Contacts of the helix formed by residues 262 - 277 (chain B) in PDB entry 2DW1
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 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260B LYS* 3.1 21.3 + - + +
261B PRO* 1.3 76.6 - - + +
263B ALA* 1.3 67.0 + - - +
264B GLY* 3.0 3.1 + - - +
265B TYR* 3.0 31.3 + - + +
266B THR* 3.2 10.7 + - - -
296B ASP* 3.8 13.7 - - - +
297B ARG* 5.4 6.1 - - - +
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Residues in contact with ALA 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 PRO 3.0 9.3 + - - +
262B GLU* 1.3 69.5 - - - +
264B GLY* 1.3 63.6 + - - +
266B THR* 3.3 0.7 + - - -
267B LEU* 2.9 25.5 + - - +
295B LEU* 4.4 5.8 - - + -
296B ASP* 5.0 4.0 + - - +
297B ARG* 5.5 5.9 - - - +
298B VAL* 3.8 28.5 - - + -
301B LEU* 3.5 26.0 - - + -
316B ILE* 3.7 16.5 - - + +
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Residues in contact with GLY 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A GLY* 4.3 15.5 - - - +
262B GLU* 3.0 2.4 + - - +
263B ALA* 1.3 78.6 - - - +
265B TYR* 1.3 61.1 + - - +
267B LEU* 3.5 1.6 + - - +
268B ASN* 3.1 24.9 + - - +
301B LEU* 3.6 14.3 - - - +
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Residues in contact with TYR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B THR* 3.3 35.4 + - - -
260B LYS* 3.5 45.4 + - + -
262B GLU* 3.0 29.4 + - + +
264B GLY* 1.3 74.2 - - - +
266B THR* 1.3 59.5 + - - +
268B ASN* 3.3 6.0 + - - +
269B ALA* 2.8 43.7 + - + +
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Residues in contact with THR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ILE* 4.1 6.9 - - + +
258B THR 4.8 1.6 - - - -
259B VAL* 4.0 12.3 - - + -
260B LYS* 2.7 41.7 + - - +
262B GLU 3.2 2.5 + - - -
263B ALA 3.8 6.3 - - - -
265B TYR* 1.3 82.6 - - - +
267B LEU* 1.3 57.2 + - - +
269B ALA* 3.7 4.0 - - - +
270B PHE* 2.8 29.1 + - - +
289B LEU* 4.0 24.7 - - + -
291B THR* 5.9 1.6 - - + -
295B LEU* 5.3 1.8 - - + -
316B ILE* 4.0 17.9 - - + -
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Residues in contact with LEU 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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565A PRO* 4.3 0.2 - - + -
566A GLY 4.0 15.7 - - - +
263B ALA 2.9 17.6 + - - +
264B GLY 3.9 3.4 - - - +
266B THR* 1.3 75.6 - - - +
268B ASN* 1.3 59.6 + - - +
270B PHE* 3.6 1.5 - - + +
271B GLY* 2.8 27.0 + - - -
301B LEU* 4.2 10.8 - - + -
302B ALA* 3.9 23.1 - - - +
303B TYR* 3.4 41.8 + - + +
314B THR* 3.8 7.4 - - - +
315B GLY* 3.6 33.2 - - - +
316B ILE* 3.9 14.1 - - + +
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Residues in contact with ASN 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A GLY 3.5 21.7 + - - +
567A GLN* 3.7 21.1 - - - +
264B GLY 3.1 15.6 + - - +
265B TYR* 3.7 4.8 - - - +
267B LEU* 1.3 80.3 - - - +
269B ALA* 1.3 58.8 + - - +
271B GLY* 3.4 0.9 + - - -
272B GLU* 2.9 36.6 + - - +
303B TYR* 3.4 11.1 + - - -
311B LYS* 3.5 20.7 + - - +
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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
----------------------------------------------------------
257B ILE* 4.1 23.6 - - + +
258B THR 5.3 0.2 - - - +
265B TYR* 2.8 36.7 + - + +
266B THR* 3.7 4.7 - - - +
268B ASN* 1.3 75.7 + - - +
270B PHE* 1.3 60.8 + - - +
272B GLU* 3.2 7.0 + - - +
273B TRP* 2.9 29.1 + - - +
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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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205B VAL* 3.7 34.8 - - + -
251B TRP* 4.5 5.8 - + - -
257B ILE* 3.9 5.7 - - + +
266B THR 2.8 18.6 + - - +
267B LEU* 3.6 5.2 - - + +
269B ALA* 1.3 76.2 - - - +
271B GLY* 1.3 57.4 + - - +
273B TRP* 3.2 23.7 + + - +
274B ARG* 2.9 28.7 + - + +
287B ALA* 3.7 24.0 - - + -
288B GLN 3.8 4.7 - - - -
289B LEU* 3.5 59.2 - - + -
314B THR* 3.9 21.3 - - + -
315B GLY 3.9 5.6 - - - -
316B ILE* 4.6 2.9 - - + -
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Residues in contact with GLY 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 LEU 2.8 16.7 + - - -
268B ASN 3.8 2.0 - - - -
270B PHE* 1.3 76.9 - - - +
272B GLU* 1.3 60.6 + - - +
274B ARG* 3.2 12.0 + - - +
275B LYS 3.2 10.7 + - - -
303B TYR* 5.2 1.1 - - - -
311B LYS* 3.4 39.6 - - - +
314B THR* 3.9 9.6 - - - -
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Residues in contact with GLU 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 ASN* 2.9 30.1 + - - +
269B ALA* 3.6 6.7 - - - +
271B GLY* 1.3 75.9 - - - +
273B TRP* 1.3 57.5 + - - +
275B LYS* 3.6 18.1 + - - +
276B THR* 3.1 37.2 + - - +
311B LYS* 2.6 33.8 + - - +
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Residues in contact with TRP 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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205B VAL* 4.0 6.1 - - + -
249B GLU* 3.7 16.8 - - - -
251B TRP* 3.8 17.0 - + - -
256B LYS* 3.5 45.1 - - + +
257B ILE* 3.8 13.2 - - + -
269B ALA 2.9 16.4 + - - +
270B PHE* 3.6 34.5 - + - +
272B GLU* 1.3 76.9 - - - +
274B ARG* 1.3 66.3 + - - +
275B LYS 3.3 0.2 - - - -
276B THR* 3.9 4.5 - - - -
277B ASP* 2.9 49.4 + - + -
278B LEU* 3.4 32.8 + - + -
281B ARG* 3.9 15.9 - - - -
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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 PHE* 2.9 16.3 + - + +
271B GLY 3.2 5.3 + - - +
273B TRP* 1.3 87.6 - - + +
275B LYS* 1.3 58.8 + - - +
276B THR 3.5 0.3 + - - -
278B LEU* 4.1 9.9 - - + -
279B LEU* 2.9 45.4 + - - +
284B HIS* 2.9 45.5 + - - +
285B ASP 2.7 36.5 + - - -
286B ASN* 3.4 2.0 - - - +
287B ALA* 3.9 12.4 - - + +
308B CYS 4.6 2.2 + - - -
309B HIS 3.0 19.6 + - - -
310B PRO* 3.0 31.1 + - - +
313B SER* 3.8 10.2 - - - -
314B THR* 4.0 20.4 - - + -
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Residues in contact with LYS 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 GLY 3.2 10.8 + - - +
272B GLU* 3.6 24.1 + - - +
274B ARG* 1.3 82.2 - - - +
276B THR* 1.3 65.8 + - + +
279B LEU* 4.4 13.0 - - + +
280B THR* 5.2 1.6 + - - -
309B HIS* 6.5 0.4 - - - -
310B PRO* 3.4 41.5 - - + +
311B LYS* 3.8 20.8 - - + +
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Residues in contact with THR 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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272B GLU* 3.1 28.0 + - - +
273B TRP* 3.9 5.5 + - - -
274B ARG 3.3 0.4 - - - -
275B LYS* 1.3 96.3 - - + +
277B ASP* 1.3 63.9 + - - +
278B LEU 4.0 0.2 - - - -
280B THR* 3.9 16.7 - - - +
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Residues in contact with ASP 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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256B LYS* 4.2 11.5 + - - +
273B TRP* 2.9 43.9 + - + +
276B THR* 1.3 81.3 + - - +
278B LEU* 1.3 54.2 + - - +
280B THR* 2.9 17.1 - - - +
281B ARG* 2.7 33.8 + - - -
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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