Contacts of the strand formed by residues 243 - 249 (chain A) in PDB entry 3SN6
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 ALA 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ARG 3.6 0.2 + - - -
43A LEU* 3.3 9.8 - - + +
44A LEU 3.0 9.5 + - - -
241A VAL* 2.9 22.0 - - - +
242A THR* 1.3 85.7 + - - +
244A ILE* 1.3 61.1 + - - +
245A ILE 3.8 0.7 - - - +
285A ILE* 4.4 0.9 - - - -
286A SER 3.4 7.9 - - - +
288A ILE* 3.9 20.9 - - + -
379A CYS* 4.1 10.5 - - - -
382A ILE* 3.5 23.1 - - + -
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Residues in contact with ILE 244 (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 LEU* 3.5 26.7 - - + +
46A LEU* 4.2 18.8 - - + -
235A ILE* 5.7 0.4 - - + -
241A VAL* 4.0 9.0 - - + -
243A ALA* 1.3 72.9 - - - +
245A ILE* 1.3 68.1 + - - +
246A PHE* 3.4 6.1 + - + +
276A ILE* 3.9 29.2 - - + -
282A LEU* 4.1 19.1 - - + -
285A ILE* 3.4 26.0 - - + -
286A SER 2.9 12.5 + - - +
287A VAL* 3.3 15.0 - - + +
288A ILE 2.9 24.0 + - - -
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Residues in contact with ILE 245 (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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43A LEU* 3.7 30.7 - - + -
44A LEU 2.8 12.4 + - - +
45A LEU* 3.5 22.0 - - + -
46A LEU* 2.9 30.0 + - - +
56A ILE* 5.7 4.3 - - + -
212A PHE* 6.4 0.4 - - + -
221A MET* 4.3 20.4 - - - -
243A ALA 3.8 0.9 + - - +
244A ILE* 1.3 70.9 - - - +
246A PHE* 1.3 63.0 + - - +
247A VAL* 4.9 0.7 - - + +
288A ILE* 3.4 17.0 - - + +
290A PHE* 3.7 28.0 - - + -
375A VAL* 3.7 27.6 - - + -
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Residues in contact with PHE 246 (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 LEU* 3.4 33.7 - - + -
47A GLY* 4.4 5.2 - - - -
48A ALA 4.8 0.9 - - - -
244A ILE* 4.3 4.9 - - + +
245A ILE* 1.3 74.5 - - - +
247A VAL* 1.3 59.5 + - - +
248A VAL* 3.4 26.0 - - + -
269A ALA* 3.5 15.9 - - - -
272A LEU* 4.0 19.3 - - + -
273A PHE* 3.4 48.2 - + + -
276A ILE* 5.2 4.9 - - + -
287A VAL* 3.7 19.3 - - + -
288A ILE 2.9 7.9 + - - +
289A LEU* 3.3 19.2 - - + +
290A PHE 2.9 24.3 + - - -
345A PHE* 4.3 4.0 - + - -
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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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45A LEU* 4.0 14.6 - - + -
46A LEU 2.9 15.8 + - - +
47A GLY* 3.3 17.0 - - - -
48A ALA 4.1 0.2 + - - -
51A SER* 3.4 17.9 + - - +
53A LYS* 3.7 27.8 - - + -
56A ILE* 4.3 12.6 - - + -
246A PHE* 1.3 73.7 - - - +
248A VAL* 1.3 61.8 + - - +
290A PHE* 3.2 23.6 - - + +
292A ASN* 4.0 28.7 - - + +
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Residues in contact with VAL 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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48A ALA* 4.9 6.5 - - + +
51A SER* 4.1 1.6 - - - -
246A PHE* 3.4 42.6 - - + -
247A VAL* 1.3 75.5 - - - +
249A ALA* 1.3 65.3 + - - +
266A LEU* 5.2 1.1 - - + -
269A ALA* 3.4 21.8 - - + -
289A LEU* 3.9 6.1 - - + -
290A PHE 2.9 5.7 + - - -
291A LEU* 3.4 28.6 - - + +
292A ASN* 2.9 22.8 + - - -
345A PHE* 3.5 20.2 - - + -
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Residues in contact with ALA 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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49A GLY 4.8 4.0 - - - +
50A GLU 4.8 1.1 - - - +
51A SER* 3.8 15.5 + - - +
248A VAL* 1.3 73.2 - - - +
250A SER* 1.3 61.8 + - - +
251A SER 4.3 0.9 - - - +
252A SER* 2.9 39.4 + - - -
266A LEU* 4.4 8.0 - - - +
292A ASN* 3.9 10.1 - - + -
293A LYS* 3.5 36.1 - - + +
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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