Contacts of the helix formed by residues 264 - 272 (chain B) in PDB entry 4YC3
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 GLU 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU* 3.5 20.9 - - - +
252B PHE* 4.4 0.9 - - - -
262B PRO 5.0 3.4 - - - +
263B PRO* 1.3 77.6 - - - +
265B ILE* 1.3 66.5 + - - +
266B GLY* 4.2 6.4 - - - +
267B ASP* 2.8 33.2 + - - +
268B PHE* 3.7 4.7 + - - -
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Residues in contact with ILE 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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41A GLU* 3.7 27.1 - - + +
42A GLU* 3.0 19.4 + - - +
252B PHE* 3.7 30.1 - - + -
264B GLU* 1.3 72.6 - - - +
266B GLY* 1.3 64.1 + - - +
268B PHE* 3.2 6.5 + - + +
269B ALA* 3.1 20.3 + - - +
278B LYS* 3.5 47.3 - - + +
281B ILE* 3.8 28.0 - - + +
282B ARG* 4.2 11.4 - - + -
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Residues in contact with GLY 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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264B GLU* 3.2 5.4 - - - +
265B ILE* 1.3 81.0 - - - +
267B ASP* 1.3 64.0 + - - +
269B ALA* 3.4 3.6 + - - +
270B PHE* 3.1 24.4 + - - +
278B LYS* 4.3 17.0 - - - +
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Residues in contact with ASP 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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215B PHE* 3.5 34.3 - - + -
263B PRO* 3.6 12.7 - - + +
264B GLU* 2.8 41.7 + - - +
266B GLY* 1.3 76.2 - - - +
268B PHE* 1.3 62.2 + - - +
270B PHE* 3.4 7.0 + - - +
271B VAL* 3.1 17.8 + - - +
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Residues in contact with PHE 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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211B VAL* 4.5 4.5 - - + -
215B PHE* 3.8 18.8 - + - -
217B LEU* 4.7 0.9 - - + -
248B VAL* 4.1 22.6 - - + +
251B MET* 3.8 27.6 - - + -
252B PHE* 3.5 43.5 - + + -
255B SER* 3.8 20.6 - - - -
263B PRO* 3.8 33.7 - - + -
264B GLU 3.7 9.2 - - - -
265B ILE* 3.2 7.5 + - + +
267B ASP* 1.3 75.1 - - - +
269B ALA* 1.3 67.3 + - - +
271B VAL* 3.4 20.0 + - + +
272B THR* 3.6 10.9 + - - +
281B ILE* 4.2 12.7 - - + +
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Residues in contact with ALA 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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265B ILE 3.1 12.8 + - - +
266B GLY* 3.8 6.7 - - - +
267B ASP 3.4 0.2 - - - -
268B PHE* 1.3 74.1 - - - +
270B PHE* 1.3 62.7 + - - +
272B THR* 2.7 27.5 + - - -
274B ASN* 3.4 18.1 + - - +
276B TYR 3.8 15.9 - - - +
277B THR* 4.9 0.4 - - - -
278B LYS* 4.3 19.1 - - + +
281B ILE* 3.9 15.3 - - + +
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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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214B LYS* 5.2 16.8 - - - -
266B GLY 3.1 17.9 + - - +
267B ASP* 3.6 8.3 - - - +
269B ALA* 1.3 76.9 - - - +
271B VAL* 1.3 60.9 + - - +
273B ASP* 3.0 25.6 + - - +
274B ASN* 3.6 22.4 - - - +
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Residues in contact with VAL 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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207B TRP* 3.5 31.0 + - + +
211B VAL* 4.1 29.4 - - + -
214B LYS* 3.9 33.0 - - + -
215B PHE* 4.1 7.2 - - + -
248B VAL* 4.7 3.4 - - + -
267B ASP 3.1 14.7 + - - +
268B PHE* 3.4 19.3 - - + +
269B ALA 3.1 0.6 - - - -
270B PHE* 1.3 79.9 - - + +
272B THR* 1.3 57.2 + - - +
273B ASP* 3.1 9.0 + - - +
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Residues in contact with THR 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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207B TRP* 4.1 9.0 - - + -
244B GLN* 4.0 16.8 + - - +
248B VAL* 3.5 34.8 - - + -
268B PHE 3.6 8.3 - - - +
269B ALA* 2.7 19.0 + - - -
271B VAL* 1.3 77.5 - - - +
273B ASP* 1.3 58.2 + - - +
275B THR* 2.7 39.7 + - - -
276B TYR* 3.6 28.8 + - + -
281B ILE* 5.9 0.4 - - + -
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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