Contacts of the strand formed by residues 218 - 226 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D ARG* 5.6 1.6 - - - +
216I PRO* 3.9 1.6 - - - +
217I ASP* 1.3 82.5 - - - +
219I ALA* 1.3 63.5 + - - +
220I ALA* 3.8 25.8 - - - +
222I TYR* 5.1 3.4 + - - -
277I GLU* 3.4 31.1 + - - +
278I VAL 3.4 8.5 - - - +
279I ASP* 5.2 5.6 - - + +
280I ILE* 4.6 3.3 - - - +
312I ASN* 5.8 4.0 + - - +
313I ILE* 3.6 5.7 - - - +
314I GLU* 2.9 70.1 + - + +
316I THR* 3.9 22.7 - - + -
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Residues in contact with ALA 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I TRP* 4.3 15.0 - - + -
191I LEU* 4.2 17.9 - - + -
218I ARG* 1.3 80.1 + - - +
220I ALA* 1.3 62.7 + - - +
276I LYS 4.6 0.2 - - - -
277I GLU* 3.7 2.9 - - - +
278I VAL* 2.9 44.2 + - + +
280I ILE* 4.9 0.6 - - + +
312I ASN 3.3 6.5 - - - +
313I ILE* 3.7 19.7 - - + -
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Residues in contact with ALA 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191I LEU* 4.6 2.0 - - - +
218I ARG* 3.8 20.2 - - - +
219I ALA* 1.3 77.3 - - - +
221I LEU* 1.3 60.8 + - - +
222I TYR* 3.6 26.9 - - + +
274I LEU* 4.0 10.5 - - + -
276I LYS 3.3 5.2 - - - +
277I GLU* 4.8 1.6 - - + -
311I PHE* 3.0 7.5 - - - +
312I ASN* 2.9 40.6 + - + +
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Residues in contact with LEU 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190I CYS* 4.1 22.0 - - - +
191I LEU* 4.1 28.2 - - + +
192I PHE* 4.1 20.9 - - + -
220I ALA* 1.3 74.1 - - - +
222I TYR* 1.3 60.8 - - - +
274I LEU* 3.7 3.8 - - - +
275I ILE* 2.8 51.3 + - + +
276I LYS* 2.9 23.5 + - + +
290I PHE* 4.8 5.6 - - + -
309I THR* 4.2 15.9 - - - -
310I TYR 3.6 15.3 - - - +
311I PHE* 4.1 3.8 - - + -
358I ILE* 5.9 0.7 - - + -
360I MET* 4.9 3.4 - - - -
372I PHE* 6.2 0.4 - - + -
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Residues in contact with TYR 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D GLY* 6.4 1.3 - - - -
218I ARG* 5.1 3.5 + - - -
220I ALA* 3.6 32.1 - - + +
221I LEU* 1.3 74.5 - - - +
223I VAL* 1.3 62.5 + - - +
272I ALA* 4.4 4.0 - - + -
273I CYS* 3.3 13.5 - - - +
274I LEU* 3.5 40.0 - - + +
275I ILE* 4.2 4.3 - - - -
309I THR* 3.0 30.1 - - - -
310I TYR* 2.9 55.2 + + + +
312I ASN* 3.4 23.0 + - - -
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Residues in contact with VAL 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222I TYR* 1.3 73.2 - - - +
224I VAL* 1.3 69.3 + - - +
272I ALA* 3.4 2.9 - - - +
273I CYS* 3.0 33.3 + - + +
275I ILE* 3.5 31.6 - - + -
294I PHE* 4.1 23.6 - - + -
296I LEU* 3.5 9.0 - - + +
307I LEU* 4.6 20.4 - - + -
308I VAL 3.2 8.1 - - - +
309I THR* 3.7 23.6 - - + -
310I TYR* 5.1 0.4 - - - -
358I ILE* 4.9 9.4 - - + -
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Residues in contact with VAL 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223I VAL* 1.3 81.7 - - - +
225I ALA* 1.3 71.8 + - - +
226I ILE* 4.0 6.1 - - + -
268I VAL* 3.5 31.4 - - + -
270I THR* 3.7 5.4 - - - +
271I ASN 3.4 19.3 - - - +
272I ALA* 3.7 13.9 - - + -
296I LEU* 3.8 7.6 - - - -
307I LEU* 3.4 3.3 - - - +
308I VAL* 2.8 39.3 + - + +
310I TYR* 4.2 15.3 - - + -
328I PRO* 5.6 2.9 - - + -
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Residues in contact with ALA 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224I VAL* 1.3 76.5 - - - +
226I ILE* 1.3 67.2 + - - +
268I VAL* 3.8 0.3 - - - +
269I VAL* 3.1 22.9 + - - -
270I THR* 3.0 28.8 + - + -
296I LEU* 3.6 6.4 - - + +
304I VAL* 3.9 20.4 - - + -
306I ALA 3.5 10.8 - - - +
307I LEU* 3.9 12.8 - - + -
354I ILE* 4.1 4.9 - - + -
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Residues in contact with ILE 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224I VAL* 4.0 3.6 - - + -
225I ALA* 1.3 80.6 - - - +
227I GLU* 1.3 60.6 + - - +
228I ASP* 3.9 25.8 - - + +
263I VAL* 4.0 23.3 - - + -
267I GLN* 3.4 14.1 - - + +
268I VAL* 3.9 24.2 - - + -
269I VAL* 4.1 6.7 - - - -
304I VAL* 3.4 4.8 - - - -
305I HIS 2.9 23.0 + - - -
306I ALA* 2.9 27.5 + - + +
308I VAL* 3.6 34.8 - - + -
339I VAL* 4.7 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