Contacts of the strand formed by residues 246 - 255 (chain B) in PDB entry 1UXI
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 ARG 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B GLN* 3.4 39.9 + - - +
238B GLU* 4.4 9.9 + - - -
239B ALA* 3.7 25.1 - - + -
244B LYS* 3.9 25.8 - - + +
245B LYS* 1.3 78.3 - - - +
247B VAL* 1.3 62.9 + - - +
248B MET* 3.5 25.3 + - + +
269B VAL 3.4 1.4 - - - +
270B ILE* 3.3 4.2 - - - -
271B LEU* 2.8 29.0 + - + +
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Residues in contact with VAL 247 (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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170B MET* 4.7 17.4 - - + +
245B LYS 3.8 5.1 + - - +
246B ARG* 1.3 74.5 - - - +
248B MET* 1.3 63.3 + - - +
268B PRO* 5.2 0.9 - - + -
269B VAL 3.4 4.7 - - - +
270B ILE* 4.2 21.3 - - + -
280B LEU* 3.9 25.4 - - + -
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Residues in contact with MET 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 3.8 11.7 - - + -
170B MET* 4.7 1.3 - - - -
235B GLN* 3.8 35.0 - - + +
236B MET* 3.8 17.9 - - - -
246B ARG* 3.5 39.0 - - + +
247B VAL* 1.3 76.6 - - - +
249B PRO* 1.3 72.9 - - + +
250B VAL* 4.1 9.0 - - + -
268B PRO* 4.1 2.7 - - - -
269B VAL* 2.8 36.0 + - - +
271B LEU* 3.7 31.0 - - + -
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Residues in contact with PRO 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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144B ALA 5.2 0.3 + - - -
145B GLY* 3.5 30.4 + - - +
146B VAL* 3.4 22.3 + - + +
149B ALA* 4.7 6.7 - - + -
169B ALA 5.6 0.7 - - - +
170B MET* 3.7 25.1 - - + -
171B LEU 3.2 29.2 - - - +
248B MET* 1.3 85.7 - - + +
250B VAL* 1.3 67.9 + - - +
266B GLY* 5.3 1.3 - - - -
267B VAL 3.3 14.4 - - - +
268B PRO* 4.0 0.4 - - + -
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE* 4.4 6.1 - - + -
142B GLY 3.8 11.7 - - - +
144B ALA* 5.4 0.7 - - - +
145B GLY 4.9 5.4 - - - +
236B MET* 3.8 24.0 - - + -
248B MET* 3.9 22.2 - - + +
249B PRO* 1.3 81.4 - - - +
251B ALA* 1.3 71.3 + - - +
252B ALA* 3.3 5.6 + - + -
266B GLY* 4.1 4.3 - - - -
267B VAL* 3.0 27.4 + - - +
269B VAL* 3.7 31.4 - - + -
271B LEU* 4.7 4.0 - - + -
276B VAL* 4.3 9.0 - - + -
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Residues in contact with ALA 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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122B LEU* 3.4 32.5 - - + -
123B ASP* 3.9 12.8 - - - +
126B THR* 4.3 5.2 - - - +
141B ILE* 3.5 8.3 - - - +
142B GLY* 3.0 29.4 + - - +
144B ALA* 5.4 2.9 - - + +
250B VAL* 1.3 71.0 - - - +
252B ALA* 1.3 58.0 + - - +
264B TYR* 3.4 16.1 - - + -
265B PHE 3.5 11.0 - - - +
266B GLY* 4.2 1.3 - - - +
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Residues in contact with ALA 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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141B ILE* 5.1 0.2 - - - -
250B VAL* 3.3 1.7 + - + -
251B ALA* 1.3 73.6 - - - +
253B TYR* 1.3 63.3 + - - +
254B LEU* 3.4 5.6 + - - +
263B ILE 3.5 0.2 - - - +
264B TYR* 3.2 9.3 - - - -
265B PHE 3.1 28.1 + - - +
267B VAL* 4.0 19.5 - - + -
269B VAL* 4.1 16.4 - - + -
276B VAL* 4.2 17.3 - - + -
279B ILE* 4.1 12.6 - - + -
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Residues in contact with TYR 253 (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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127B TYR* 4.2 8.1 - + - -
137B LYS* 3.6 48.0 + - + +
252B ALA* 1.3 72.5 - - - +
254B LEU* 1.3 69.1 + - - +
255B THR* 3.7 21.3 + - + +
257B GLN* 5.0 0.2 + - - -
261B ASN* 5.0 1.0 + - - -
262B ASP* 2.6 41.4 + - - +
263B ILE 3.6 16.2 - - - -
264B TYR* 3.1 41.0 - + + +
279B ILE* 3.4 18.9 - - - +
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Residues in contact with LEU 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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252B ALA 3.8 12.8 - - - +
253B TYR* 1.3 85.0 - - - +
255B THR* 1.3 65.9 + - - +
256B GLY 3.7 0.4 - - - -
257B GLN* 3.4 21.1 - - + +
258B TYR* 4.8 1.8 - - + -
260B LEU* 3.6 40.8 - - + +
261B ASN* 3.5 0.7 + - - -
262B ASP 3.0 22.7 + - - -
263B ILE* 3.0 16.7 + - + +
265B PHE* 3.7 22.9 - - + -
267B VAL* 3.9 27.1 - - + -
279B ILE* 3.9 17.3 - - + -
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Residues in contact with THR 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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253B TYR* 3.7 23.7 + - + +
254B LEU* 1.3 77.9 - - - +
256B GLY* 1.3 56.7 + - - +
257B GLN* 2.7 21.8 + - - -
261B ASN* 3.2 20.9 + - - +
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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