Contacts of the helix formed by residues 262 - 277 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LYS* 2.9 11.3 - - + -
261A PRO* 1.3 77.7 - - + +
263A ALA* 1.3 65.2 + - - +
264A GLY* 3.4 6.1 + - - -
265A TYR* 2.6 53.6 + - + +
266A THR* 3.2 13.0 + - - -
296A ASP* 3.5 12.7 + - - +
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A PRO 3.2 6.6 + - - +
262A GLU* 1.3 70.9 - - - +
264A GLY* 1.3 64.7 + - - +
266A THR* 3.1 4.6 + - - -
267A LEU* 2.8 24.3 + - - +
295A LEU* 4.6 10.1 - - + -
296A ASP* 4.8 3.0 + - + +
298A VAL* 3.9 24.2 - - + -
301A LEU* 3.5 22.7 - - + -
316A ILE* 3.8 14.1 - - + +
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Residues in contact with GLY 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A GLU* 3.4 7.0 + - - +
263A ALA* 1.3 79.2 - - - +
265A TYR* 1.3 62.5 + - - +
267A LEU 3.3 0.3 + - - -
268A ASN* 3.1 25.3 + - - +
301A LEU* 3.8 4.1 - - - +
566B GLY* 3.5 29.0 - - - -
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Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A THR* 3.4 31.9 + - - -
260A LYS* 3.4 45.0 + - + -
262A GLU* 2.6 38.7 + - + +
264A GLY* 1.3 73.0 - - - +
266A THR* 1.3 63.8 + - - +
268A ASN* 3.3 9.0 + - - +
269A ALA* 3.0 41.0 + - + +
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ILE* 4.0 8.0 - - + +
258A THR 4.9 0.7 - - - -
259A VAL* 4.1 17.4 - - + -
260A LYS* 2.8 40.5 + - - +
262A GLU 3.2 2.3 + - - -
263A ALA 3.1 8.1 + - - -
265A TYR* 1.3 80.6 - - - +
267A LEU* 1.3 63.3 + - - +
269A ALA* 4.0 2.6 - - - -
270A PHE* 3.0 22.9 + - - +
289A LEU* 4.2 20.6 - - + -
291A THR* 5.9 1.1 - - + -
295A LEU* 5.3 0.9 - - + -
316A ILE* 4.0 18.2 - - + -
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ALA 2.8 18.5 + - - +
264A GLY 3.9 3.6 - - - +
266A THR* 1.3 73.0 - - - +
268A ASN* 1.3 58.6 + - - +
270A PHE* 3.4 1.1 + - + +
271A GLY* 2.9 26.2 + - - -
301A LEU* 3.9 10.5 - - + +
302A ALA* 4.0 11.2 - - - +
303A TYR* 3.5 33.3 + - + -
314A THR* 3.8 14.4 - - - +
315A GLY* 3.6 31.2 - - - +
316A ILE* 3.8 17.6 - - + +
565B PRO* 3.9 25.8 - - + -
566B GLY 4.1 4.3 - - - +
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Residues in contact with ASN 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLY 3.1 17.0 + - - +
265A TYR* 3.6 8.4 + - - +
267A LEU* 1.3 75.5 - - - +
269A ALA* 1.3 62.9 + - - +
271A GLY* 3.4 1.6 + - - -
272A GLU* 3.0 33.4 + - - +
303A TYR* 3.4 12.4 + - - +
311A LYS* 2.9 30.9 + - - +
566B GLY* 4.0 18.1 - - - +
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ILE* 4.1 23.7 - - + +
258A THR 5.5 0.4 - - - +
265A TYR* 3.0 35.6 + - + +
266A THR 4.1 3.1 - - - +
268A ASN* 1.3 77.3 - - - +
270A PHE* 1.3 61.4 + - - +
272A GLU* 3.1 8.8 + - - +
273A TRP* 2.8 30.3 + - - +
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A VAL* 3.8 23.6 - - + -
251A TRP* 4.5 5.2 - + - -
257A ILE* 3.9 10.9 - - + +
266A THR 3.0 18.8 + - - +
267A LEU* 3.7 5.4 - - + +
269A ALA* 1.3 76.2 - - - +
271A GLY* 1.3 53.5 + - - +
273A TRP* 3.3 33.2 + + - +
274A ARG* 2.8 37.7 + - + +
287A ALA* 3.5 33.0 - - + -
288A GLN 3.9 2.5 - - - -
289A LEU* 3.7 48.5 - - + -
314A THR* 3.9 20.0 - - + -
315A GLY 4.0 5.2 - - - -
316A ILE* 4.5 3.4 - - + -
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Residues in contact with GLY 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LEU 2.9 17.6 + - - -
268A ASN* 3.7 2.0 - - - -
269A ALA 3.2 0.2 - - - -
270A PHE* 1.3 78.4 - - - +
272A GLU* 1.3 55.9 + - - +
274A ARG* 3.4 6.0 + - - +
275A LYS* 3.0 28.8 + - - +
303A TYR* 5.2 1.1 - - - -
311A LYS* 3.2 32.9 - - - -
314A THR* 4.0 7.0 - - - -
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASN* 3.0 24.8 + - - +
269A ALA* 3.5 9.4 - - - +
271A GLY* 1.3 71.1 - - - +
273A TRP* 1.3 62.4 + - - +
275A LYS* 3.1 15.5 + - - +
276A THR* 2.8 45.2 + - + +
311A LYS* 2.9 34.2 + - - +
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Residues in contact with TRP 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A VAL* 4.1 5.6 - - + -
249A GLU* 3.7 33.0 - - - -
251A TRP* 3.6 25.1 - + - -
256A LYS* 3.6 30.6 - - + +
257A ILE* 3.7 15.0 - - + -
269A ALA 2.8 19.7 + - - +
270A PHE* 3.6 33.2 - + - +
272A GLU* 1.3 73.0 - - - +
274A ARG* 1.3 69.4 - - - +
276A THR* 3.9 5.8 - - - -
277A ASP* 2.8 66.2 + - + +
278A LEU* 3.5 28.3 + - + -
281A ARG* 4.1 4.7 - - - -
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A PHE* 2.8 22.2 + - + +
271A GLY 3.5 5.2 - - - +
273A TRP* 1.3 86.0 - - + +
275A LYS* 1.3 57.9 + - - +
278A LEU* 3.5 9.5 + - + -
279A LEU* 2.8 42.7 + - - +
284A HIS* 2.9 62.2 + - - +
285A ASP 3.4 16.4 + - - -
286A ASN 3.6 0.6 - - - +
287A ALA* 4.0 11.5 - - + +
308A CYS* 4.8 2.4 + - - +
309A HIS 3.0 18.4 + - - -
310A PRO* 2.8 40.4 + - - +
313A SER* 3.8 12.1 - - - -
314A THR* 3.8 22.2 - - + -
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLY 3.0 17.5 + - - +
272A GLU* 3.6 18.7 + - - +
274A ARG* 1.3 79.0 - - - +
276A THR* 1.3 70.3 + - + +
277A ASP 3.7 0.2 + - - -
279A LEU* 4.3 11.2 - - - +
280A THR* 4.5 6.9 + - - -
310A PRO* 3.6 43.2 + - + +
311A LYS* 3.8 18.8 - - + +
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Residues in contact with THR 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLU* 2.8 35.1 + - + +
273A TRP* 3.8 7.6 + - - -
275A LYS* 1.3 89.7 - - + +
277A ASP* 1.3 62.6 + - - +
280A THR* 3.9 14.6 + - - +
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Residues in contact with ASP 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LYS* 4.6 5.5 + - - +
273A TRP* 2.8 44.5 + - + +
275A LYS 3.4 0.6 - - - -
276A THR* 1.3 82.3 - - - +
278A LEU* 1.3 70.0 + - - +
279A LEU 3.4 0.9 - - - -
280A THR* 2.8 24.3 + - - +
281A ARG* 2.8 39.8 + - - +
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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