Contacts of the helix formed by residues 254 - 269 (chain A) in PDB entry 2HD5
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 THR 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ASN 5.7 0.4 - - - +
252A ALA 3.7 8.9 + - - +
253A HIS* 1.3 80.2 - - - +
255A ALA* 1.3 58.3 + - - +
257A VAL* 3.2 12.5 - - + +
258A GLU* 2.4 54.1 + - - +
310A GLU* 3.1 25.8 - - - +
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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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253A HIS* 5.9 1.3 - - - +
254A THR* 1.3 78.9 + - - +
256A LEU* 1.3 57.5 + - - +
258A GLU* 3.6 15.4 - - - +
259A GLU* 3.0 35.1 + - + +
282A GLN* 3.1 31.2 - - - +
283A ARG* 3.8 7.0 - - - +
310A GLU* 3.5 0.4 + - - -
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Residues in contact with LEU 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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255A ALA* 1.3 75.7 - - - +
257A VAL* 1.3 67.3 + - - +
259A GLU* 3.4 0.3 + - - -
260A PHE* 2.9 27.2 + - - +
279A PHE* 3.8 23.8 - - + -
282A GLN* 3.9 9.4 - - + -
283A ARG* 3.5 50.3 - - + +
284A TYR* 3.5 23.3 - - + -
303A LEU* 4.2 4.3 - - + +
306A GLY* 3.6 30.3 - - - -
307A LEU* 3.8 9.9 - - + +
310A GLU* 3.1 14.6 + - - +
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Residues in contact with VAL 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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241A TYR* 5.1 5.4 - - + -
242A CYS* 6.3 1.3 - - - -
244A TYR* 3.9 31.9 - - - +
254A THR* 3.2 26.2 - - + +
256A LEU* 1.3 73.4 - - - +
258A GLU* 1.3 59.1 + - + +
260A PHE* 5.5 2.7 - - + -
261A ALA* 2.9 30.8 + - + +
307A LEU* 3.7 23.3 - - + +
310A GLU* 2.8 30.3 + - + +
311A VAL* 4.1 20.9 - - + -
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Residues in contact with GLU 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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244A TYR* 4.5 19.4 - - + +
254A THR* 2.4 45.7 + - - +
255A ALA* 3.6 15.2 - - - +
256A LEU 3.2 0.2 - - - -
257A VAL* 1.3 80.2 - - + +
259A GLU* 1.3 63.8 + - - +
261A ALA* 3.8 1.4 - - - +
262A LYS* 2.9 42.4 + - + +
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Residues in contact with GLU 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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255A ALA* 3.0 19.9 + - + +
256A LEU 4.2 1.8 - - - +
258A GLU* 1.3 79.2 - - + +
260A PHE* 1.3 67.4 + - - +
262A LYS* 3.0 31.1 + - - +
263A LEU* 3.0 23.7 + - - +
278A GLU* 3.0 39.3 - - - +
279A PHE* 3.9 23.5 + - + +
282A GLN* 3.9 17.9 - - + +
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Residues in contact with PHE 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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229A LEU* 3.9 30.7 - - + -
232A LEU* 4.1 18.8 - - + -
238A LEU* 4.0 29.2 - - + -
242A CYS* 3.7 25.6 - - - -
256A LEU 2.9 19.0 + - - +
257A VAL* 3.7 5.8 - - + +
259A GLU* 1.3 78.6 - - - +
261A ALA* 1.3 64.1 + - - +
263A LEU* 3.2 6.9 + - + +
264A ILE* 3.0 42.1 + - + +
279A PHE* 3.9 20.7 - + + -
303A LEU* 4.3 2.7 - - + -
307A LEU* 3.8 34.3 - - + -
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Residues in contact with ALA 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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242A CYS* 3.8 24.4 - - + +
244A TYR* 3.4 40.6 - - + -
257A VAL* 2.9 19.9 + - + +
258A GLU 3.9 0.9 - - - +
260A PHE* 1.3 79.9 - - + +
262A LYS* 1.3 57.5 + - - +
264A ILE* 3.2 1.9 + - - +
265A GLN* 2.8 34.9 + - - +
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Residues in contact with LYS 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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244A TYR* 4.9 5.6 - - + -
258A GLU* 2.9 28.3 + - + +
259A GLU* 3.0 38.0 + - - +
261A ALA* 1.3 75.9 - - - +
263A LEU* 1.3 54.8 + - - +
265A GLN* 3.5 16.6 - - - +
266A THR* 2.7 40.0 + - - +
278A GLU* 3.7 12.3 + - - -
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Residues in contact with LEU 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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216A LEU* 3.9 11.7 - - + -
229A LEU* 3.5 37.2 - - + -
259A GLU 3.0 17.0 + - - +
260A PHE* 3.2 6.7 + - + +
262A LYS* 1.3 77.2 - - - +
264A ILE* 1.3 65.0 + - + +
266A THR* 3.1 5.6 + - - -
267A ILE* 3.0 35.4 + - + +
274A VAL* 3.4 31.4 - - + -
275A SER 4.1 12.1 - - - +
276A PRO* 3.9 12.8 - - + -
279A PHE* 4.0 17.7 - - + -
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Residues in contact with ILE 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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229A LEU* 4.6 4.7 - - + +
232A LEU 5.6 0.2 - - - +
233A SER* 4.0 28.5 - - - +
238A LEU* 6.2 0.2 - - + -
239A ARG* 3.8 25.1 - - + -
242A CYS* 4.0 11.0 - - + -
243A LEU* 4.2 7.9 - - + -
260A PHE* 3.0 51.6 + - + +
261A ALA 3.2 4.7 + - - +
263A LEU* 1.3 80.0 - - + +
265A GLN* 1.3 64.8 + - - +
266A THR 3.2 0.2 + - - -
267A ILE* 3.2 10.6 + - + +
268A TRP* 3.0 42.2 + - + +
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Residues in contact with GLN 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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242A CYS 2.8 28.8 + - - +
243A LEU* 3.6 23.1 - - + +
244A ARG* 2.9 41.9 + - - +
261A ALA 2.8 23.5 + - - +
262A LYS* 3.5 20.8 - - - +
264A ILE* 1.3 73.1 - - - +
266A THR* 1.3 58.9 + - - +
268A TRP 3.5 0.5 + - - -
269A THR* 2.9 34.0 + - + +
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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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262A LYS* 2.7 25.8 + - - +
263A LEU* 3.6 5.6 - - - -
264A ILE 3.1 0.2 - - - -
265A GLN* 1.3 76.3 - - - +
267A ILE* 1.3 61.2 + - - +
269A THR* 3.4 7.5 + - - +
270A SER* 2.6 37.4 + - - +
274A VAL* 3.9 28.7 - - + -
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Residues in contact with ILE 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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212A GLY* 3.4 31.7 + - - +
213A LEU 4.3 0.3 + - - -
214A ALA* 4.1 23.0 - - + +
216A LEU* 4.2 25.8 - - + -
229A LEU* 5.3 2.9 - - + +
230A GLN* 4.5 11.0 - - - +
233A SER* 3.7 28.7 - - - +
263A LEU* 3.0 29.5 + - + +
264A ILE* 3.2 15.2 + - + +
266A THR* 1.3 77.3 - - - +
268A TRP* 1.3 64.6 + - + +
270A SER* 3.6 13.0 + - - -
274A VAL* 4.4 13.9 - - + -
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Residues in contact with TRP 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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211A GLN* 3.6 42.1 + - - -
212A GLY* 3.5 23.6 - - - -
233A SER* 2.8 34.1 + - - -
234A ASN* 3.5 22.2 - - - -
239A ARG* 3.3 42.3 - - + +
243A LEU* 4.1 19.7 - - + -
264A ILE* 3.0 37.9 + - + +
265A GLN 4.3 0.2 - - - +
266A THR 3.2 0.2 - - - -
267A ILE* 1.3 78.5 - - + +
269A THR* 1.3 61.4 + - + +
270A SER 3.4 3.0 - - - +
471A SER* 3.9 12.6 - - - -
472A PRO* 3.8 15.0 - - + -
473A GLY* 5.4 2.2 - - - -
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Residues in contact with THR 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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243A LEU* 5.9 2.7 - - + -
265A GLN* 2.9 21.8 + - + +
266A THR* 3.4 9.9 + - - +
267A ILE 3.4 0.2 - - - -
268A TRP* 1.3 81.5 - - + +
270A SER* 1.3 61.7 + - - +
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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