Contacts of the strand formed by residues 246 - 255 (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 ARG 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A GLN* 3.4 38.6 + - - +
238A GLU* 4.3 11.3 + - - -
239A ALA* 3.8 14.6 - - + -
244A LYS* 3.8 28.3 - - + +
245A LYS* 1.3 78.2 - - - +
247A VAL* 1.3 62.2 + - - +
248A MET* 3.1 30.9 + - + -
269A VAL 3.3 2.3 - - - +
270A ILE* 3.3 1.9 - - - -
271A LEU* 2.8 29.7 + - - +
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Residues in contact with VAL 247 (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* 4.5 16.3 - - + +
245A LYS 4.6 5.4 - - - +
246A ARG* 1.3 76.0 + - - +
248A MET* 1.3 65.4 + - - +
269A VAL 3.3 5.6 - - - +
270A ILE* 4.4 17.7 - - + -
280A LEU* 3.9 25.4 - - + -
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Residues in contact with MET 248 (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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146A VAL* 3.7 23.8 - - + -
170A MET* 4.4 2.7 - - - -
235A GLN* 4.7 11.9 - - + +
236A MET* 3.9 12.6 - - + -
239A ALA* 3.7 10.3 - - + -
246A ARG* 3.1 35.0 - - + -
247A VAL* 1.3 78.0 - - - +
249A PRO* 1.3 72.6 - - + +
250A VAL* 3.8 12.1 - - + -
268A PRO* 4.2 3.4 - - - -
269A VAL* 2.9 33.4 + - - +
271A LEU* 3.4 38.8 - - + -
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Residues in contact with PRO 249 (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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144A ALA 5.1 0.3 + - - -
145A GLY* 3.3 40.3 + - - +
146A VAL* 3.3 12.9 + - + +
149A ALA* 4.6 9.6 - - + -
169A ALA 5.4 2.0 - - - +
170A MET* 3.7 20.4 - - + -
171A LEU 3.2 26.2 - - - +
248A MET* 1.3 88.1 - - + +
250A VAL* 1.3 64.5 + - - +
266A GLY* 5.4 0.9 - - - -
267A VAL 3.3 14.6 - - - +
268A PRO* 4.1 0.9 - - + -
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 4.5 6.7 - - + -
142A GLY 3.6 11.7 - - - +
144A ALA 5.3 0.4 - - - +
145A GLY 4.8 3.4 - - - +
236A MET* 3.4 28.0 - - + -
248A MET* 3.6 23.5 + - + +
249A PRO* 1.3 79.1 - - - +
251A ALA* 1.3 64.7 + - - +
252A ALA 2.9 9.2 + - - -
266A GLY* 4.1 4.7 - - - -
267A VAL* 3.0 23.7 + - - +
269A VAL* 3.6 29.8 - - + -
271A LEU* 4.6 4.0 - - + -
276A VAL* 4.2 14.6 - - + -
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Residues in contact with ALA 251 (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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122A LEU* 3.4 32.8 - - + -
123A ASP* 3.7 14.8 - - - +
126A THR* 4.5 3.4 - - - +
141A ILE* 3.5 6.4 - - - +
142A GLY* 3.0 30.0 + - - +
144A ALA* 5.2 4.5 - - + +
250A VAL* 1.3 68.4 - - - +
252A ALA* 1.3 58.8 + - - +
264A TYR* 3.4 14.2 - - + -
265A PHE 3.4 12.8 - - - +
266A GLY* 4.1 2.1 - - - +
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Residues in contact with ALA 252 (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* 5.2 0.4 - - - -
250A VAL* 2.9 11.2 + - + +
251A ALA* 1.3 73.4 - - - +
253A TYR* 1.3 62.8 + - - +
254A LEU* 3.5 3.3 + - - +
263A ILE 3.4 0.3 - - - +
264A TYR* 3.1 12.2 - - - -
265A PHE* 2.8 28.4 + - - +
267A VAL* 4.0 16.8 - - + -
269A VAL* 4.2 5.6 - - + -
276A VAL* 3.9 27.8 - - + -
279A ILE* 4.2 10.1 - - + -
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Residues in contact with TYR 253 (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 7.4 - + - -
137A LYS* 3.4 46.9 + - + +
138A GLU* 5.3 4.8 - - - +
252A ALA* 1.3 72.8 - - - +
254A LEU* 1.3 62.2 + - - +
255A THR* 3.6 29.0 + - + +
261A ASN* 4.7 1.7 + - - -
262A ASP* 2.5 53.5 + - - +
263A ILE 3.4 12.8 - - - -
264A TYR* 3.3 37.1 - + + +
279A ILE* 3.7 15.3 - - - +
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Residues in contact with LEU 254 (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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252A ALA 4.1 3.6 - - - +
253A TYR* 1.3 77.4 - - - +
255A THR* 1.3 63.0 + - - +
256A GLY 3.6 0.9 - - - -
257A GLN* 3.4 26.9 - - + +
258A TYR* 4.9 1.3 - - + -
260A LEU* 3.6 42.0 - - + +
261A ASN* 3.3 0.3 + - - -
262A ASP* 2.8 29.1 + - - -
263A ILE* 2.9 14.7 + - + +
265A PHE* 3.5 34.1 - - + -
267A VAL* 3.8 31.9 - - + -
279A ILE* 4.2 9.4 - - + -
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Residues in contact with THR 255 (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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253A TYR* 3.6 31.5 + - + +
254A LEU* 1.3 75.7 - - - +
256A GLY* 1.3 56.9 + - - +
257A GLN* 2.8 20.7 + - - -
260A LEU 3.6 0.2 - - - -
261A ASN* 3.2 18.9 - - - +
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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