Contacts of the helix formed by residues 254 - 270 (chain A) in PDB entry 2DH3
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 ASP 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A LEU 3.5 0.8 + - - -
253A LYS* 1.3 105.6 + - - +
255A ALA* 1.3 66.9 + - - +
256A SER* 3.4 4.0 - - - -
257A SER* 3.1 27.1 + - - +
258A PHE* 3.2 21.5 - - + -
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Residues in contact with ALA 255 (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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249A ILE* 3.8 19.3 - - + +
252A LEU* 3.3 29.2 + - + +
253A LYS 3.2 3.4 - - - -
254A ASP* 1.3 73.7 - - - +
256A SER* 1.3 64.1 + - - +
258A PHE* 3.1 14.9 + - - +
259A LEU* 3.1 19.7 + - + +
290A LEU* 4.0 20.9 - - + -
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Residues in contact with SER 256 (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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254A ASP* 4.7 2.1 + - - -
255A ALA* 1.3 79.2 - - - +
257A SER* 1.3 65.8 + - - +
259A LEU* 4.1 7.6 - - - -
260A ALA* 3.2 9.4 + - - +
289A SER 4.3 15.5 - - - -
290A LEU* 4.4 8.6 - - - +
293A SER* 2.9 41.4 + - - -
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Residues in contact with SER 257 (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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254A ASP* 3.1 24.4 + - - +
256A SER* 1.3 82.7 + - - +
258A PHE* 1.3 64.5 + - - +
260A ALA* 3.5 7.7 + - - +
261A GLU* 3.4 19.4 + - - +
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Residues in contact with PHE 258 (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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222A VAL* 3.8 23.6 - - + -
223A ASP* 5.7 0.9 - - - -
226A ALA* 3.3 28.5 - - + -
252A LEU* 4.4 9.4 - - + -
253A LYS* 3.4 21.3 - - + -
254A ASP* 3.2 30.9 + - + -
255A ALA 3.1 6.0 + - - +
257A SER* 1.3 74.7 - - - +
259A LEU* 1.3 64.6 + - - +
260A ALA 3.1 2.0 - - - -
261A GLU* 3.3 12.8 + - - +
262A TRP* 3.0 59.7 + + + -
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Residues in contact with LEU 259 (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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246A VAL* 4.2 16.8 - - + -
249A ILE* 4.4 23.3 - - + -
252A LEU* 5.8 2.0 - - + -
255A ALA* 3.1 25.1 + - + +
256A SER* 4.1 7.4 - - - +
257A SER 3.4 0.2 - - - -
258A PHE* 1.3 76.4 - - - +
260A ALA* 1.3 58.0 + - - +
262A TRP* 4.3 15.9 - - + -
263A GLN* 3.1 28.9 + - - +
275A LEU* 4.0 6.1 - - + +
277A ALA* 3.8 30.5 - - + -
290A LEU* 4.6 14.1 - - + +
293A SER* 4.3 4.9 - - - +
294A ASN* 4.9 0.6 - - - +
297A LEU* 3.9 27.6 - - + +
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Residues in contact with ALA 260 (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 SER 3.2 7.4 + - - +
257A SER* 3.5 12.1 - - - +
258A PHE 3.1 0.2 - - - -
259A LEU* 1.3 76.7 - - - +
261A GLU* 1.3 65.4 + - - +
263A GLN* 3.5 2.1 - - - +
264A ASN* 3.1 32.3 + - - +
293A SER* 3.3 21.9 + - - +
294A ASN* 4.1 12.5 - - + +
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Residues in contact with GLU 261 (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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230A LYS* 3.3 40.5 - - - +
257A SER 3.4 7.9 + - - +
258A PHE* 3.3 16.4 + - - +
260A ALA* 1.3 79.7 - - - +
262A TRP* 1.3 69.9 + - - +
264A ASN* 3.1 20.5 + - - +
265A ILE* 3.1 21.6 + - + +
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Residues in contact with TRP 262 (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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217A TRP* 4.1 25.8 - + - -
226A ALA* 4.1 11.6 + - + -
229A VAL* 3.8 28.5 - - + +
230A LYS* 4.0 16.0 - - + +
233A LEU* 3.8 28.0 - - + +
246A VAL* 4.8 10.3 - - + -
252A LEU* 4.1 18.4 - - + -
258A PHE* 3.0 53.3 + + + +
259A LEU* 4.3 19.3 - - + +
261A GLU* 1.3 89.3 + - - +
263A GLN* 1.3 64.4 + - - +
265A ILE* 3.4 5.8 + - + +
266A THR* 2.8 30.9 + - - -
275A LEU* 4.1 14.6 - - + -
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Residues in contact with GLN 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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259A LEU 3.1 21.3 + - - +
260A ALA 3.5 3.8 - - - +
262A TRP* 1.3 75.8 - - - +
264A ASN* 1.3 58.5 + - - +
266A THR* 3.4 3.4 + - - -
267A LYS* 2.9 56.3 + - + +
275A LEU* 3.7 26.8 + - + +
294A ASN* 3.3 35.9 - - + +
296A ASP* 3.3 38.8 + - - +
297A LEU* 3.8 8.2 - - + +
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Residues in contact with ASN 264 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ALA* 3.1 19.7 + - - +
261A GLU* 3.1 12.4 + - + +
263A GLN* 1.3 75.4 - - - +
265A ILE* 1.3 60.7 + - + +
267A LYS* 4.4 4.1 - - - +
268A GLY* 3.0 24.6 + - - -
294A ASN* 3.5 17.1 + - - +
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Residues in contact with ILE 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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230A LYS* 3.8 44.2 - - + +
233A LEU* 4.3 27.1 - - + -
234A GLU* 4.2 23.3 - - + +
237A LEU* 4.4 7.5 - - + +
261A GLU* 3.1 18.1 + - + +
262A TRP* 3.8 10.1 - - + +
263A GLN 3.4 0.2 - - - -
264A ASN* 1.3 75.2 - - + +
266A THR* 1.3 64.7 + - - +
268A GLY* 3.3 2.0 + - - -
269A PHE* 3.3 21.0 + - - +
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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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233A LEU* 4.3 18.2 - - - +
237A LEU* 4.4 12.7 - - + +
243A GLY* 5.1 0.4 - - - -
244A PHE* 4.3 10.8 - - + -
262A TRP 2.8 20.5 + - - -
263A GLN* 3.4 8.9 + - - +
265A ILE* 1.3 79.5 - - - +
267A LYS* 1.3 61.2 + - - +
268A GLY 3.4 0.3 + - - -
269A PHE* 3.5 9.4 + - - +
270A SER 3.3 11.3 + - - +
273A ARG* 3.6 28.1 - - + +
274A LEU 3.7 26.0 - - - +
275A LEU* 4.6 6.8 - - + +
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Residues in contact with LYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LYS* 5.1 2.0 - - - +
118A TRP* 3.1 36.8 - - - -
263A GLN* 2.9 49.1 + - + +
264A ASN* 4.4 4.3 - - - +
266A THR* 1.3 71.0 - - - +
268A GLY* 1.3 65.5 + - - +
270A SER* 3.1 20.2 - - - +
271A GLU* 3.4 35.3 + - - +
273A ARG 3.2 15.3 + - - +
274A LEU* 4.7 3.6 - - - +
275A LEU 5.4 0.9 - - - +
296A ASP* 3.1 28.8 + - + +
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Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A ASN 3.0 20.0 + - - -
265A ILE* 3.7 2.5 - - - -
266A THR 3.2 0.4 - - - -
267A LYS* 1.3 75.3 - - - +
269A PHE* 1.3 67.1 + - - +
270A SER* 4.4 0.2 - - - -
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Residues in contact with PHE 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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234A GLU* 5.6 0.4 - - - -
237A LEU* 3.6 55.9 - - + -
238A GLN* 4.2 21.8 - - + -
265A ILE 3.3 7.1 + - - +
266A THR 3.7 9.6 - - - +
267A LYS 3.3 0.4 - - - -
268A GLY* 1.3 78.0 - - - +
270A SER* 1.3 63.3 + - - +
273A ARG* 3.9 32.1 - - + -
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Residues in contact with SER 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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266A THR 3.3 10.8 + - - +
267A LYS* 3.1 14.0 - - - +
268A GLY 3.4 0.6 - - - -
269A PHE* 1.3 85.0 - - - +
271A GLU* 1.3 64.2 + - - +
272A ASP* 3.1 18.5 + - - +
273A ARG* 3.5 33.6 + - - +
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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