Contacts of the helix formed by residues 261 - 275 (chain B) in PDB entry 3DL2
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 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260B GLN* 1.3 76.7 - - - +
262B TYR* 1.3 64.3 + - - +
263B LEU* 4.2 5.0 + - - +
264B ASP* 3.2 33.7 + - - +
265B VAL* 3.1 19.3 + - - +
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Residues in contact with TYR 262 (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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260B GLN 4.7 0.2 - - - -
261B SER* 1.3 74.2 - - - +
263B LEU* 1.3 62.7 + - - +
265B VAL* 3.4 11.4 + - + +
266B VAL* 3.1 28.5 + - + +
295B PRO* 3.5 35.7 - - + +
298B ILE* 4.9 1.2 - - - +
465B LEU* 3.6 33.4 - - + +
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Residues in contact with LEU 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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261B SER* 3.3 4.6 + - - +
262B TYR* 1.3 79.3 - - - +
264B ASP* 1.3 65.2 + - - +
266B VAL* 3.1 7.9 - - - +
267B GLN* 3.0 31.6 + - + +
465B LEU* 3.8 27.6 - - + +
468B GLN* 3.8 39.7 - - + +
469B LEU* 4.0 19.1 - - + -
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Residues in contact with ASP 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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260B GLN* 5.0 7.8 - - + -
261B SER* 3.2 29.2 + - - +
263B LEU* 1.3 82.8 - - - +
265B VAL* 1.3 61.2 + - + +
267B GLN* 3.7 6.4 - - - +
268B SER* 3.0 28.6 + - - -
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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
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255B SER* 5.6 5.1 - - - -
260B GLN* 3.6 33.4 - - + +
261B SER 3.1 15.5 + - - +
262B TYR* 3.7 16.2 - - + +
263B LEU 3.3 0.2 - - - -
264B ASP* 1.3 73.8 - - - +
266B VAL* 1.3 64.9 + - - +
268B SER* 2.6 25.7 + - - +
269B ASN* 3.2 7.9 + - + +
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Residues in contact with VAL 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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262B TYR* 3.1 19.2 + - + +
263B LEU* 3.1 26.0 - - + +
265B VAL* 1.3 77.5 - - - +
267B GLN* 1.3 51.0 + - - +
269B ASN* 3.1 8.3 + - - +
270B VAL* 2.8 34.5 + - + +
295B PRO* 4.1 25.4 - - + -
298B ILE* 3.8 28.9 - - + -
299B MET* 4.6 2.0 - - - -
465B LEU* 4.1 18.2 - - + -
469B LEU* 3.8 18.2 - - + -
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Residues in contact with GLN 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 3.0 21.3 + - + +
264B ASP* 3.7 8.7 - - - +
265B VAL 3.3 0.2 - - - -
266B VAL* 1.3 77.3 - - - +
268B SER* 1.3 52.0 + - - +
270B VAL* 3.2 7.0 + - - +
271B ASP* 2.7 71.7 + - - +
468B GLN 4.7 1.4 - - - +
469B LEU* 3.4 16.0 - - + +
470B LYS* 2.8 55.8 + - + +
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B SER* 2.8 27.2 + - - +
264B ASP 3.0 13.9 + - - -
265B VAL* 2.6 25.2 + - - +
267B GLN* 1.3 74.6 - - - +
269B ASN* 1.3 60.3 + - - +
271B ASP* 3.5 8.8 + - - +
272B MET* 3.1 21.5 + - - +
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Residues in contact with ASN 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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253B VAL 4.2 3.0 + - - -
254B ASN* 3.2 20.9 - - - +
255B SER* 3.1 31.3 - - - +
265B VAL* 3.2 7.6 + - + +
266B VAL* 3.1 12.4 + - - +
268B SER* 1.3 79.1 + - - +
270B VAL* 1.3 64.8 + - - +
272B MET* 3.3 6.7 + - - +
273B PHE* 3.1 34.1 + - - -
293B SER* 4.2 2.3 - - - -
294B GLN 2.9 25.9 - - - +
299B MET* 3.6 22.3 - - + +
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Residues in contact with VAL 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 VAL* 2.8 25.3 + - + +
267B GLN* 3.5 10.3 - - - +
269B ASN* 1.3 73.2 - - - +
271B ASP* 1.3 56.9 + - - +
273B PHE* 3.1 5.0 + - - +
274B ARG* 2.8 41.7 + - + +
298B ILE* 4.5 0.2 - - + -
299B MET* 4.0 16.4 - - - -
302B VAL* 3.8 33.8 - - + +
469B LEU* 4.2 19.7 - - + -
470B LYS 3.6 24.7 - - - +
471B LEU* 4.7 4.9 - - + -
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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 GLN* 2.7 52.6 + - - +
268B SER* 3.8 8.5 - - - +
269B ASN 3.3 0.2 - - - -
270B VAL* 1.3 72.9 - - - +
272B MET* 1.3 63.3 + - - +
274B ARG* 3.1 36.1 + - - +
275B ALA* 3.4 13.2 + - - +
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Residues in contact with MET 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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215B LEU* 5.6 9.0 - - + +
253B VAL* 3.8 31.6 - - + -
254B ASN 3.6 29.6 - - - +
255B SER 4.4 5.8 - - - +
268B SER 3.1 14.5 + - - +
269B ASN* 3.5 13.5 - - - +
270B VAL 3.3 0.2 - - - -
271B ASP* 1.3 76.4 - - - +
273B PHE* 1.3 63.6 + - + +
275B ALA* 3.4 14.7 + - - +
276B LEU* 3.4 23.8 + - + +
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Residues in contact with PHE 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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251B PHE* 3.9 26.0 - + + -
253B VAL* 3.8 25.1 - - + -
269B ASN* 3.1 24.0 + - - +
270B VAL 3.5 7.2 - - - +
272B MET* 1.3 78.0 - - + +
274B ARG* 1.3 59.5 + - - +
276B LEU* 3.0 7.8 + - + -
277B VAL* 2.9 45.1 + - + +
291B VAL* 4.4 7.2 - - + -
293B SER* 3.2 34.8 - - - -
299B MET* 3.5 25.1 - - + -
302B VAL* 4.2 3.1 - - + -
303B THR* 3.4 27.1 - - - -
306B LEU* 3.5 10.9 - - + +
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Residues in contact with ARG 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 VAL* 2.8 20.8 + - + +
271B ASP* 3.1 37.2 + - - +
272B MET 3.3 0.4 - - - -
273B PHE* 1.3 75.6 - - - +
275B ALA* 1.3 57.4 + - - +
276B LEU 3.3 0.4 - - - -
278B PRO* 3.4 22.0 - - - +
306B LEU* 3.6 28.7 - - + +
470B LYS* 3.4 32.4 + - - +
471B LEU* 3.6 27.4 + - - +
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Residues in contact with ALA 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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240B LEU* 4.7 8.7 - - - +
271B ASP 3.4 8.2 + - - +
272B MET* 3.4 9.2 + - - +
273B PHE 3.2 0.6 - - - -
274B ARG* 1.3 77.0 - - - +
276B LEU* 1.3 60.1 + - - +
278B PRO* 4.5 1.6 - - - -
279B ALA* 5.0 3.7 - - - +
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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