Contacts of the helix formed by residues 259 - 269 (chain A) in PDB entry 1EJC
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 LEU 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A ARG* 3.3 28.9 - - + +
233A ILE* 5.8 0.2 - - + -
235A THR* 3.5 35.9 - - + +
236A GLY* 4.6 3.1 - - - +
239A LEU* 4.8 4.0 - - + -
255A GLN 4.6 3.6 - - - +
256A PRO 3.0 10.5 + - - +
258A THR* 1.3 94.7 - - - +
260A ASP* 1.3 64.9 + - - +
261A ALA 3.3 2.5 - - - -
262A VAL* 3.2 32.2 + - + -
263A LEU* 2.9 32.6 + - + +
280A ILE* 3.8 14.6 - - + -
303A PRO* 5.8 2.0 - - + -
306A MET* 5.5 1.6 - - + -
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Residues in contact with ASP 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 PRO 3.9 2.3 - - - +
257A ASP* 3.9 28.4 - - - +
258A THR 3.8 1.6 - - - -
259A LEU* 1.3 74.9 - - - +
261A ALA* 1.3 64.8 + - - +
263A LEU* 4.0 5.3 - - - +
264A ALA* 3.0 25.2 + - - +
267A ARG* 5.0 0.9 + - - -
299A HIS* 6.2 0.2 - - - -
300A PRO* 5.4 7.5 - - + +
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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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259A LEU 3.3 0.6 - - - -
260A ASP* 1.3 79.2 - - - +
262A VAL* 1.3 62.4 + - - +
264A ALA* 3.4 6.2 + - - +
265A LYS* 3.0 25.8 + - - +
300A PRO 3.7 16.3 + - - +
301A ALA* 3.8 2.9 - - - +
302A PHE* 3.6 38.7 - - + +
303A PRO* 4.8 1.3 - - + -
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Residues in contact with VAL 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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236A GLY* 4.6 12.6 - - - -
239A LEU* 4.9 0.2 - - + -
259A LEU* 3.2 32.6 + - + +
261A ALA* 1.3 73.5 - - - +
263A LEU* 1.3 71.0 + - + +
265A LYS* 3.2 6.8 + - - +
266A LEU* 3.0 39.8 + - + +
302A PHE* 4.2 10.3 - - + -
303A PRO* 3.8 33.0 - - + -
306A MET* 4.1 11.0 - - + -
310A PHE* 3.9 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
----------------------------------------------------------
239A LEU* 3.6 31.4 - - + -
256A PRO* 4.2 16.2 - - + +
259A LEU* 2.9 27.6 + - + +
260A ASP* 4.0 4.7 - - - +
262A VAL* 1.3 77.6 - - + +
264A ALA* 1.3 63.3 + - - +
266A LEU* 3.2 2.4 + - + -
267A ARG* 3.0 46.3 + - - +
273A ILE* 3.7 18.1 - - + +
275A THR* 3.9 27.8 - - + -
280A ILE* 4.1 18.2 - - + -
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Residues in contact with ALA 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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260A ASP 3.0 19.0 + - - +
261A ALA* 3.7 5.6 - - - +
263A LEU* 1.3 76.2 - - - +
265A LYS* 1.3 63.2 + - - +
267A ARG* 3.3 21.5 + - - +
268A GLU* 3.1 31.9 + - - +
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Residues in contact with LYS 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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261A ALA 3.0 17.7 + - - +
262A VAL 3.6 4.9 - - - +
264A ALA* 1.3 76.9 - - - +
266A LEU* 1.3 64.2 + - - +
268A GLU* 2.8 36.3 + - - +
269A ALA* 3.1 18.9 + - - +
292A VAL* 3.8 16.3 - - + +
293A THR* 2.7 31.8 + - - +
294A VAL* 4.1 11.4 - - + +
295A ARG 5.8 0.2 - - - +
302A PHE* 4.3 13.0 - - + -
310A PHE* 3.5 28.8 - - + -
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Residues in contact with LEU 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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239A LEU* 3.8 23.6 - - + -
240A VAL* 4.4 6.5 - - + +
243A ALA* 4.1 15.3 - - + -
262A VAL* 3.0 32.8 + - + +
263A LEU* 3.7 2.7 - - + +
265A LYS* 1.3 75.3 - - - +
267A ARG* 1.3 63.1 + - - +
269A ALA* 3.0 15.4 + - + +
270A GLY 3.2 0.5 + - - -
271A ALA* 3.1 24.4 + - + +
273A ILE* 3.6 18.2 - - + -
282A LEU* 3.7 17.0 - - + -
310A PHE* 3.5 24.0 - - + -
313A LEU* 3.9 20.6 - - + -
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Residues in contact with ARG 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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260A ASP 5.0 1.0 + - - -
263A LEU* 3.0 32.8 + - - +
264A ALA* 3.5 38.6 - - - +
265A LYS 3.2 0.2 - - - -
266A LEU* 1.3 75.8 - - - +
268A GLU* 1.3 58.1 + - + +
270A GLY* 2.9 19.8 + - - -
271A ALA 3.7 18.4 + - - +
273A ILE* 4.2 33.5 + - + +
275A THR* 5.1 5.1 - - - +
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Residues in contact with GLU 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 ALA* 3.1 22.8 + - - +
265A LYS* 2.8 44.6 + - - +
267A ARG* 1.3 75.3 - - - +
269A ALA* 1.3 59.4 + - - +
270A GLY* 3.1 1.5 + - - -
290A LYS* 4.2 10.0 - - - +
291A ALA 4.9 0.7 - - - +
292A VAL* 3.7 16.6 - - + +
293A THR 5.0 1.4 + - - -
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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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243A ALA* 6.1 0.9 - - + -
265A LYS 3.1 9.9 + - - +
266A LEU* 3.0 16.8 + - + +
268A GLU* 1.3 76.2 - - - +
270A GLY* 1.3 57.9 + - - +
271A ALA* 3.6 1.1 - - + +
284A MET* 4.0 3.3 - - + +
288A ARG 4.6 0.5 - - - +
289A PRO* 3.5 13.8 - - + +
290A LYS* 2.9 46.4 + - - +
292A VAL* 3.6 6.9 - - + +
310A PHE* 6.0 0.2 - - + -
313A LEU* 4.2 22.0 - - + -
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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