Contacts of the strand formed by residues 272 - 278 (chain D) in PDB entry 3MY0
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 GLN 272 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D ILE* 3.9 17.3 - - + -
231D PHE 5.4 2.2 - - - +
264D MET* 3.6 3.8 - - - -
265D THR* 3.0 35.2 + - - +
268D ASN* 6.0 4.3 - - + -
270D SER* 3.3 7.6 + - - +
271D THR* 1.3 75.8 - - - +
273D LEU* 1.3 66.1 + - - +
274D TRP* 3.8 18.6 - - - +
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Residues in contact with LEU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D LYS 3.6 0.9 - - - +
230D ILE* 4.2 0.2 - - - +
231D PHE* 3.1 38.7 + - + +
232D SER 6.2 0.2 - - - -
233D SER* 6.2 0.2 - - - -
236D GLU* 3.6 40.8 - - + +
239D TRP* 2.8 66.9 - - + -
263D ASP 3.6 4.3 - - - -
264D MET* 4.3 19.5 - - + +
271D THR 5.6 2.0 - - - +
272D GLN* 1.3 75.1 - - - +
274D TRP* 1.3 65.1 + - - +
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Residues in contact with TRP 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ALA* 3.6 26.7 - - + -
202D VAL* 4.9 13.7 - - + -
204D LEU* 4.0 28.7 - - + -
228D VAL* 3.7 23.1 - - + -
229D LYS 3.5 3.4 - - - +
230D ILE* 3.6 24.3 - - + +
239D TRP* 3.0 18.6 + - - +
262D SER* 3.5 1.7 + - - -
263D ASP* 2.8 37.6 + - + +
265D THR* 3.4 31.6 - - + +
267D ARG* 4.5 17.0 - - + -
268D ASN* 4.9 12.4 - - + +
272D GLN* 3.7 16.3 - - + +
273D LEU* 1.3 82.9 - - - +
275D LEU* 1.3 60.9 + - - +
276D ILE* 4.2 15.3 - - + -
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Residues in contact with LEU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ALA 3.7 0.9 - - - +
228D VAL* 3.5 1.6 - - - -
229D LYS* 2.8 41.1 + - + +
231D PHE* 3.8 21.3 - - + -
239D TRP* 4.6 2.0 - - + -
242D GLU* 3.4 44.0 - - + +
243D THR* 4.6 7.4 - - - +
246D TYR* 4.4 8.7 - - + -
259D PHE* 3.4 34.1 - - + -
261D ALA 3.6 3.8 - - - +
262D SER* 4.0 11.7 - - - +
274D TRP* 1.3 74.5 - - - +
276D ILE* 1.3 60.5 + - - +
277D THR* 4.1 17.3 + - + +
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Residues in contact with ILE 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D VAL* 4.5 5.8 - - + -
199D ALA* 3.7 39.3 - - + +
202D VAL* 4.3 6.3 - - + -
226D VAL* 4.0 24.5 - - + -
227D ALA 3.2 9.0 - - - +
228D VAL* 4.0 20.0 - - + -
259D PHE* 4.2 1.4 - - - -
260D ILE* 3.0 37.6 + - + -
261D ALA* 2.9 34.8 + - + +
263D ASP* 5.3 2.0 - - + +
274D TRP* 4.3 12.1 - - + -
275D LEU* 1.3 74.0 - - - +
277D THR* 1.3 68.3 + - - +
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Residues in contact with THR 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D VAL* 3.5 10.7 - - - +
227D ALA* 2.8 38.3 + - - +
229D LYS* 6.4 0.9 - - + -
246D TYR* 5.3 4.3 - - + -
257D LEU* 3.4 27.0 - - + +
258D GLY 3.1 17.5 - - - +
259D PHE* 4.6 6.1 - - + -
260D ILE* 3.7 9.6 - - - +
275D LEU* 4.1 26.0 - - + +
276D ILE* 1.3 80.1 - - - +
278D HIS* 1.3 70.6 + - - +
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Residues in contact with HIS 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D GLU* 6.1 0.9 - - - -
225D SER 5.0 1.6 - - - -
226D VAL* 5.0 0.9 - - - +
227D ALA* 3.5 4.7 - - - +
257D LEU* 3.6 12.1 - - + +
258D GLY* 3.0 32.4 + - - +
259D PHE 5.2 2.2 + - - -
260D ILE* 4.0 24.1 - - + +
277D THR* 1.3 91.5 + - - +
279D TYR* 1.3 60.9 + - - +
280D HIS* 4.2 21.9 + - + +
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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