Contacts of the strand formed by residues 251 - 256 (chain B) in PDB entry 1I2M
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 PHE 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B HIS* 3.8 2.9 + - - -
203B GLN* 4.1 2.6 - - - +
247B CYS* 3.6 2.1 - - - -
248B GLY* 2.9 40.6 + - - +
249B ALA 3.8 4.4 - - - -
250B TYR* 1.3 88.1 - - + +
252B THR* 1.3 65.8 + - - +
253B PHE* 3.8 22.0 - + - -
264B PHE 3.4 14.1 - - - +
265B GLY* 4.0 0.4 - - - -
266B LEU* 3.7 19.5 - - + +
271B GLN* 3.7 20.4 - - + -
272B LEU* 4.0 10.1 - - + -
301B GLY* 4.0 4.0 - - - -
302B GLY 3.3 27.8 - - - -
303B GLN 3.7 13.9 - - - -
305B HIS 3.7 14.8 - - - -
306B THR* 3.4 20.9 - - - -
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Residues in contact with THR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B HIS* 2.8 26.5 + - - -
185B VAL* 3.9 20.6 - - + +
193B LEU* 4.9 5.2 - - + -
203B GLN 3.0 11.6 + - - -
245B ALA* 5.1 0.7 - - + -
246B PHE 3.3 15.5 - - - +
247B CYS* 4.4 0.7 - - - +
251B PHE* 1.3 73.2 - - - +
253B PHE* 1.3 74.6 + - - +
263B GLY* 3.2 5.5 - - - -
264B PHE* 2.8 60.4 + - + -
272B LEU* 4.2 1.8 - - - +
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Residues in contact with PHE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ALA* 3.2 3.6 - - - +
246B PHE* 2.8 40.8 + - + +
247B CYS 5.9 0.4 - - - -
248B GLY 5.5 2.2 - - - -
251B PHE* 3.8 23.1 - + - -
252B THR* 1.3 78.3 - - - +
254B ALA* 1.3 61.9 + - - +
261B VAL* 4.1 6.3 - - + -
262B TYR 3.3 4.9 - - - -
271B GLN 3.4 22.7 - - - -
272B LEU* 3.7 11.0 - - + -
286B LEU* 3.5 31.9 - - + -
289B PHE* 4.2 7.2 - + - -
299B PHE* 3.6 51.8 - + + -
300B SER 5.0 2.2 - - - -
306B THR* 3.7 26.0 - - + -
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LEU* 4.1 21.1 - - + -
242B PHE* 3.5 27.1 - - + -
244B ASP 3.5 9.2 - - - +
245B ALA* 4.5 0.9 - - + -
246B PHE* 5.3 0.2 - - - -
253B PHE* 1.3 76.3 - - - +
255B ILE* 1.3 63.9 + - - +
256B SER 3.9 0.4 + - - -
260B HIS 3.6 1.0 - - - +
261B VAL* 3.6 2.2 - - - -
262B TYR* 2.7 44.7 + - + +
264B PHE* 4.9 5.8 - - + -
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Residues in contact with ILE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B PHE* 3.4 5.1 - - - +
243B GLN* 2.8 41.3 + - + +
244B ASP* 3.0 15.3 + - + +
246B PHE* 3.9 28.0 - - + -
254B ALA* 1.3 74.6 - - - +
256B SER* 1.3 71.1 + - - +
259B GLY* 3.9 21.5 - - - +
260B HIS 3.3 5.4 - - - +
261B VAL* 4.7 6.3 - - + -
296B TRP* 3.3 33.2 - - + +
297B VAL* 4.4 4.5 - - - +
299B PHE* 4.2 16.4 - - + -
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Residues in contact with SER 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B VAL* 3.7 17.3 - - - -
241B ARG 3.2 14.4 - - - -
242B PHE* 3.8 5.5 - - - -
243B GLN* 3.0 12.8 + - - -
254B ALA 3.9 0.4 + - - -
255B ILE* 1.3 75.9 - - - +
257B HIS* 1.3 66.0 + - - +
258B GLU* 3.4 17.6 + - - +
259B GLY* 2.8 11.6 + - - -
260B HIS* 2.9 39.9 + - - +
262B TYR* 4.1 8.7 - - - -
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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