Contacts of the helix formed by residues 294 - 305 (chain B) in PDB entry 1SVU
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 SER 294 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B TYR* 5.9 1.3 - - - -
292B HIS* 2.9 13.8 + - - -
293B PRO* 1.3 73.7 - - - +
295B THR* 1.3 54.9 + - - +
296B SER* 3.0 8.5 + - - -
297B GLN* 2.4 55.6 + - - +
298B ALA 2.8 10.9 + - - -
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Residues in contact with THR 295 (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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205B LEU* 5.8 2.9 - - - +
276B PRO* 3.5 21.1 - - - +
292B HIS 4.7 0.2 - - - -
293B PRO 2.9 10.2 + - - -
294B SER* 1.3 70.0 - - - +
296B SER* 1.3 67.0 + - - +
298B ALA* 3.9 10.9 - - - -
299B TYR* 3.1 37.6 + - - -
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Residues in contact with SER 296 (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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261B LYS* 5.1 5.4 - - - +
294B SER* 2.8 7.3 + - - -
295B THR* 1.3 84.5 - - - +
297B GLN* 1.3 65.4 + - - +
299B TYR* 3.3 12.1 - - - +
300B LYS* 3.2 20.4 + - - +
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Residues in contact with GLN 297 (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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42B ASP* 5.0 0.9 - - - +
44B TYR* 3.2 54.1 - - + -
292B HIS* 3.5 19.7 - - + +
294B SER* 2.4 38.9 + - - +
296B SER* 1.3 71.2 + - - +
298B ALA* 1.3 51.6 + - - +
299B TYR 2.7 15.2 + - - -
300B LYS* 2.7 30.8 + - - +
301B GLN* 2.8 25.0 + - - +
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Residues in contact with ALA 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B PRO* 3.7 26.0 - - + -
291B VAL* 4.5 3.6 - - + -
292B HIS* 3.5 39.5 - - + +
294B SER 2.8 8.9 + - - +
295B THR* 3.9 7.0 - - - +
297B GLN* 1.3 72.8 - - - +
299B TYR* 1.3 58.9 + - - +
301B GLN* 4.2 4.0 - - - -
302B PHE* 2.8 39.4 + - + +
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Residues in contact with TYR 299 (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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205B LEU* 3.2 19.4 - - + +
252B SER 4.6 2.3 - - - +
253B ALA* 4.5 1.9 - - - -
260B ALA 5.0 0.2 - - - -
261B LYS* 3.8 26.7 - - + -
262B THR* 3.6 13.8 - - + +
273B LYS* 3.7 22.6 - - + +
274B LEU 2.4 28.0 + - - -
276B PRO* 3.1 33.0 - - + +
279B CYS* 3.6 21.6 - - - -
295B THR* 3.1 25.6 + - - +
296B SER* 3.3 12.8 - - - +
297B GLN 2.7 1.8 + - - -
298B ALA* 1.3 76.0 - - - +
300B LYS* 1.3 65.6 + - - +
302B PHE* 3.5 2.9 + - - +
303B GLY* 2.9 21.0 + - - -
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Residues in contact with LYS 300 (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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253B ALA* 3.1 33.8 - - + +
254B TYR* 6.1 5.6 - - + +
261B LYS* 4.6 3.5 - - + +
296B SER 3.2 7.4 + - - +
297B GLN* 2.7 28.4 + - - +
299B TYR* 1.3 72.9 - - - +
301B GLN* 1.3 67.0 + - - +
303B GLY 2.8 11.8 + - - -
304B ASN* 3.1 6.4 + - - +
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Residues in contact with GLN 301 (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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21B LEU* 3.1 39.0 - - + +
42B ASP* 4.1 3.0 + - - -
44B TYR* 3.0 33.9 - - - +
45B ALA* 3.3 16.9 - - - +
48B VAL* 3.3 15.8 - - - +
292B HIS* 3.4 14.8 - - - +
297B GLN* 2.8 23.5 + - - +
298B ALA* 4.1 3.4 - - - +
300B LYS* 1.3 72.4 - - + +
302B PHE* 1.3 55.1 + - - +
304B ASN* 2.5 35.2 + - - +
305B SER 2.9 10.0 + - - -
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Residues in contact with PHE 302 (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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21B LEU* 3.7 20.4 - - + -
251B LEU* 5.0 2.6 - - + +
276B PRO 3.8 11.7 - - - -
279B CYS* 4.2 15.5 - - + -
280B ALA* 3.1 40.4 - - + -
283B MET* 2.9 46.8 - - + +
285B TYR* 3.8 29.6 - + - -
289B TYR* 4.9 5.8 - + - -
291B VAL* 3.3 33.4 - - + -
292B HIS 5.4 0.2 - - - -
298B ALA* 2.8 30.9 + - + +
299B TYR 3.9 2.5 - - - +
301B GLN* 1.3 80.0 - - - +
303B GLY* 1.3 58.2 + - - +
304B ASN 3.1 0.5 + - - -
305B SER* 3.6 2.6 + - - +
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Residues in contact with GLY 303 (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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163B ARG* 3.1 19.8 + - - -
165B ARG* 5.8 0.3 + - - -
251B LEU* 3.7 16.4 - - - +
252B SER* 3.8 2.1 - - - -
253B ALA* 3.3 29.9 + - - +
299B TYR 2.9 9.7 + - - -
300B LYS 2.8 10.1 + - - -
302B PHE* 1.3 76.3 - - - +
304B ASN* 1.3 57.4 + - - +
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Residues in contact with ASN 304 (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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163B ARG* 4.5 0.2 + - - -
165B ARG* 4.4 13.3 + - - -
253B ALA* 2.8 27.0 - - - +
254B TYR* 5.3 11.8 - - - -
300B LYS* 3.7 9.1 + - - +
301B GLN* 2.5 23.2 + - - +
303B GLY* 1.3 73.0 - - - +
305B SER* 1.3 69.9 + - - +
306B VAL* 5.0 0.3 - - - +
402B SAH 4.1 41.2 - - + +
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.7 18.6 - - - -
23B GLY* 4.0 0.3 - - - -
163B ARG* 3.0 17.3 + - - -
165B ARG* 5.2 0.3 + - - -
283B MET* 3.2 5.7 - - - +
285B TYR* 2.2 36.9 + - - -
301B GLN 2.9 9.6 + - - -
302B PHE* 3.6 6.7 + - - -
304B ASN* 1.3 88.9 - - - +
306B VAL* 1.3 64.4 + - - +
402B SAH 2.4 32.7 + - - -
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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