Contacts of the strand formed by residues 250 - 256 (chain V) in PDB entry 1I84
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 LYS 250 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184V THR* 4.4 10.3 - - - +
187V THR* 5.0 4.3 - - - -
228V ASN* 3.3 35.2 + - - +
231V LEU* 5.5 5.9 - - + +
232V GLU* 5.4 4.9 - - - +
236V ASN* 5.7 0.6 + - - -
246V SER* 4.3 10.5 + - - -
248V PHE* 4.1 27.0 - - + -
249V GLY* 1.3 76.1 - - - +
251V PHE* 1.3 57.4 + - - +
252V ILE* 3.8 22.7 - - + -
267V ILE* 5.2 11.2 - - + -
268V GLU 3.7 7.9 - - - -
269V THR* 5.2 2.0 - - - -
270V TYR* 3.6 4.0 - - - -
463V ILE 4.0 0.2 - - - +
464V LEU* 3.4 1.4 - - - +
465V ASP* 2.6 79.5 + - + +
466V ILE* 4.4 0.2 - - - +
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Residues in contact with PHE 251 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172V SER* 5.6 0.2 - - - -
174V LEU* 5.8 0.2 - - + -
250V LYS* 1.3 73.4 - - - +
252V ILE* 1.3 57.6 + - - +
253V ARG* 3.8 27.6 + - + +
266V ASN 4.8 0.2 - - - -
267V ILE* 3.9 0.8 - - - +
268V GLU* 3.1 37.4 + - + +
270V TYR* 3.4 22.7 - - + +
460V PHE* 4.5 9.4 - + - -
462V GLY* 4.4 23.8 - - - -
463V ILE 3.6 5.2 - - - -
464V LEU* 3.6 21.3 - - + -
670V LEU* 3.5 16.2 - - + -
673V THR* 4.3 17.7 - - + -
674V LEU* 3.5 25.6 - - + -
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Residues in contact with ILE 252 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187V THR* 3.6 29.6 - - + -
191V ILE* 4.3 22.7 - - + -
224V LEU* 5.2 5.4 - - + -
228V ASN* 4.6 4.7 - - - +
250V LYS* 3.8 29.8 - - + -
251V PHE* 1.3 74.8 - - - +
253V ARG* 1.3 68.5 + - - +
254V ILE* 4.2 10.3 + - + -
265V ALA* 5.3 2.0 - - + -
266V ASN 3.6 12.1 - - - +
267V ILE* 4.2 17.7 - - + +
461V LEU 3.7 2.8 - - - +
462V GLY* 3.8 1.7 - - - -
463V ILE* 3.0 47.4 + - + +
465V ASP* 5.0 0.4 - - + -
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Residues in contact with ARG 253 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251V PHE* 3.8 19.3 + - + +
252V ILE* 1.3 75.5 - - - +
254V ILE* 1.3 59.8 + - - +
255V ASN* 2.7 36.3 + - - +
265V ALA* 3.0 6.6 - - - +
266V ASN* 2.8 55.6 + - + +
459V SER 5.7 0.2 - - - -
460V PHE* 3.0 63.9 - - + +
461V LEU 3.6 1.8 - - - +
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Residues in contact with ILE 254 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191V ILE* 4.4 18.8 - - + -
194V LEU* 5.0 7.2 - - + -
224V LEU* 4.0 29.6 - - + -
252V ILE* 4.6 4.9 - - + -
253V ARG* 1.3 75.5 - - - +
255V ASN* 1.3 62.8 + - - +
256V PHE* 3.3 37.0 - - + -
262V ILE* 3.4 16.6 - - + -
264V GLY 3.5 4.9 - - - +
265V ALA* 4.3 4.0 - - + -
460V PHE* 2.9 6.8 - - - -
461V LEU* 2.7 42.3 + - + +
463V ILE* 4.2 25.1 - - + -
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Residues in contact with ASN 255 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253V ARG* 2.7 43.8 + - - +
254V ILE* 1.3 73.9 - - - +
256V PHE* 1.3 56.7 + - - +
262V ILE* 3.5 3.1 - - - -
263V VAL* 2.7 41.9 + - + +
264V GLY* 2.9 33.2 + - - +
265V ALA* 3.9 3.8 - - - +
266V ASN* 4.8 2.6 + - - +
451V ASP* 4.1 13.1 + - - -
459V SER 3.3 4.5 - - - +
460V PHE* 3.4 7.6 - - - +
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Residues in contact with PHE 256 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161V TYR* 4.0 16.2 - + - -
164V MET* 3.0 46.7 - - + -
165V LEU* 5.7 0.4 - - + -
194V LEU* 3.3 33.0 - - + -
198V ALA* 4.4 2.7 - - + -
254V ILE* 3.3 24.7 - - + -
255V ASN* 1.3 74.2 - - - +
257V ASP* 1.3 66.5 + - - +
260V GLY* 4.4 7.0 - - - -
261V TYR 3.0 9.2 - - - +
262V ILE* 3.5 28.3 - - + -
263V VAL* 3.8 4.2 - - - +
458V ALA 3.5 5.5 + - - -
459V SER* 2.7 44.0 + - - +
461V LEU* 3.7 13.5 - - + -
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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