Contacts of the strand formed by residues 261 - 272 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A TYR* 4.7 1.8 + - - -
254A LEU 3.3 3.0 + - - -
255A THR* 3.2 31.7 - - - +
256A GLY* 4.2 4.5 - - - +
259A GLY 4.4 0.2 + - - -
260A LEU* 1.3 76.0 - - - +
262A ASP* 1.3 96.1 + - - +
263A ILE* 3.4 12.3 - - - +
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Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A TYR* 2.7 32.7 + - - -
253A TYR* 2.5 36.8 + - - +
254A LEU 2.8 5.9 + - - -
261A ASN* 1.3 88.9 - - - +
263A ILE* 1.3 64.5 + - - +
303A LEU* 4.4 1.9 - - - +
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Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TYR* 4.1 9.0 - - - -
252A ALA 3.4 0.3 - - - +
253A TYR* 3.4 10.3 - - - -
254A LEU* 2.9 34.0 + - + +
260A LEU* 4.2 22.0 - - + -
261A ASN 3.4 11.4 - - - +
262A ASP* 1.3 88.3 - - - +
264A TYR* 1.3 62.2 + - - +
265A PHE* 3.8 34.9 + - + -
296A ALA* 4.5 12.1 - - + +
299A VAL* 4.7 5.8 - - + -
300A ARG* 4.3 18.8 - - + +
303A LEU* 3.9 18.8 - - + -
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Residues in contact with TYR 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ASP* 3.6 41.0 + - - +
126A THR* 3.6 18.8 - - + -
127A TYR* 3.3 30.3 - + + -
130A ALA* 3.6 27.8 - - + +
137A LYS* 3.1 28.1 + - + +
140A VAL* 3.0 29.2 + - - +
251A ALA* 3.4 13.9 - - + -
252A ALA* 3.1 21.1 - - - -
253A TYR* 3.3 33.4 - + + +
263A ILE* 1.3 73.7 - - - +
265A PHE* 1.3 59.3 + - - +
299A VAL* 3.7 11.6 - - - +
303A LEU* 4.8 1.8 - - - +
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Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ASP* 3.9 2.5 - - - -
173A GLY* 3.6 12.3 - - - -
174A GLY 3.5 19.7 - - - -
251A ALA* 3.8 5.4 - - - -
252A ALA 2.8 29.5 + - - +
254A LEU* 3.5 22.4 - - + -
258A TYR* 6.0 0.2 - + - -
260A LEU* 3.6 24.2 - - + -
263A ILE* 3.8 15.0 + - + -
264A TYR* 1.3 73.9 - - - +
266A GLY* 1.3 60.2 + - - +
267A VAL* 3.0 21.1 + - + +
292A LEU* 3.4 33.4 - - + -
295A SER* 3.7 1.6 - - - -
296A ALA* 3.3 38.1 - - - -
299A VAL* 3.6 18.6 - - + -
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Residues in contact with GLY 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ASP* 3.8 4.2 + - - -
144A ALA* 6.3 1.8 - - - -
145A GLY* 6.0 4.5 - - - -
171A LEU 5.0 2.2 - - - -
172A MET* 3.4 11.5 - - - +
173A GLY* 2.7 49.3 + - - -
249A PRO* 5.4 1.3 - - - -
250A VAL 3.7 10.3 - - - -
251A ALA* 4.1 4.7 - - - -
265A PHE* 1.3 71.5 - - - +
267A VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A MET* 4.1 5.6 - - + -
249A PRO* 3.3 5.1 - - - +
250A VAL 3.0 26.6 + - - +
252A ALA* 4.0 9.2 - - + -
254A LEU* 3.8 29.8 - - + -
258A TYR* 4.1 15.5 - - + -
265A PHE* 3.0 18.5 + - + +
266A GLY* 1.3 79.0 - - - +
268A PRO* 1.3 72.3 - - + +
269A VAL* 3.6 12.6 + - + +
279A ILE* 3.7 25.8 - - + -
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Residues in contact with PRO 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A MET* 3.4 28.3 - - + -
172A MET* 3.8 18.2 - - + -
247A VAL* 5.2 0.2 - - + -
248A MET 3.6 6.5 - - - +
249A PRO* 4.1 3.6 - - + -
258A TYR* 3.7 14.6 - - - +
267A VAL* 1.3 86.8 - - + +
269A VAL* 1.3 62.6 + - - +
279A ILE* 3.7 1.9 - - - +
280A LEU* 2.9 57.1 + - + +
282A LEU* 4.0 14.6 - - + -
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ARG 3.3 0.9 - - - +
247A VAL* 3.3 5.2 - - - +
248A MET* 2.9 39.0 + - + +
250A VAL* 3.6 26.0 - - + -
252A ALA* 4.2 1.1 - - + -
267A VAL* 3.6 24.5 - - + +
268A PRO* 1.3 80.1 - - - +
270A ILE* 1.3 65.4 + - - +
271A LEU* 4.0 19.1 - - + +
276A VAL* 4.0 22.4 - - + -
278A LYS 3.1 16.4 - - - +
279A ILE* 4.2 4.0 - - + -
280A LEU* 4.5 4.9 - - - +
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A LYS* 4.0 33.2 - - + +
246A ARG 3.3 3.6 - - - -
247A VAL* 4.4 17.3 - - + -
269A VAL* 1.3 74.8 - - - +
271A LEU* 1.3 57.4 + - - +
276A VAL 4.0 0.5 - - - -
277A GLU* 3.0 38.2 + - + +
278A LYS* 3.0 40.4 + - + -
280A LEU* 4.5 14.1 - - + -
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ILE* 3.7 20.9 - - + -
236A MET* 4.0 31.0 - - + +
239A ALA* 3.9 18.6 - - + +
240A VAL* 4.0 9.2 - - + -
245A LYS* 3.1 22.0 + - - -
246A ARG 2.8 13.9 + - - -
248A MET* 3.4 38.1 - - + -
250A VAL* 4.6 2.9 - - + -
269A VAL* 3.7 11.5 + - + -
270A ILE* 1.3 70.5 - - - +
272A GLY* 1.3 60.2 + - - +
275A GLY* 3.6 28.9 - - - +
276A VAL* 4.1 3.6 - - + +
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Residues in contact with GLY 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ALA 3.8 7.6 - - - -
240A VAL* 3.4 23.9 - - - +
243A ASP* 3.5 7.6 - - - -
245A LYS* 4.2 5.2 - - - -
270A ILE 3.8 2.0 + - - -
271A LEU* 1.3 74.8 - - - +
273A ALA* 1.3 65.9 + - - -
274A GLY 3.1 2.7 - - - -
275A GLY* 3.0 19.3 + - - -
277A GLU* 3.5 12.0 - - - +
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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