Contacts of the strand formed by residues 276 - 282 (chain B) in PDB entry 3S9L
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 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B VAL* 4.2 4.5 - - + +
253B SER 3.8 12.1 - - - +
255B VAL* 4.6 6.5 - - + -
271B ALA* 3.2 37.5 + - + +
272B GLU* 4.4 4.5 - - - +
275B ASN* 1.3 76.0 - - - +
277B ILE* 1.3 75.0 + - - +
278B GLY 4.4 10.3 - - - +
279B VAL* 4.9 2.0 - - + -
332B ILE* 4.6 13.7 - - + +
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Residues in contact with ILE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B VAL* 3.4 42.9 - - + +
229B THR 3.9 18.6 - - - +
230B GLY* 5.7 0.4 - - - -
252B GLY* 3.4 19.1 - - - +
253B SER* 3.3 27.1 + - - +
254B ILE* 3.9 12.1 - - + -
275B ASN* 5.0 0.9 - - + +
276B ALA* 1.3 84.6 - - - +
278B GLY* 1.3 61.1 + - - +
332B ILE* 3.3 15.1 - - - +
333B PRO* 4.0 1.4 - - - +
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Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B VAL* 4.6 6.5 - - - -
254B ILE* 3.7 21.7 - - - +
255B VAL* 3.0 22.9 + - - +
276B ALA* 4.4 0.2 - - - +
277B ILE* 1.3 82.3 + - - +
279B VAL* 1.3 71.5 + - - +
332B ILE* 3.5 8.2 - - - +
333B PRO 4.0 4.5 - - - -
375B LEU* 5.5 2.5 - - - -
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Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 4.5 1.2 - - - +
255B VAL* 3.4 19.3 - - + +
257B VAL* 4.3 22.0 - - + -
267B LYS* 5.2 2.0 - - + -
268B VAL* 4.1 23.3 - - + +
271B ALA* 3.9 18.6 - - + -
276B ALA* 4.9 0.7 - - + -
278B GLY* 1.3 80.5 - - - +
280B LEU* 1.3 63.0 + - - +
281B ILE* 5.0 0.7 - - + +
332B ILE* 4.3 12.3 - - + -
333B PRO 3.4 7.3 + - - +
334B VAL* 3.2 26.9 - - + +
335B GLN 3.1 23.9 + - - -
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B VAL* 6.6 0.2 - - + -
232B LEU* 5.8 1.3 - - + -
254B ILE* 5.6 4.5 - - + -
255B VAL 3.0 11.9 + - - +
256B ILE* 3.0 17.8 - - + +
257B VAL* 2.7 33.1 + - - -
279B VAL* 1.3 75.8 - - - +
281B ILE* 1.3 54.9 + - - +
335B GLN* 3.3 12.3 - - + +
337B ILE* 4.5 18.8 - - + -
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Residues in contact with ILE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL* 3.5 21.3 - - + +
259B ALA 5.3 3.8 - - - +
264B PHE* 4.8 16.2 - - + -
267B LYS* 5.0 2.0 - - + -
279B VAL* 4.2 1.8 - - + +
280B LEU* 1.3 71.5 - - - +
282B TYR* 1.3 59.6 + - - +
297B PHE* 2.9 31.9 - - + -
334B VAL* 5.2 6.8 - - + +
335B GLN 3.3 6.6 + - - -
336B THR* 3.5 8.4 - - + -
337B ILE* 3.3 17.3 + - - -
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Residues in contact with TYR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B ILE* 4.4 8.7 - - + -
257B VAL 2.8 10.3 + - - +
258B ARG* 3.3 26.9 - - + +
259B ALA 3.7 2.6 + - - -
281B ILE* 1.3 75.7 - - - +
283B MET* 1.3 63.5 + - - +
284B ASP 4.0 0.5 + - - -
297B PHE* 3.7 6.3 - - - -
337B ILE* 3.8 27.8 - - + +
338B SER 4.6 0.2 - - - +
342B ALA* 4.1 20.9 - - + -
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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