Contacts of the strand formed by residues 295 - 301 (chain A) in PDB entry 1Y24
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 ILE 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A TRP* 5.8 1.3 - - + -
248A PHE* 3.4 36.8 - - + -
279A VAL* 6.1 0.7 - - + +
282A GLN* 3.7 33.2 - - + +
283A ILE* 3.7 29.6 - - + +
285A GLN* 5.5 3.1 - - + +
293A THR* 3.6 12.8 + - - +
294A PRO* 1.3 79.0 - - - +
296A TYR* 1.3 59.6 + - - +
297A ASN* 5.1 2.7 - - - +
330A GLN 5.0 5.6 - - - +
331A ASN* 2.8 36.4 - - - +
332A LEU* 3.0 27.6 + - + +
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Residues in contact with TYR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLN* 5.7 0.4 - - - -
130A PHE* 4.1 10.3 - + + -
176A ASN* 4.0 14.3 + - - -
217A ARG* 3.8 19.9 + - - -
247A PHE* 3.7 40.8 - + + -
248A PHE 2.7 11.3 + - - +
249A THR* 3.2 6.3 - - + -
250A GLY 3.0 23.9 + - - -
294A PRO* 3.9 21.1 - - + +
295A ILE* 1.3 77.5 - - - +
297A ASN* 1.3 60.1 + - - +
298A ASP* 3.2 20.5 - - - +
331A ASN* 3.2 8.3 - - - -
332A LEU* 4.2 14.5 - - + +
333A LEU* 3.6 40.6 - - + +
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Residues in contact with ASN 297 (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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250A GLY* 3.1 27.0 + - - +
251A GLU 5.2 0.2 - - - -
252A ALA* 4.9 12.3 - - + +
278A VAL 5.9 0.4 + - - -
279A VAL* 3.2 27.8 - - - +
282A GLN* 5.9 5.1 - - - +
295A ILE* 5.1 3.0 - - - +
296A TYR* 1.3 72.1 + - - +
298A ASP* 1.3 52.4 + - - +
299A GLU 2.9 10.2 + - - +
300A ALA* 4.0 6.3 + - + -
331A ASN* 3.1 21.9 + - - +
333A LEU 2.8 11.7 + - - -
334A LEU* 3.4 25.9 - - + +
335A ALA* 2.8 26.7 + - - +
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Residues in contact with ASP 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A CYS* 5.3 1.7 - - - -
89A ARG* 3.0 36.8 + - + +
130A PHE* 3.2 27.8 - - - -
132A LEU* 3.6 29.9 - - + +
178A GLU* 5.1 0.9 - - - +
249A THR* 3.0 26.7 - - - +
250A GLY 3.5 5.6 + - - +
296A TYR* 3.2 15.4 - - - +
297A ASN* 1.3 69.3 - - - +
299A GLU* 1.3 57.4 + - - +
333A LEU* 4.9 6.2 - - - +
335A ALA* 3.5 17.7 - - - +
337A THR* 4.5 0.2 - - - +
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Residues in contact with GLU 299 (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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89A ARG* 3.1 34.5 + - - +
91A HIS* 4.6 1.0 + - - -
181A ASN* 3.7 15.2 + - - +
182A GLU* 3.8 6.8 - - - +
250A GLY 4.2 2.1 + - - +
251A GLU* 3.3 28.1 - - + +
252A ALA* 2.7 33.5 + - - +
297A ASN 2.9 3.6 + - - -
298A ASP* 1.3 75.3 - - - +
300A ALA* 1.3 54.6 + - - +
301A ASP* 4.2 4.7 - - - +
304A VAL* 3.3 28.4 - - - +
335A ALA 3.6 2.9 - - - -
337A THR* 3.5 17.0 - - + +
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Residues in contact with ALA 300 (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* 3.3 11.2 - - + +
275A GLN* 4.6 8.5 - - - +
297A ASN* 4.2 3.8 - - + +
299A GLU* 1.3 73.2 - - - +
301A ASP* 1.3 60.0 + - - +
323A VAL* 6.0 1.6 - - + -
334A LEU* 4.1 34.5 - - + -
335A ALA 2.8 14.7 + - - +
336A ASN* 3.2 19.5 + - - +
337A THR* 3.0 22.0 + - - -
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Residues in contact with ASP 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLU* 4.7 0.4 - - - +
252A ALA 3.1 6.5 + - - +
253A GLY* 3.6 3.6 - - - -
254A VAL* 4.0 2.3 + - - +
275A GLN* 3.3 20.2 + - - +
299A GLU* 4.5 7.7 - - - +
300A ALA* 1.3 73.6 - - - +
302A PRO* 1.3 77.3 - - + +
303A LEU 3.0 32.6 - - - +
304A VAL* 3.3 20.1 + - - +
323A VAL* 6.5 0.9 - - - -
336A ASN* 5.5 1.6 - - - +
337A THR* 3.1 37.5 + - - +
357A PRO* 4.4 5.0 - - + +
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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