Contacts of the strand formed by residues 247 - 252 (chain B) in PDB entry 2YTZ
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 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B GLY* 4.0 29.8 - - - +
205B ALA* 4.8 2.7 - - + -
206B ARG* 3.6 31.4 - - + +
243B THR 4.4 1.6 - - - +
244B LEU* 3.2 32.0 + - + +
245B GLU 4.1 1.4 - - - +
246B LYS* 1.3 82.6 - - - +
248B GLY* 1.3 59.6 + - - +
263B GLN* 3.7 6.2 - - - +
264B GLY 2.9 29.4 + - - +
265B PHE* 4.3 16.2 - - + +
275B PRO* 4.9 12.1 - - + -
276B VAL 3.3 14.8 - - - +
277B TRP* 4.4 10.5 - - + -
278B LEU* 4.5 0.7 - - - -
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Residues in contact with GLY 248 (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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247B LEU* 1.3 78.3 - - - +
249B TYR* 1.3 70.4 + - - -
262B GLU 3.1 13.5 - - - -
264B GLY 3.6 6.9 + - - -
275B PRO* 3.5 1.6 - - - +
276B VAL* 2.9 37.5 + - - +
278B LEU* 3.4 11.8 - - - +
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Residues in contact with TYR 249 (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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266A LEU* 3.8 16.8 - - + +
248B GLY* 1.3 79.0 - - - -
250B ILE* 1.3 66.1 + - - +
251B TYR* 4.6 2.9 - - + -
260B GLU 3.7 0.2 - - - +
261B LEU* 3.5 4.9 - - - +
262B GLU* 2.8 44.2 + - + +
264B GLY 3.4 15.3 - - - -
265B PHE 2.6 29.4 + - - -
266B LEU* 3.9 3.8 - - - +
267B PRO* 3.3 52.9 - - + +
272B ALA* 4.2 7.2 - - + -
273B TYR 3.3 22.9 - - - +
274B GLY 3.6 2.5 - - - -
275B PRO* 3.3 39.9 - - + +
276B VAL* 4.5 0.9 - - - -
278B LEU* 4.1 1.8 - - - +
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Residues in contact with ILE 250 (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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187B LEU* 4.4 17.3 - - + -
195B VAL* 3.8 20.2 - - + -
198B ARG* 5.3 2.5 - - - -
249B TYR* 1.3 79.0 - - - +
251B TYR* 1.3 77.0 + - - +
252B PHE* 4.8 0.4 - - + -
259B PHE* 4.6 1.3 - - + -
260B GLU 3.3 4.9 - - - +
261B LEU* 4.1 13.9 - - + -
272B ALA* 3.7 1.6 - - - -
273B TYR* 2.8 43.7 + - + +
276B VAL* 3.9 28.5 - - + -
278B LEU* 4.9 2.7 - - + -
320B LEU* 3.7 42.4 - - + -
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Residues in contact with TYR 251 (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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249B TYR* 4.6 3.8 - - + -
250B ILE* 1.3 76.8 - - - +
252B PHE* 1.3 60.6 + - - +
258B LYS 4.0 0.4 - - - +
259B PHE* 3.1 6.6 - - - +
260B GLU* 2.7 61.2 + - + +
262B GLU* 2.6 34.1 + - + -
267B PRO* 3.5 7.0 - - + +
269B ARG* 3.2 63.8 + - + +
270B PRO 3.2 22.9 - - - -
271B ASN* 3.4 15.5 - - + -
272B ALA* 3.4 16.8 - - + -
273B TYR* 4.3 1.8 - - - -
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Residues in contact with PHE 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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187B LEU* 3.9 38.6 - - + -
188B ARG 5.4 4.5 - - - -
189B GLY* 6.1 0.7 - - - -
190B GLU* 3.7 38.1 - - + -
191B LEU* 3.4 32.5 - - + -
250B ILE* 4.8 1.1 - - + -
251B TYR* 1.3 76.1 - - - +
253B ASP* 1.3 73.5 + - - +
254B ASP* 3.6 21.8 + - + +
257B GLY* 3.6 28.7 - - - -
258B LYS 3.8 1.3 - - - -
259B PHE* 4.0 11.9 - - + -
271B ASN 5.1 0.2 + - - -
273B TYR* 4.0 15.7 + - + -
330B ARG* 4.3 0.4 - - - -
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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