Contacts of the helix formed by residues 287 - 297 (chain D) in PDB entry 1EJI
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 287 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224D TYR* 4.9 10.6 + - - +
285D TYR 4.7 6.7 - - - +
286D TYR* 1.3 72.8 - - - +
288D LEU* 1.3 66.5 + - - +
289D GLU* 3.3 2.7 - - - -
290D SER* 3.1 19.8 + - - +
291D LEU* 3.2 39.6 + - + +
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Residues in contact with LEU 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D LEU* 3.6 37.0 - - + -
224D TYR* 3.6 26.9 - - + +
249D HIS* 4.0 14.4 - - + +
250D VAL* 4.3 5.2 - - + -
269D TYR* 4.0 11.7 - - + -
270D ARG* 3.4 33.7 - - + +
286D TYR* 3.4 31.7 - - + -
287D GLU* 1.3 78.3 - - - +
289D GLU* 1.3 64.4 + - - +
290D SER 3.2 0.3 + - - -
291D LEU* 3.2 1.2 + - + +
292D ILE* 2.8 33.7 + - + +
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Residues in contact with GLU 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D TYR* 3.3 36.4 + - + +
270D ARG 4.6 1.6 + - - -
271D LYS* 3.5 36.5 + - + +
286D TYR 5.2 2.2 + - - +
287D GLU 3.3 0.9 - - - -
288D LEU* 1.3 77.2 - - - +
290D SER* 1.3 58.1 + - - +
293D ASN* 3.0 52.9 + - - +
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Residues in contact with SER 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D GLU* 3.1 16.4 + - - -
289D GLU* 1.3 81.9 - - - +
291D LEU* 1.3 65.2 + - - +
293D ASN* 4.3 2.6 - - - +
294D SER* 2.8 32.2 + - - -
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Residues in contact with LEU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ALA* 3.5 29.8 - - + +
131D LEU* 4.0 21.3 - - + -
224D TYR* 5.3 2.7 - - - +
287D GLU* 3.2 44.0 + - + +
288D LEU 3.9 3.8 - - - +
290D SER* 1.3 77.7 - - - +
292D ILE* 1.3 66.7 + - - +
294D SER* 3.4 6.3 + - - -
295D ALA* 3.0 17.3 + - - +
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Residues in contact with ILE 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ASN* 5.0 2.7 - - - +
126D ALA 5.3 1.6 - - - +
127D VAL* 4.6 8.5 - - + -
130D ALA* 3.7 17.0 - - + -
131D LEU* 4.4 13.7 - - + -
250D VAL* 4.2 15.9 - - + -
267D ILE* 3.8 40.8 - - + -
269D TYR* 3.8 39.5 - - + -
288D LEU* 2.8 25.5 + - + +
289D GLU 4.3 0.7 - - - +
291D LEU* 1.3 68.8 - - - +
293D ASN* 1.3 67.5 + - - +
295D ALA* 2.8 14.4 + - - +
296D VAL* 3.1 14.0 + - + +
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Residues in contact with ASN 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D TYR* 2.8 42.8 + - + +
113D VAL 4.5 1.7 - - - +
114D ASN* 2.7 34.7 + - - +
269D TYR* 3.3 23.3 + - - -
289D GLU* 3.0 35.3 + - - +
290D SER* 4.3 2.7 - - - +
292D ILE* 1.3 76.8 - - - +
294D SER* 1.3 59.6 + - - +
296D VAL 3.4 0.3 + - - -
297D PHE 3.0 16.0 + - - +
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Residues in contact with SER 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D SER* 2.8 23.0 + - - -
291D LEU* 3.7 5.6 - - - -
292D ILE 3.1 0.8 - - - -
293D ASN* 1.3 76.2 - - - +
295D ALA* 1.3 67.5 + - - +
297D PHE 3.1 12.6 - - - +
298D PRO* 3.5 6.6 - - - +
299D GLY* 2.9 22.5 + - - -
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Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ALA* 3.4 28.9 - - - +
129D THR* 4.4 10.5 - - + -
130D ALA* 3.5 21.5 - - + +
291D LEU 3.0 5.4 + - - +
292D ILE 2.8 9.7 + - - +
294D SER* 1.3 75.8 - - - +
296D VAL* 1.3 54.0 + - - +
299D GLY* 3.1 4.8 - - - -
300D LEU* 2.7 41.6 + - + +
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Residues in contact with VAL 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D TYR* 3.4 15.3 - - - +
114D ASN* 3.5 28.3 - - - +
116D GLN* 4.0 13.5 - - + +
117D PRO* 4.8 3.1 - - + -
126D ALA* 4.3 17.7 - - + -
267D ILE* 4.4 10.8 - - + -
292D ILE* 3.1 14.7 + - + +
295D ALA* 1.3 77.2 - - - +
297D PHE* 1.3 56.7 + - + +
300D LEU* 3.4 4.4 + - - +
301D GLN* 2.7 65.9 + - + +
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Residues in contact with PHE 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LEU* 4.4 12.3 - - + -
75D GLU* 3.3 53.6 - - + +
76D GLY* 4.3 5.2 - - - -
77D TYR* 4.0 19.6 - + + +
82D TYR* 3.9 33.9 - + - -
116D GLN* 4.8 4.9 - - - +
293D ASN 3.0 15.2 + - - +
294D SER* 3.1 7.5 + - - +
296D VAL* 1.3 83.5 - - + +
298D PRO* 1.3 80.6 - - + +
299D GLY 3.1 4.0 - - - +
301D GLN* 3.1 26.0 - - + -
302D GLY* 3.4 17.7 - - - +
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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