Contacts of the strand formed by residues 218 - 226 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216H PRO* 3.9 1.8 - - - +
217H ASP* 1.3 80.2 + - - +
219H ALA* 1.3 64.0 + - - +
220H ALA* 3.8 25.7 - - - +
222H TYR* 5.2 3.4 + - - -
277H GLU* 3.1 33.9 + - - +
278H VAL 3.4 10.3 - - - +
279H ASP* 5.0 7.0 - - + +
280H ILE* 4.5 3.4 - - - +
312H ASN* 5.8 3.4 + - - +
313H ILE* 3.8 6.8 - - - +
314H GLU* 2.8 70.2 + - + +
316H THR* 4.1 20.4 - - + -
349M ARG* 5.7 1.0 - - - +
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Residues in contact with ALA 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H TRP* 4.3 14.6 - - + -
191H LEU* 4.1 16.8 - - + -
218H ARG* 1.3 79.0 + - - +
220H ALA* 1.3 63.0 + - - +
277H GLU* 3.6 1.9 - - - +
278H VAL* 2.8 45.4 + - + +
312H ASN 3.4 7.2 - - - -
313H ILE* 3.7 20.9 - - + -
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Residues in contact with ALA 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H LEU* 4.5 2.6 - - - +
218H ARG* 3.8 20.9 - - - +
219H ALA* 1.3 78.5 - - - +
221H LEU* 1.3 59.6 + - - +
222H TYR* 3.7 22.5 - - + +
274H LEU* 4.0 9.4 - - + -
276H LYS 3.3 9.6 - - - +
277H GLU* 4.7 1.6 - - - -
311H PHE* 3.1 6.6 - - - +
312H ASN* 2.9 38.0 + - + +
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Residues in contact with LEU 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H CYS* 4.1 22.4 - - - +
191H LEU* 4.1 18.6 - - + +
192H PHE* 4.2 19.7 - - + -
220H ALA* 1.3 72.3 - - - +
222H TYR* 1.3 62.2 - - - +
274H LEU* 3.7 4.2 - - - +
275H ILE* 2.9 50.9 + - + -
276H LYS* 2.9 23.1 + - + +
290H PHE* 4.8 6.3 - - + -
309H THR* 4.1 16.6 - - + +
310H TYR 3.6 15.7 - - - +
311H PHE* 4.0 12.3 - - + -
358H ILE* 5.9 0.9 - - + -
360H MET* 4.8 4.3 - - - -
372H PHE* 6.2 0.2 - - + -
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Residues in contact with TYR 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H ARG* 5.2 2.9 + - - -
220H ALA* 3.7 31.2 - - + +
221H LEU* 1.3 77.2 - - - +
223H VAL* 1.3 62.7 + - - +
272H ALA* 4.3 4.9 - - + -
273H CYS* 3.2 11.7 - - - +
274H LEU* 3.7 40.9 - - + +
275H ILE* 4.3 3.6 - - - -
308H VAL 4.4 0.2 - - - -
309H THR* 3.1 31.6 - - - +
310H TYR* 2.8 55.7 + + + +
312H ASN* 3.3 22.4 + - - -
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Residues in contact with VAL 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222H TYR* 1.3 72.4 - - - +
224H VAL* 1.3 70.6 + - - +
272H ALA* 3.3 2.1 - - - +
273H CYS* 2.9 40.0 + - + +
275H ILE* 3.5 33.7 - - + -
294H PHE* 4.1 16.6 - - + -
296H LEU* 3.4 9.2 - - + +
307H LEU* 4.7 20.0 - - + -
308H VAL 3.4 6.3 - - - +
309H THR* 3.7 24.2 - - + -
310H TYR* 5.2 0.2 - - - -
358H ILE* 4.9 9.9 - - + -
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Residues in contact with VAL 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223H VAL* 1.3 84.6 - - - +
225H ALA* 1.3 64.3 + - - +
226H ILE* 4.0 8.3 - - + -
268H VAL* 3.6 37.7 - - + -
270H THR* 3.6 6.3 - - - +
271H ASN 3.4 17.7 - - - +
272H ALA* 3.7 14.4 - - + -
296H LEU* 3.8 7.6 - - - +
307H LEU* 3.4 4.9 - - - +
308H VAL* 2.8 39.7 + - + +
310H TYR* 4.2 14.1 - - + -
328H PRO* 5.5 3.1 - - + -
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Residues in contact with ALA 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224H VAL* 1.3 75.9 - - - +
226H ILE* 1.3 67.4 + - - +
269H VAL* 3.0 25.2 + - - +
270H THR* 3.0 28.6 + - + -
296H LEU* 3.7 5.6 - - + +
304H VAL* 3.9 23.1 - - + -
306H ALA 3.5 4.7 - - - -
307H LEU* 3.9 13.9 - - + -
354H ILE* 4.1 6.5 - - + -
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Residues in contact with ILE 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224H VAL* 4.0 4.0 - - + -
225H ALA* 1.3 80.0 - - - +
227H GLU* 1.3 60.8 - - - +
228H ASP* 3.9 28.0 - - + +
263H VAL* 4.0 17.7 - - + -
267H GLN* 3.3 24.5 - - - +
268H VAL* 4.0 19.1 - - + -
269H VAL* 4.2 6.3 - - - -
304H VAL* 3.3 4.4 - - - -
305H HIS 2.9 24.1 + - - -
306H ALA* 2.9 28.0 + - + +
308H VAL* 3.7 32.1 - - + -
328H PRO* 6.2 0.2 - - + -
339H VAL* 4.7 3.4 - - + -
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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