Contacts of the strand formed by residues 261 - 272 (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 ASN 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253B TYR* 5.0 1.2 + - - -
254B LEU 3.5 2.6 + - - -
255B THR* 3.2 32.3 + - - +
256B GLY* 4.3 5.4 - - - +
259B GLY 4.3 0.8 + - - +
260B LEU* 1.3 76.2 - - - +
262B ASP* 1.3 92.5 + - - +
263B ILE* 3.5 4.7 - - - +
300B ARG* 3.2 13.7 + - - -
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Residues in contact with ASP 262 (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* 3.0 32.0 + - - -
253B TYR* 2.6 36.0 + - - +
254B LEU 3.0 4.9 + - - -
261B ASN* 1.3 91.1 - - - +
263B ILE* 1.3 56.8 + - - +
300B ARG* 2.9 21.8 + - - +
307B LYS* 3.9 10.7 + - - -
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Residues in contact with ILE 263 (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* 4.1 7.4 - - - -
252B ALA 3.5 0.9 - - - +
253B TYR* 3.6 8.8 - - - -
254B LEU* 3.0 33.8 + - + +
260B LEU* 4.2 20.6 - - + -
261B ASN 3.9 11.0 - - - +
262B ASP* 1.3 77.8 - - - +
264B TYR* 1.3 71.8 + - - +
265B PHE* 3.6 14.7 + - + -
296B ALA* 4.0 16.2 - - + +
299B VAL* 3.7 31.2 - - + -
300B ARG* 3.8 15.7 - - + +
303B LEU* 3.8 8.7 - - + -
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Residues in contact with TYR 264 (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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123B ASP* 3.6 39.7 - - - +
126B THR* 3.6 13.9 - - + -
127B TYR* 3.3 33.8 - + + +
130B ALA* 3.5 32.3 - - + +
137B LYS* 3.0 20.6 + - + +
140B VAL* 2.8 29.7 + - - +
251B ALA* 3.4 17.7 - - + -
252B ALA* 3.2 14.8 - - - -
253B TYR* 3.1 34.5 - + + -
263B ILE* 1.3 82.6 - - - +
265B PHE* 1.3 60.2 + - - +
299B VAL* 3.6 3.6 - - - +
303B LEU* 4.8 1.0 - - - +
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Residues in contact with PHE 265 (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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123B ASP* 3.9 3.1 - - - -
172B MET* 5.3 0.4 - - + -
173B GLY* 3.5 22.2 - - - -
174B GLY 3.7 6.5 - - - -
251B ALA* 3.9 4.9 - - - +
252B ALA 3.1 27.0 + - - +
254B LEU* 3.7 17.9 - - + -
258B TYR* 6.1 0.2 - + - -
260B LEU* 3.7 13.5 - - + -
263B ILE* 3.6 15.7 + - + -
264B TYR* 1.3 73.1 - - - +
266B GLY* 1.3 78.0 + - - +
267B VAL* 3.2 14.0 + - + +
292B LEU* 3.4 34.8 - - + -
295B SER* 3.5 12.6 - - - -
296B ALA* 3.3 39.5 - - + -
299B VAL* 3.7 16.6 - - + -
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Residues in contact with GLY 266 (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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123B ASP* 3.9 4.0 + - - -
144B ALA* 6.4 1.6 - - - -
145B GLY* 6.2 2.9 - - - -
171B LEU 5.1 1.8 - - - -
172B MET* 3.2 11.8 - - - +
173B GLY 2.9 46.7 + - - -
249B PRO* 5.3 1.8 - - - -
250B VAL 3.3 13.5 - - - -
251B ALA* 4.2 1.3 - - - -
265B PHE* 1.3 74.6 - - - +
267B VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 267 (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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172B MET* 4.2 2.7 - - - -
249B PRO* 3.9 4.9 - - - -
250B VAL 3.0 23.8 + - - +
252B ALA* 4.0 8.5 - - + -
254B LEU* 3.9 30.7 - - + -
258B TYR* 3.9 23.6 - - + -
265B PHE* 3.7 17.7 - - + +
266B GLY* 1.3 80.9 - - - +
268B PRO* 1.3 73.9 - - + +
269B VAL* 3.4 13.5 + - + +
279B ILE* 3.9 20.6 - - + -
292B LEU* 6.5 0.2 - - + -
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Residues in contact with PRO 268 (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* 3.5 26.9 - - + -
172B MET* 3.7 25.4 - - + -
247B VAL* 5.2 1.1 - - + -
248B MET 3.6 7.0 - - - +
249B PRO* 4.0 3.1 - - + -
258B TYR* 3.8 15.5 - - - +
267B VAL* 1.3 87.1 - - + +
269B VAL* 1.3 61.1 + - - +
279B ILE* 3.8 1.7 - - - +
280B LEU* 2.9 47.9 + - + +
282B LEU* 4.0 17.5 - - + -
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Residues in contact with VAL 269 (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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246B ARG 3.4 0.2 - - - +
247B VAL* 3.4 7.6 - - - +
248B MET* 2.8 39.8 + - + +
250B VAL* 3.7 32.1 - - + -
252B ALA* 4.1 2.9 - - + -
267B VAL* 3.6 21.8 - - + +
268B PRO* 1.3 79.9 - - - +
270B ILE* 1.3 72.9 + - - +
271B LEU* 4.3 8.1 - - + +
276B VAL* 4.0 24.9 - - + -
278B LYS 3.2 14.1 - - - +
279B ILE* 4.2 3.1 - - + -
280B LEU* 4.4 2.7 - - - +
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Residues in contact with ILE 270 (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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245B LYS* 3.8 31.0 - - + +
246B ARG 3.3 2.9 - - - -
247B VAL* 4.2 18.8 - - + -
269B VAL* 1.3 79.5 - - - +
271B LEU* 1.3 60.4 + - - +
275B GLY 3.6 0.3 - - - +
276B VAL* 3.9 2.8 - - - -
277B GLU* 2.9 42.8 + - + +
278B LYS* 2.9 37.2 + - + +
280B LEU* 4.3 15.7 - - + -
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Residues in contact with LEU 271 (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* 3.8 24.9 - - + -
236B MET* 3.8 26.2 - - + +
239B ALA* 3.7 25.2 - - + +
240B VAL* 4.1 9.0 - - + -
245B LYS* 2.9 24.4 + - - -
246B ARG 2.8 22.0 + - - +
248B MET* 3.7 31.0 - - + -
250B VAL* 4.7 1.6 - - + -
269B VAL* 3.9 5.3 - - + -
270B ILE* 1.3 73.7 - - - +
272B GLY* 1.3 59.0 + - - +
275B GLY* 3.2 28.5 - - - +
276B VAL* 4.1 4.5 - - + +
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Residues in contact with GLY 272 (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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239B ALA 3.7 9.4 - - - -
240B VAL* 3.7 16.3 - - - +
243B ASP* 3.5 7.6 - - - -
245B LYS 4.2 2.5 - - - -
270B ILE 4.0 0.6 + - - -
271B LEU* 1.3 76.8 - - - +
273B ALA* 1.3 57.4 + - - +
274B GLY 3.0 3.4 - - - -
275B GLY* 2.6 34.2 + - - -
277B GLU* 3.2 13.9 + - - -
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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