Contacts of the helix formed by residues 287 - 297 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A TYR* 4.8 11.0 + - - +
285A TYR 5.1 4.7 - - - +
286A TYR* 1.3 73.6 - - - +
288A LEU* 1.3 68.1 + - - +
289A GLU* 3.3 2.9 - - - -
290A SER* 3.1 21.4 + - - +
291A LEU* 3.2 39.4 + - + +
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Residues in contact with LEU 288 (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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131A LEU* 3.6 36.8 - - + -
224A TYR* 3.6 27.6 - - + +
249A HIS* 3.9 15.5 - - + +
250A VAL* 4.4 5.6 - - + -
269A TYR* 4.0 11.7 - - + -
270A ARG* 3.4 34.3 - - + +
286A TYR* 3.5 29.0 - - + -
287A GLU* 1.3 78.5 - - - +
289A GLU* 1.3 65.6 + - - +
290A SER 3.2 0.2 + - - -
291A LEU* 3.2 2.1 + - + +
292A ILE* 2.8 33.2 + - + +
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Residues in contact with GLU 289 (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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112A GLY* 5.4 0.9 - - - -
269A TYR* 3.3 45.4 + - + +
270A ARG 4.6 1.2 + - - -
271A LYS* 4.0 31.7 + - + +
286A TYR 5.4 0.6 + - - +
287A GLU 3.3 1.3 - - - -
288A LEU* 1.3 77.6 - - - +
290A SER* 1.3 65.1 + - - +
293A ASN* 3.0 41.4 + - - +
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Residues in contact with SER 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLU* 3.1 15.9 + - - -
289A GLU* 1.3 80.9 - - - +
291A LEU* 1.3 66.1 + - - +
293A ASN* 4.3 2.4 - - - +
294A SER* 2.8 32.4 + - - -
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Residues in contact with LEU 291 (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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130A ALA* 3.4 30.0 - - + +
131A LEU* 3.9 22.0 - - + -
224A TYR* 5.4 2.0 - - - +
287A GLU* 3.2 41.0 + - + +
288A LEU 3.2 4.3 + - - +
290A SER* 1.3 80.6 - - - +
292A ILE* 1.3 63.8 + - - +
294A SER* 3.4 4.7 + - - -
295A ALA* 3.0 19.9 + - - +
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Residues in contact with ILE 292 (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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114A ASN* 5.1 2.5 - - - +
126A ALA 5.4 1.3 - - - +
127A VAL* 4.7 7.6 - - + -
130A ALA* 3.7 16.4 - - + -
131A LEU* 4.4 14.4 - - + -
250A VAL* 4.2 15.5 - - + -
267A ILE* 3.7 42.0 - - + -
269A TYR* 3.8 38.4 - - + -
288A LEU* 2.8 24.8 + - + +
289A GLU 4.3 0.9 - - - +
291A LEU* 1.3 69.7 - - - +
293A ASN* 1.3 68.1 + - - +
294A SER 3.0 1.0 + - - -
295A ALA* 3.0 10.6 + - - +
296A VAL* 3.1 16.6 + - + +
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Residues in contact with ASN 293 (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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77A TYR* 2.5 45.8 + - + +
113A VAL 4.6 2.1 + - - +
114A ASN* 2.6 35.6 + - - +
269A TYR* 3.3 24.3 + - - -
289A GLU* 3.0 33.0 + - - +
290A SER* 4.3 2.9 - - - +
292A ILE* 1.3 76.2 - - - +
294A SER* 1.3 60.3 + - - +
296A VAL 3.5 0.3 + - - -
297A PHE 3.3 9.9 + - - +
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Residues in contact with SER 294 (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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290A SER* 2.8 24.5 + - - -
291A LEU* 3.7 3.8 - - - -
292A ILE 3.1 0.6 - - - -
293A ASN* 1.3 75.0 - - - +
295A ALA* 1.3 66.7 + - - +
296A VAL 3.1 1.3 - - - -
297A PHE 2.9 27.6 + - - +
298A PRO* 3.6 4.1 - - - +
299A GLY* 3.2 7.3 + - - -
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Residues in contact with ALA 295 (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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126A ALA 3.5 13.2 - - - +
129A THR* 4.1 13.5 - - + -
130A ALA* 3.5 36.8 - - + +
291A LEU 3.0 7.3 + - - +
292A ILE 3.0 2.4 + - - +
294A SER* 1.3 76.8 - - - +
296A VAL* 1.3 53.6 + - - +
299A GLY* 3.1 6.0 - - - -
300A LEU* 2.7 41.3 + - + +
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Residues in contact with VAL 296 (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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77A TYR* 3.4 18.8 - - - +
114A ASN* 3.7 26.9 - - - +
116A GLN* 4.2 9.9 - - + +
117A PRO* 5.0 2.7 - - + -
126A ALA* 4.1 20.2 - - + -
267A ILE* 4.3 11.2 - - + -
292A ILE* 3.1 13.8 + - + +
293A ASN 3.6 0.4 - - - +
294A SER 3.1 0.8 - - - -
295A ALA* 1.3 77.4 - - - +
297A PHE* 1.3 57.4 + - + +
300A LEU* 4.5 4.9 - - - +
301A GLN* 2.8 56.4 + - - +
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Residues in contact with PHE 297 (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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75A GLU* 3.4 46.0 - - + +
76A GLY* 4.4 3.8 - - - -
77A TYR* 4.2 20.4 - + + +
82A TYR* 3.3 33.4 - + - -
116A GLN* 4.9 4.3 - - - +
293A ASN 3.3 10.1 + - - +
294A SER* 2.9 16.1 + - - +
296A VAL* 1.3 84.8 - - + +
298A PRO* 1.3 85.5 - - + +
299A GLY 3.3 0.2 - - - +
301A GLN* 3.0 26.5 - - + +
302A GLY* 3.4 16.8 - - - +
149B LEU* 4.2 6.3 - - + -
601B THF 4.1 11.0 - + - -
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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