Contacts of the helix formed by residues 266 - 279 (chain B) in PDB entry 1ISS
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 GLY 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B ASN 3.4 2.5 + - - -
265B ALA* 1.3 79.6 - - - +
267B GLU* 1.3 66.8 + - - -
268B LYS* 3.0 6.0 + - - -
269B SER* 3.1 17.5 + - - -
270B PHE* 3.3 9.2 + - - -
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Residues in contact with GLU 267 (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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266B GLY* 1.3 72.0 - - - -
268B LYS* 1.3 62.2 + - - +
270B PHE* 3.1 13.3 + - + +
271B ASP* 2.9 29.0 + - - +
301B SER* 5.1 0.9 + - - +
305B ARG* 3.2 46.5 + - - +
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Residues in contact with LYS 268 (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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266B GLY* 3.0 3.3 - - - -
267B GLU* 1.3 77.2 - - - +
269B SER* 1.3 66.1 + - - +
271B ASP* 2.9 22.0 + - - +
272B ARG* 2.9 15.8 + - - +
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Residues in contact with SER 269 (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 ILE* 3.9 9.6 - - - +
265B ALA* 3.9 23.6 - - - +
266B GLY* 3.1 13.6 + - - -
268B LYS* 1.3 79.0 - - - +
270B PHE* 1.3 64.2 + - - +
272B ARG* 3.3 32.6 + - - +
273B LEU* 2.9 21.0 + - - +
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Residues in contact with PHE 270 (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 ILE* 3.5 33.9 - - + -
262B TYR 4.6 3.6 - - - -
263B SER 4.6 13.2 - - - -
265B ALA 4.1 11.4 - - - -
266B GLY 3.3 10.9 + - - -
267B GLU* 3.1 18.1 + - + +
268B LYS 2.9 1.4 + - - -
269B SER* 1.3 78.0 - - - +
271B ASP* 1.3 54.2 + - - +
273B LEU* 2.6 44.1 + - + +
274B LEU* 2.9 6.6 + - - +
294B MET 4.4 7.0 - - - -
295B THR* 4.0 20.6 - - + -
298B GLY* 3.4 41.1 - - - +
299B LEU* 4.7 1.3 - - - -
301B SER* 5.7 0.7 - - - -
302B ALA* 4.3 6.2 - - + +
305B ARG* 4.0 10.8 - - - +
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Residues in contact with ASP 271 (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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267B GLU* 2.9 19.7 + - - +
268B LYS* 2.9 12.3 + - - +
270B PHE* 1.3 72.0 - - - +
272B ARG* 1.3 64.5 + - - +
274B LEU* 3.1 12.3 + - - +
275B ARG* 2.9 23.4 + - - +
302B ALA* 4.0 14.9 - - - +
305B ARG* 3.0 38.6 + - - +
306B LEU* 5.0 5.4 + - - +
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Residues in contact with ARG 272 (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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268B LYS* 2.9 11.9 + - - +
269B SER* 3.3 33.8 + - - +
271B ASP* 1.3 75.5 - - - +
273B LEU* 1.3 63.2 + - - +
275B ARG* 3.2 33.4 + - - +
276B LYS* 3.0 23.6 + - - +
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Residues in contact with LEU 273 (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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230B VAL* 4.4 25.6 - - + -
257B HIS* 5.4 1.7 + - + +
259B ASP* 3.6 41.5 - - + +
260B LYS 5.1 2.2 - - - +
261B ILE* 4.2 25.1 - - + -
269B SER 2.9 12.0 + - - +
270B PHE* 2.6 32.1 + - + +
272B ARG* 1.3 70.8 - - - +
274B LEU* 1.3 64.8 + - - +
276B LYS* 3.3 4.6 + - - +
277B LEU* 3.0 25.8 + - + +
295B THR* 5.4 2.9 - - + -
299B LEU* 4.3 21.1 - - + -
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Residues in contact with LEU 274 (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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270B PHE 2.9 9.4 + - - +
271B ASP* 3.4 9.9 - - - +
273B LEU* 1.3 75.4 - - - +
275B ARG* 1.3 56.6 + - - +
277B LEU* 2.8 8.6 + - + +
278B ARG* 2.7 47.2 + - + +
299B LEU* 4.4 15.0 - - + +
302B ALA* 2.9 40.4 - - + +
303B MET* 3.8 25.4 - - + +
306B LEU* 3.8 26.0 - - + -
308B VAL* 4.5 3.6 - - + -
312B PHE* 4.1 22.0 - - + -
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Residues in contact with ARG 275 (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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271B ASP 2.9 13.2 + - - +
272B ARG* 3.2 37.1 + - - +
274B LEU* 1.3 79.2 - - - +
276B LYS* 1.3 67.1 + - - +
277B LEU 2.6 2.6 + - - -
278B ARG* 2.8 15.5 + - - +
279B GLU* 3.1 34.0 + - + +
306B LEU* 6.2 1.3 - - - -
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Residues in contact with LYS 276 (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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257B HIS* 3.4 39.3 + - + +
259B ASP* 5.1 4.3 - - - +
272B ARG* 3.0 9.9 + - + +
273B LEU* 3.7 9.4 - - - +
275B ARG* 1.3 79.1 - - - +
277B LEU* 1.3 61.1 - - - +
279B GLU* 4.0 20.8 - - - +
280B ARG* 4.1 7.1 + - - +
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Residues in contact with LEU 277 (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 SER* 3.2 27.1 - - - +
230B VAL* 4.0 21.8 - - + -
257B HIS* 4.5 14.1 - - + -
273B LEU* 3.0 14.8 + - + +
274B LEU* 2.8 12.2 + - + +
275B ARG 2.6 4.4 + - - -
276B LYS* 1.3 73.4 - - - +
278B ARG* 1.3 64.3 + - - +
280B ARG* 3.2 20.6 + - - +
284B ALA* 4.4 4.3 - - + +
287B VAL* 3.6 28.5 - - + -
299B LEU* 4.8 20.9 - - + -
312B PHE* 4.2 21.5 - - + -
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Residues in contact with ARG 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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274B LEU* 2.7 32.1 + - + +
275B ARG* 2.8 9.8 + - - +
277B LEU* 1.3 67.3 - - - +
279B GLU* 1.3 54.5 + - - +
280B ARG 2.7 17.0 + - - -
281B LEU* 3.0 26.4 - - + +
306B LEU* 3.2 35.8 - - - +
308B VAL* 4.0 9.4 - - - +
311B GLU* 3.2 35.9 + - - -
312B PHE* 3.7 23.6 - - + -
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Residues in contact with GLU 279 (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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275B ARG* 3.1 38.1 + - + +
276B LYS* 4.0 13.7 - - - +
278B ARG* 1.3 76.5 - - + +
280B ARG* 1.3 64.3 + - + +
281B LEU 3.6 5.6 + - - +
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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