Contacts of the strand formed by residues 249 - 254 (chain D) in PDB entry 3M0V
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 ALA 249 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207D TYR* 3.7 8.4 - - + -
216D LEU* 3.2 12.6 - - + +
218D SER* 6.1 0.9 - - - +
242D ALA* 3.4 13.0 - - - +
245D LEU* 3.7 34.8 - - + -
246D GLY 3.0 11.0 + - - +
247D PRO 3.2 0.2 - - - -
248D LYS* 1.3 77.7 - - - +
250D GLN* 1.3 64.0 + - - +
276D LYS* 2.9 26.9 + - - -
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Residues in contact with GLN 250 (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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215D LYS* 2.8 42.4 + - - +
216D LEU 2.8 6.5 + - - +
217D PHE* 3.3 10.4 - - + -
218D SER* 3.1 25.6 + - - -
242D ALA* 3.9 7.0 - - - -
247D PRO 4.6 10.8 + - - +
248D LYS 3.9 2.9 + - - +
249D ALA* 1.3 80.4 - - - +
251D CYS* 1.3 64.3 + - - +
275D GLY 3.2 28.7 + - - +
276D LYS* 3.7 5.6 - - + +
277D LEU 4.0 10.9 + - - -
278D GLY* 3.5 24.8 - - - +
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Residues in contact with CYS 251 (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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217D PHE* 5.1 0.4 - - - -
218D SER 3.7 4.5 - - - -
220D HIS* 5.3 0.2 - - - +
238D ASN* 3.3 51.4 - - + +
239D TYR* 3.8 7.9 - - - -
242D ALA* 3.8 12.3 - - - -
250D GLN* 1.3 72.9 - - - +
252D LEU* 1.3 61.4 + - - +
253D VAL* 4.1 0.6 + - - -
271D LEU* 4.0 23.6 - - + -
276D LYS* 2.8 21.9 + - - +
277D LEU* 3.8 4.5 - - - +
278D GLY* 2.8 27.5 + - - -
279D GLY 3.5 2.8 + - - +
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Residues in contact with LEU 252 (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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177D THR* 3.8 19.1 - - + +
217D PHE* 4.1 16.2 - - + -
218D SER 2.9 13.5 + - - +
219D GLU* 3.7 34.4 - - + +
220D HIS* 3.8 12.6 + - - -
238D ASN* 4.7 0.2 - - - -
250D GLN 4.0 0.2 + - - -
251D CYS* 1.3 74.4 - - - +
253D VAL* 1.3 67.5 + - - +
254D ASP 3.9 1.4 + - - -
279D GLY 3.5 14.1 - - - +
281D HIS* 3.5 43.5 - - + +
325D MET* 3.5 31.6 - - + -
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Residues in contact with VAL 253 (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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220D HIS* 4.2 10.5 - - + -
252D LEU* 1.3 75.5 - - - +
254D ASP* 1.3 64.3 + - - +
255D LEU* 3.8 7.0 + - + -
258D HIS* 3.6 25.4 - - + +
264D ILE* 4.3 15.0 - - + -
267D ILE* 4.6 6.5 - - + -
268D VAL* 4.7 4.5 - - + -
271D LEU* 3.6 30.5 - - + -
277D LEU* 3.9 13.9 - - + -
279D GLY 3.0 6.6 + - - +
280D PHE* 3.3 21.7 - - + -
281D HIS 2.9 24.4 + - - +
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Residues in contact with ASP 254 (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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219D GLU* 3.2 17.9 - - + +
220D HIS* 5.2 2.2 + - - -
252D LEU 3.9 2.6 + - - -
253D VAL* 1.3 72.7 - - - +
255D LEU* 1.3 63.5 + - - +
256D GLY* 3.0 10.7 + - - -
257D HIS* 3.0 37.6 + - - +
258D HIS* 3.2 12.0 + - - -
281D HIS* 3.3 12.3 - - + +
283D ASN* 2.9 24.6 + - - -
289D ASP* 4.0 1.0 - - - +
327D ASP* 3.1 5.4 - - - +
507D MN 2.2 31.5 + - - -
508D MN 3.8 1.1 + - - -
2004D RNS 3.1 2.4 + - - -
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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