Contacts of the helix formed by residues 262 - 274 (chain B) in PDB entry 1PUF
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 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B TYR* 4.7 0.4 + - - -
260B TYR 3.4 3.9 + - - -
261B PRO* 1.3 76.0 - - - +
263B GLU* 1.3 66.3 + - - +
264B GLU* 3.3 21.2 + - - +
265B ALA* 3.0 23.0 + - - +
266B LYS* 2.8 20.4 + - - +
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Residues in contact with GLU 263 (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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262B SER* 1.3 72.9 - - - +
264B GLU* 1.3 74.1 + - + +
266B LYS* 3.0 15.0 + - - +
267B GLU* 3.0 32.8 + - - +
277B VAL* 5.3 3.2 - - + +
28E G 5.4 7.6 - - - +
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Residues in contact with GLU 264 (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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262B SER* 3.3 18.1 + - - +
263B GLU* 1.3 91.5 + - + +
265B ALA* 1.3 61.2 + - - +
267B GLU* 3.3 16.8 + - - +
268B GLU* 3.3 21.1 + - - +
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Residues in contact with ALA 265 (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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251B TYR* 3.9 17.7 - - + +
261B PRO* 3.8 9.9 - - + -
262B SER* 3.0 29.9 + - - +
264B GLU* 1.3 74.8 - - - +
266B LYS* 1.3 64.4 + - - +
268B GLU* 3.5 6.2 + - - +
269B LEU* 3.2 29.3 + - - +
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Residues in contact with LYS 266 (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 PRO* 3.5 37.9 - - + +
262B SER 2.8 15.4 + - - +
263B GLU* 3.5 12.8 - - - +
265B ALA* 1.3 74.7 - - - +
267B GLU* 1.3 60.5 + - - +
269B LEU* 3.4 2.4 + - - +
270B ALA* 2.8 30.8 + - - +
277B VAL* 4.0 20.0 - - + -
280B VAL* 3.9 20.2 - - + +
281B SER* 2.8 37.4 + - - +
284B PHE* 6.0 1.8 - - - -
28E G 5.1 1.2 - - - -
29E T 2.8 29.4 + - - -
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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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263B GLU* 3.0 19.1 + - - +
264B GLU* 3.6 19.9 - - - +
265B ALA 3.3 0.4 - - - -
266B LYS* 1.3 76.8 - - - +
268B GLU* 1.3 57.3 + - - +
270B ALA* 3.3 3.5 + - - +
271B LYS* 2.9 32.4 + - - +
277B VAL* 3.6 23.6 - - + -
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Residues in contact with GLU 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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264B GLU 3.3 12.2 + - - +
265B ALA* 4.0 6.5 - - - +
267B GLU* 1.3 75.1 - - - +
269B LEU* 1.3 67.5 + - + +
271B LYS* 3.2 18.5 + - - +
272B LYS* 3.0 49.8 + - - +
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Residues in contact with LEU 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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247B ILE* 3.7 28.3 - - + +
248B LEU* 4.6 7.9 - - + -
251B TYR* 3.8 47.3 - - + -
261B PRO* 4.5 4.3 - - + -
265B ALA 3.2 23.9 + - - +
266B LYS 3.9 2.7 - - - +
268B GLU* 1.3 74.5 - - + +
270B ALA* 1.3 68.5 + - - +
271B LYS 3.1 0.2 + - - -
272B LYS* 3.1 13.2 + - - +
273B CYS* 2.9 29.8 + - - -
280B VAL* 4.4 13.5 - - + -
284B PHE* 4.0 22.9 - - + -
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Residues in contact with ALA 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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266B LYS 2.8 19.2 + - - +
267B GLU 3.4 6.1 - - - +
269B LEU* 1.3 76.7 - - - +
271B LYS* 1.3 56.5 + - - +
274B GLY* 3.0 24.1 + - - -
275B ILE* 3.1 31.1 + - - +
276B THR 3.9 10.5 - - - -
277B VAL* 3.9 9.9 - - + +
280B VAL* 3.7 17.2 - - + +
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Residues in contact with LYS 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 16.7 + - + +
268B GLU* 3.4 24.1 + - - +
269B LEU 3.0 0.2 - - - -
270B ALA* 1.3 75.6 - - + +
272B LYS* 1.3 65.8 + - + +
273B CYS 3.2 0.9 + - - -
274B GLY* 3.3 10.6 + - - -
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Residues in contact with LYS 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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244B ALA* 5.8 0.2 - - - -
247B ILE* 3.9 46.7 - - + +
268B GLU* 3.0 41.1 + - - +
269B LEU* 3.8 15.2 - - - +
271B LYS* 1.3 76.7 - - + +
273B CYS* 1.3 60.7 + - - +
274B GLY 3.8 0.2 + - - -
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Residues in contact with CYS 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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241B ASN* 4.7 8.1 + - - -
244B ALA* 3.7 47.8 - - + +
247B ILE* 3.9 20.4 - - - -
248B LEU* 4.0 18.6 - - - -
269B LEU 2.9 19.6 + - - +
272B LYS* 1.3 77.8 - - - +
274B GLY* 1.3 61.5 + - - +
275B ILE* 3.8 23.8 - - + +
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Residues in contact with GLY 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 ALA 3.0 7.0 + - - -
271B LYS 3.3 9.5 + - - -
272B LYS 3.8 0.2 + - - -
273B CYS* 1.3 78.7 - - - +
275B ILE* 1.3 62.4 + - - +
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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