Contacts of the helix formed by residues 259 - 270 (chain A) in PDB entry 1EG4
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 ILE 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A GLY* 3.7 31.2 - - - +
238A LEU* 3.9 15.7 - - + +
239A HIS* 3.5 32.7 + - + +
242A ILE* 3.7 39.5 - - + -
254A PHE 5.7 0.2 - - - +
256A GLY 4.5 2.7 - - - +
257A SER 3.5 1.0 + - - -
258A ASN* 1.3 74.2 + - - +
260A GLU* 1.4 74.3 + - - +
261A PRO* 3.4 2.0 - - - -
262A SER* 3.0 17.3 + - - +
263A VAL* 3.0 15.5 + - + +
291A SER* 4.4 12.3 - - - -
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Residues in contact with GLU 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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231A GLN* 5.2 5.5 - - - +
232A ARG* 6.1 0.3 - - - -
235A GLY* 5.6 2.1 - - - -
258A ASN* 2.8 27.4 + - - +
259A ILE* 1.4 79.2 - - - +
261A PRO* 1.3 65.9 - - + +
263A VAL* 3.2 17.7 + - + +
264A ARG* 3.0 46.4 + - + +
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Residues in contact with PRO 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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255A GLY 5.8 2.7 - - - +
258A ASN* 3.3 25.8 - - + +
259A ILE 3.4 1.1 - - - -
260A GLU* 1.3 96.0 - - + +
262A SER* 1.3 55.0 + - - +
264A ARG* 3.5 28.0 + - - +
265A SER* 2.9 28.3 + - - -
268A GLN* 5.3 0.2 - - - +
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Residues in contact with SER 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LEU* 4.0 11.4 - - - -
254A PHE 5.3 0.3 + - - -
255A GLY* 5.9 2.1 - - - -
258A ASN 5.6 0.2 + - - -
259A ILE* 3.0 12.6 + - - -
261A PRO* 1.3 74.3 - - - +
263A VAL* 1.3 67.9 + - - +
265A SER* 3.2 7.7 + - - -
266A CYS* 2.8 20.3 + - - +
284A TRP* 3.5 15.0 - - - -
289A PRO* 5.9 0.9 - - - -
290A GLN* 6.0 0.3 - - - +
291A SER* 3.5 37.0 + - - -
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLN* 3.5 44.2 - - + +
234A LEU* 4.2 11.0 - - + -
235A GLY* 3.6 31.2 - - - +
238A LEU* 3.8 12.1 - - + -
259A ILE* 3.0 20.7 + - + +
260A GLU* 3.5 18.2 - - + +
262A SER* 1.3 77.8 - - - +
264A ARG* 1.3 63.1 + - - +
266A CYS* 3.2 2.1 + - - +
267A PHE* 3.0 27.8 + - + -
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Residues in contact with ARG 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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231A GLN* 4.7 12.8 - - - +
260A GLU* 3.0 43.6 + - + +
261A PRO* 3.6 38.0 - - - +
263A VAL* 1.3 74.8 - - + +
265A SER* 1.3 59.0 + - - +
267A PHE* 3.3 6.5 + - - +
268A GLN* 2.8 45.3 + - + +
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Residues in contact with SER 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 PRO 2.9 19.0 + - - -
262A SER* 3.2 8.7 + - - -
264A ARG* 1.3 75.7 - - - +
266A CYS* 1.3 57.2 + - - +
268A GLN* 3.3 16.2 + - - +
269A PHE* 2.9 30.7 + - - +
284A TRP* 4.4 12.1 + - - -
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Residues in contact with CYS 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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234A LEU* 3.6 25.6 - - + -
262A SER 2.8 13.5 + - - +
263A VAL 3.2 7.6 + - - +
265A SER* 1.3 71.7 - - - +
267A PHE* 1.4 64.2 + - - +
269A PHE* 3.2 5.7 + - - +
270A ALA* 3.0 21.0 + - - +
276A ILE* 3.9 21.3 - - - -
280A LEU* 4.5 5.2 - - - -
281A PHE* 5.0 1.1 - - - -
284A TRP* 3.6 51.4 - - + +
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Residues in contact with PHE 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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229A CYS 3.5 12.3 - - - -
230A ASP 3.5 21.5 - - - -
231A GLN* 3.5 47.3 - - + +
234A LEU* 3.8 22.7 - - + -
263A VAL* 3.0 22.5 + - + +
264A ARG* 4.0 3.1 - - - +
266A CYS* 1.4 77.7 - - + +
268A GLN* 1.3 61.2 + - - +
270A ALA* 3.2 10.8 + - + +
271A ASN 3.3 0.2 + - - -
272A ASN* 2.8 31.2 + - - +
273A LYS 3.2 27.6 - - - +
274A PRO 3.8 15.3 - - - -
276A ILE* 4.0 24.7 - - + -
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Residues in contact with GLN 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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261A PRO 5.3 0.2 - - - +
264A ARG* 2.8 39.0 + - + +
265A SER* 3.7 15.2 + - - +
267A PHE* 1.3 71.1 - - - +
269A PHE* 1.3 57.7 + - - +
271A ASN* 2.9 21.0 + - - -
272A ASN* 3.6 21.1 - - - +
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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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265A SER* 2.9 13.9 + - - +
266A CYS 3.2 10.3 - - - +
268A GLN* 1.3 77.3 - - - +
270A ALA* 1.3 56.0 + - - +
271A ASN* 3.3 4.2 + - - +
280A LEU* 3.9 25.4 - - + +
283A ASP* 4.0 11.7 - - + -
284A TRP* 3.4 52.9 - + + +
287A LEU* 3.7 27.8 - - + -
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Residues in contact with ALA 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 CYS 3.0 12.1 + - - +
267A PHE* 3.2 11.8 + - + +
269A PHE* 1.3 73.1 - - - +
271A ASN* 1.3 69.1 + - - +
272A ASN 3.3 1.0 + - - -
273A LYS* 3.2 23.6 + - + +
276A ILE* 3.7 17.5 - - + -
280A LEU* 3.6 30.5 - - + -
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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