Contacts of the helix formed by residues 264 - 275 (chain B) in PDB entry 3C3A
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 ILE 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B VAL* 5.5 0.2 - - + -
220B ILE* 3.3 37.0 - - + -
243B PHE* 5.0 0.4 - - + -
260B GLU 4.2 9.2 - - - +
261B GLY* 3.0 18.4 + - - +
263B LYS* 1.3 76.9 - - + +
265B VAL* 1.3 72.7 + - + +
266B LYS 3.1 3.6 - - - -
267B ASP* 2.9 25.8 + - + +
268B LEU* 2.6 51.3 + - + +
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B THR* 3.8 27.6 - - + +
243B PHE* 3.8 36.6 - - + -
246B VAL* 4.3 11.7 - - + -
247B LEU* 4.1 18.8 - - + -
261B GLY 3.7 14.1 - - - +
262B ALA* 3.7 12.8 - - - +
263B LYS 3.6 0.8 - - - -
264B ILE* 1.3 81.8 - - + +
266B LYS* 1.3 58.9 + - - +
268B LEU* 3.2 6.3 + - - +
269B MET* 2.8 44.2 + - + +
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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
----------------------------------------------------------
246B VAL* 5.6 4.4 - - + +
247B LEU* 6.0 1.6 - - - -
262B ALA 4.8 1.2 + - - -
263B LYS 4.6 6.7 + - - +
264B ILE 3.0 1.4 + - - -
265B VAL* 1.3 82.0 - - - +
267B ASP* 1.3 69.5 + - - +
269B MET* 3.3 5.5 + - - +
270B SER* 2.9 30.1 + - - -
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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
----------------------------------------------------------
263B LYS 5.1 3.0 - - - +
264B ILE* 2.9 20.3 + - + +
266B LYS* 1.3 89.4 + - - +
268B LEU* 1.3 53.5 + - + +
270B SER* 3.0 9.2 + - - -
271B LYS* 2.8 35.4 + - - +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ILE* 3.8 16.8 - - + +
223B ILE* 3.9 22.4 - - + -
224B ASN* 3.9 33.7 - - + +
227B LEU* 3.4 19.1 - - + +
243B PHE* 3.8 24.0 - - + -
264B ILE* 2.6 43.9 + - + +
265B VAL* 3.4 7.6 - - - +
267B ASP* 1.3 78.6 - - + +
269B MET* 1.3 58.2 + - - +
271B LYS* 3.4 2.8 + - + -
272B ALA* 3.1 23.7 + - - +
279B ILE* 5.6 0.3 - - - +
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Residues in contact with MET 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B PHE* 3.9 25.8 - - + -
247B LEU* 3.7 38.6 - - + -
265B VAL* 2.8 28.0 + - + +
266B LYS* 3.9 5.6 - - - +
268B LEU* 1.3 73.2 - - - +
270B SER* 1.3 62.2 + - - +
272B ALA* 4.0 4.0 - - + +
273B GLU* 3.3 25.1 + - - +
279B ILE* 4.1 38.8 - - + -
281B LEU* 5.3 1.3 - - + -
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LYS* 2.9 19.2 + - - -
267B ASP* 3.0 13.0 + - - -
269B MET* 1.3 76.7 - - - +
271B LYS* 1.3 59.2 + - - +
273B GLU* 3.4 6.5 - - - +
274B LYS* 2.8 46.5 + - - +
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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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224B ASN* 2.8 40.9 + - - +
227B LEU* 4.1 12.6 - - + -
228B ASP* 2.7 44.4 + - - -
267B ASP 2.8 18.6 + - - +
268B LEU* 3.7 6.7 - - + +
270B SER* 1.3 74.0 - - - +
272B ALA* 1.3 56.8 + - - +
274B LYS* 3.2 13.6 + - + +
275B ASN* 2.9 47.6 + - - +
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Residues in contact with ALA 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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227B LEU* 3.9 10.5 - - + +
268B LEU 3.1 16.6 + - - +
269B MET* 4.0 7.2 - - + +
271B LYS* 1.3 76.4 - - - +
273B GLU* 1.3 52.4 + - - +
275B ASN 3.4 0.3 + - - -
276B GLY 2.8 11.6 + - - -
277B VAL* 2.7 54.1 + - + +
279B ILE* 3.8 27.6 - - + -
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Residues in contact with GLU 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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269B MET 3.3 17.5 + - - +
270B SER* 3.4 8.3 - - - +
272B ALA* 1.3 75.7 - - - +
274B LYS* 1.3 65.6 + - - +
275B ASN 3.2 0.5 + - - -
276B GLY* 3.3 10.9 + - - -
277B VAL 5.2 1.1 - - - -
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Residues in contact with LYS 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 SER* 2.8 36.0 + - - +
271B LYS* 3.2 17.0 - - + +
273B GLU* 1.3 74.2 + - - +
275B ASN* 1.3 66.8 + - - +
276B GLY 3.7 0.5 + - - -
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Residues in contact with ASN 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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227B LEU* 3.1 28.0 + - - +
228B ASP* 3.8 8.5 + - - +
230B VAL 4.8 3.0 - - - +
231B ASN* 5.9 0.2 - - - -
271B LYS* 2.9 45.2 + - - +
274B LYS* 1.3 86.3 - - - +
276B GLY* 1.3 63.9 + - - +
277B VAL* 3.3 12.4 + - + +
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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
------------------------------------------------------------
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