLU* 3.6 3.1 - - - +
278J VAL* 2.9 42.8 + - + +
280J ILE* 5.0 0.6 - - + +
312J ASN 3.3 7.2 - - - +
313J ILE* 3.7 20.6 - - + -
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Residues in contact with ALA 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191J LEU* 4.6 1.8 - - - +
218J ARG* 3.8 17.7 - - - +
219J ALA* 1.3 77.8 - - - +
221J LEU* 1.3 61.1 + - - +
222J TYR* 3.6 28.6 - - + +
274J LEU* 3.9 10.5 - - + -
276J LYS 3.3 6.5 - - - +
277J GLU* 4.8 1.8 - - + -
311J PHE* 3.0 7.3 - - - -
312J ASN* 2.8 37.9 + - + +
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Residues in contact with LEU 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J CYS* 4.1 30.5 - - - +
191J LEU* 4.2 11.0 - - + +
192J PHE* 4.3 19.1 - - + -
220J ALA* 1.3 73.7 - - - +
222J TYR* 1.3 63.0 + - - +
274J LEU* 3.6 4.7 - - - +
275J ILE* 2.9 50.1 + - + +
276J LYS* 2.8 23.3 + - + +
290J PHE* 4.9 5.4 - - + -
309J THR* 4.1 13.7 - - + +
310J TYR 3.4 20.4 - - - +
311J PHE* 4.0 8.1 - - + -
358J ILE* 5.9 1.3 - - + -
360J MET* 5.0 4.0 - - - -
372J PHE* 6.1 0.7 - - + -
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Residues in contact with TYR 222 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J ARG* 5.0 3.5 + - - -
220J ALA* 3.6 30.5 - - + +
221J LEU* 1.3 74.5 - - - +
223J VAL* 1.3 64.0 + - - +
272J ALA* 4.4 4.5 - - + -
273J CYS 3.2 13.5 - - - +
274J LEU* 3.5 40.1 - - + +
275J ILE* 4.2 4.0 - - - -
309J THR* 3.0 30.7 - - - +
310J TYR* 2.9 53.2 + + + +
312J ASN* 3.2 24.5 + - - -
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Residues in contact with VAL 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222J TYR* 1.3 71.9 - - - +
224J VAL* 1.3 71.6 + - - +
272J ALA* 3.4 2.1 - - - +
273J CYS* 3.0 33.8 + - + +
275J ILE* 3.5 32.5 - - + -
294J PHE* 4.1 24.0 - - + -
296J LEU* 3.4 8.9 - - + +
307J LEU* 4.6 20.6 - - + -
308J VAL 3.3 6.1 - - - +
309J THR* 3.6 24.2 - - + -
310J TYR* 5.2 0.4 - - - -
340J PHE* 6.2 0.2 - - + -
358J ILE* 4.9 9.4 - - + -
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Residues in contact with VAL 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223J VAL* 1.3 81.5 - - - +
225J ALA* 1.3 64.0 + - - +
226J ILE* 4.0 8.1 - - + -
268J VAL* 3.5 38.6 - - + -
270J THR* 3.7 5.8 - - - +
271J ASN 3.4 17.9 - - - +
272J ALA* 3.7 15.0 - - + -
296J LEU* 3.7 7.2 - - - -
307J LEU* 3.3 7.8 - - - +
308J VAL* 2.9 38.0 + - + +
310J TYR* 4.3 13.9 - - + -
328J PRO* 5.6 2.9 - - + -
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Residues in contact with ALA 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224J VAL* 1.3 74.2 - - - +
226J ILE* 1.3 68.9 + - - +
268J VAL* 3.6 1.2 - - - -
269J VAL* 2.9 26.2 + - - +
270J THR* 3.0 27.7 + - + -
296J LEU* 3.7 10.0 - - + +
304J VAL* 3.9 20.0 - - + -
306J ALA 3.4 9.4 - - - +
307J LEU* 4.0 5.6 - - + -
354J ILE* 4.0 7.2 - - + -
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Residues in contact with ILE 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224J VAL* 4.0 3.6 - - + -
225J ALA* 1.3 80.0 - - - +
227J GLU* 1.3 61.4 + - - +
228J ASP* 3.8 27.8 - - + +
263J VAL* 4.0 14.8 - - + -
267J GLN* 3.3 26.5 - - - +
268J VAL* 3.8 20.6 - - + -
269J VAL* 4.2 4.0 - - - -
303J TYR 4.1 2.5 - - - -
304J VAL* 3.3 5.6 - - - -
305J HIS 2.9 23.4 + - - -
306J ALA* 2.9 28.7 + - + +
308J VAL* 3.6 32.3 - - + -
339J VAL* 4.7 3.6 - - + -
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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