Contacts of the strand formed by residues 268 - 275 (chain A) in PDB entry 1IZC
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 TYR 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A THR* 3.7 9.7 + - - +
207A PHE* 5.8 1.2 - - - +
236A MET* 3.8 23.4 - - + +
239A PHE* 5.5 0.3 - - - -
240A SER* 6.1 0.9 - - - -
250A ILE* 3.3 39.7 - - + +
251A PHE 4.5 0.2 - - - -
252A GLY* 3.9 32.3 - - - -
253A GLY 4.7 3.4 - - - -
263A LEU* 2.9 54.8 + - + +
264A ILE* 3.7 6.2 - - - -
266A GLN* 3.9 21.5 + - + -
267A GLY* 1.3 78.7 - - - +
269A ARG* 1.3 76.5 + - - +
271A ILE* 3.9 17.3 - - + -
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Residues in contact with ARG 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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32A LEU* 4.5 4.3 - - + +
35A ALA* 3.4 34.4 + - + -
36A MET* 4.1 16.0 + - + +
39A PRO* 3.8 22.6 - - - +
42A THR* 3.5 19.8 - - - -
43A LEU* 2.9 31.0 + - - +
249A PRO* 3.7 29.6 - - + -
250A ILE 2.8 6.2 + - - -
264A ILE* 2.8 35.4 + - - +
267A GLY* 3.4 18.8 + - - +
268A TYR* 1.3 95.9 + - - +
270A ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 270 (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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32A LEU* 4.5 3.8 - - + -
43A LEU* 3.4 12.3 - - + -
66A PHE* 4.2 16.4 - - + -
99A ILE* 5.3 0.7 - - + -
250A ILE 3.4 2.5 + - - +
251A PHE* 3.3 42.6 - - + -
252A GLY 3.0 24.9 + - - +
268A TYR* 3.7 0.6 - - - -
269A ARG* 1.3 80.5 - - - +
271A ILE* 1.3 63.1 + - - +
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Residues in contact with ILE 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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42A THR* 3.9 21.8 - - + -
43A LEU 2.8 12.7 + - - +
44A MET* 3.5 8.3 - - - -
45A GLY 2.9 23.2 + - - -
66A PHE* 3.6 4.0 - - - -
252A GLY 3.3 5.6 - - - +
253A GLY 4.1 0.4 - - - -
254A ALA* 3.8 33.2 - - + +
260A VAL* 4.2 21.5 - - + -
263A LEU* 3.9 30.1 - - + -
264A ILE* 4.2 4.3 - - + -
268A TYR* 3.9 18.2 - - + -
270A ALA* 1.3 78.2 - - - +
272A ALA* 1.3 67.8 + - - +
273A VAL* 3.3 7.5 + - + +
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Residues in contact with ALA 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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45A GLY 3.4 10.5 - - - +
47A ALA* 4.3 20.2 - - + +
66A PHE* 3.8 13.5 - - + -
68A TRP* 5.3 4.9 - - + -
252A GLY 2.8 15.2 + - - +
253A GLY* 3.4 1.8 - - - -
254A ALA 2.9 23.7 + - - -
271A ILE* 1.3 69.5 - - - +
273A VAL* 1.3 59.0 + - - +
274A GLN 3.4 1.3 - - - -
275A PHE* 3.5 22.9 - - + -
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Residues in contact with VAL 273 (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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44A MET* 4.2 19.5 - - + -
45A GLY 2.8 23.6 + - - +
254A ALA* 4.4 11.8 - - + +
257A VAL* 3.9 26.3 - - + +
260A VAL* 4.1 20.2 - - + -
271A ILE* 3.8 24.5 - - + +
272A ALA* 1.3 73.9 - - - +
274A GLN* 1.3 74.1 + - + +
275A PHE* 4.4 4.9 - - - -
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Residues in contact with GLN 274 (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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45A GLY 3.9 1.0 + - - -
46A VAL* 3.5 16.7 - - + -
47A ALA* 2.9 23.4 + - - +
257A VAL* 5.0 8.5 - - - +
272A ALA* 3.4 1.4 + - - +
273A VAL* 1.3 92.1 + - + +
275A PHE* 1.3 86.4 + - - +
279A GLY* 3.6 21.9 - - - -
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Residues in contact with PHE 275 (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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46A VAL* 4.9 0.4 - - - -
47A ALA* 3.6 23.8 - - + -
253A GLY* 4.3 6.7 - - - -
254A ALA 3.6 27.6 - - - -
255A LEU* 4.9 11.0 - - + -
272A ALA* 3.5 34.1 - - + -
273A VAL 4.4 0.7 - - - -
274A GLN* 1.3 93.7 + - - +
276A ASP* 1.3 61.6 + - - +
277A VAL 3.4 1.1 - - - +
278A TRP* 4.5 30.3 - + + +
279A GLY* 2.7 31.0 + - - -
282A ARG* 6.1 2.7 - - - -
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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