Contacts of the strand formed by residues 250 - 255 (chain D) in PDB entry 2VM8
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 LEU 250 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D LEU* 4.7 6.3 - - + -
194D ILE* 5.0 0.7 - - - -
195D ALA* 3.3 22.9 - - + +
197D VAL* 3.4 26.9 - - + -
239D ALA* 3.7 7.0 - - + +
240D ILE* 3.4 48.9 - - + +
243D ALA* 3.6 22.0 - - + -
249D PRO* 1.3 73.5 - - - +
251D TYR* 1.3 62.9 + - - +
252D ILE* 3.7 12.6 - - + -
272D THR* 5.4 0.9 - - + -
273D VAL 3.0 12.2 + - - +
274D VAL* 3.2 9.8 - - + -
275D TYR* 2.9 29.9 + - - -
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Residues in contact with TYR 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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72D VAL* 2.8 35.3 - - - +
194D ILE* 3.7 16.4 - - + -
195D ALA 2.8 13.1 + - - +
196D GLN* 3.3 24.1 - - + -
197D VAL* 3.0 28.2 + - - +
250D LEU* 1.3 79.0 - - - +
252D ILE* 1.3 66.5 + - - +
253D THR* 3.9 4.5 - - + -
275D TYR* 3.2 23.8 - + + +
277D GLU* 2.9 36.6 + - + +
328D VAL* 3.3 14.0 - - + +
391D VAL* 4.5 7.9 - - + -
392D PHE* 3.5 33.7 - + - -
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Residues in contact with ILE 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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197D VAL* 3.5 25.6 - - + +
199D ALA* 4.8 6.5 - - + +
232D GLU* 5.7 1.3 - - + +
236D VAL* 3.7 38.1 - - + -
239D ALA* 4.6 4.7 - - + -
250D LEU* 3.7 25.8 - - + -
251D TYR* 1.3 74.2 - - - +
253D THR* 1.3 70.8 + - - +
254D LYS 5.5 0.2 - - - +
255D VAL* 3.4 14.6 - - + +
264D ILE* 3.7 25.4 - - + -
274D VAL* 3.8 12.3 - - + -
275D TYR 2.7 11.4 + - - +
277D GLU* 3.1 22.0 + - - +
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Residues in contact with THR 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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73D HIS* 3.8 18.0 - - + +
75D ARG* 5.7 0.3 + - - -
107D HIS* 4.6 0.7 - - + -
165D LEU* 3.7 22.1 - - + +
196D GLN* 3.5 30.5 - - + +
197D VAL 3.0 25.9 + - - +
198D HIS* 4.0 11.1 + - - +
199D ALA 5.5 1.4 + - - -
251D TYR* 3.5 5.8 + - + -
252D ILE* 1.3 83.3 - - - +
254D LYS* 1.3 77.9 + - - +
255D VAL 3.3 0.2 + - - -
277D GLU* 3.1 14.8 - - - +
305D PRO* 5.1 2.4 - - - +
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Residues in contact with LYS 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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73D HIS* 3.4 35.0 - - + +
75D ARG* 4.5 13.6 - - - +
198D HIS* 4.7 9.4 + - - +
232D GLU* 3.8 2.1 - - - +
253D THR* 1.3 79.7 - - - +
255D VAL* 1.3 64.1 + - - +
256D MET* 3.3 20.7 + - - +
277D GLU* 2.7 21.0 + - - -
279D ILE* 4.3 12.6 - - + -
303D THR* 4.1 12.4 + - - +
304D SER 2.6 30.7 + - - +
305D PRO* 3.4 20.5 - - + +
332D ALA* 3.6 19.9 + - + +
334D CYS* 6.3 0.4 - - - +
353D GLU* 6.3 0.6 - - - +
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Residues in contact with VAL 255 (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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232D GLU* 3.8 4.9 - - - +
252D ILE* 3.4 28.3 - - + +
253D THR 4.3 0.4 - - - -
254D LYS* 1.3 73.2 - - - +
256D MET* 1.3 56.7 + - - +
257D SER 4.2 2.7 - - - +
260D SER* 3.0 22.7 - - - +
261D ALA* 3.7 27.4 - - + +
264D ILE* 3.7 20.6 - - + -
276D GLY* 4.0 1.1 - - - -
277D GLU 3.1 17.6 + - - +
278D PRO* 3.6 16.1 - - + +
282D SER* 3.0 17.8 + - - -
317D LEU* 3.7 7.7 - - + +
326D LEU* 4.3 5.2 - - + -
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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