Contacts of the helix formed by residues 287 - 297 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B TYR* 4.8 11.9 + - - +
285B TYR 5.0 4.8 - - - +
286B TYR* 1.3 73.2 - - - +
288B LEU* 1.3 67.3 + - - +
289B GLU* 3.3 2.2 - - - -
290B SER* 3.1 20.6 + - - +
291B LEU* 3.2 40.6 + - + +
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 3.5 36.8 - - + -
224B TYR* 3.6 27.8 - - + +
249B HIS* 4.0 14.6 - - + +
250B VAL* 4.4 4.7 - - + -
269B TYR* 4.0 11.2 - - + -
270B ARG* 3.3 35.7 - - + +
286B TYR* 3.5 28.8 - - + +
287B GLU* 1.3 77.7 - - - +
289B GLU* 1.3 65.6 + - - +
290B SER 3.1 0.2 + - - -
291B LEU* 3.2 1.5 + - + +
292B ILE* 2.8 33.6 + - + +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B TYR* 3.3 36.1 + - + +
270B ARG 4.6 1.2 + - - -
271B LYS* 3.0 42.6 + - + +
286B TYR 5.4 1.7 + - - +
287B GLU 3.3 1.1 - - - -
288B LEU* 1.3 77.6 - - - +
290B SER* 1.3 60.0 + - - +
293B ASN* 3.0 53.0 + - - +
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Residues in contact with SER 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 3.1 16.1 + - - +
289B GLU* 1.3 81.4 - - - +
291B LEU* 1.3 66.4 + - - +
293B ASN* 4.3 2.0 - - - +
294B SER* 2.8 32.1 + - - -
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ALA* 3.5 30.5 - - + +
131B LEU* 3.9 22.2 - - + -
224B TYR* 5.4 2.0 - - - +
287B GLU* 3.2 42.1 + - + +
288B LEU 3.2 4.8 + - - +
290B SER* 1.3 77.0 - - - +
292B ILE* 1.3 66.3 + - - +
294B SER* 3.4 5.7 + - - -
295B ALA* 3.0 18.4 + - - +
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Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ASN* 5.0 2.0 - - - +
126B ALA 5.3 1.3 - - - +
127B VAL* 4.7 8.1 - - + -
130B ALA* 3.7 17.3 - - + -
131B LEU* 4.5 13.0 - - + -
250B VAL* 4.2 16.6 - - + -
267B ILE* 3.7 41.7 - - + -
269B TYR* 3.7 39.7 - - + -
288B LEU* 2.8 25.1 + - + +
289B GLU 4.3 0.7 - - - +
291B LEU* 1.3 69.7 - - - +
293B ASN* 1.3 68.3 + - - +
295B ALA* 2.9 13.3 + - - +
296B VAL* 3.0 15.6 + - + +
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Residues in contact with ASN 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B TYR* 2.5 42.8 + - + +
113B VAL 4.6 1.9 + - - +
114B ASN* 2.6 35.4 + - - +
269B TYR* 3.3 23.4 + - - -
289B GLU* 3.0 35.3 + - - +
290B SER* 4.3 2.0 - - - +
292B ILE* 1.3 77.1 - - - +
294B SER* 1.3 59.0 + - - +
297B PHE 3.1 14.7 + - - +
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LYS* 5.2 7.4 + - - -
600A THF 3.8 20.5 + - - -
290B SER* 2.8 24.1 + - - -
291B LEU* 3.7 4.3 - - - -
292B ILE 3.1 0.6 - - - -
293B ASN* 1.3 75.5 - - - +
295B ALA* 1.3 66.2 + - - +
297B PHE 3.1 19.0 - - - +
298B PRO* 3.6 1.6 - - - +
299B GLY* 3.1 15.2 + - - -
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ALA 3.5 25.1 - - - +
129B THR* 4.2 12.8 - - + -
130B ALA* 3.6 22.7 - - + +
291B LEU 3.0 5.5 + - - +
292B ILE 2.9 8.7 + - - +
294B SER* 1.3 73.6 - - - +
296B VAL* 1.3 60.5 + - - +
299B GLY* 3.4 4.3 - - - -
300B LEU* 2.8 36.2 + - - +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 3.5 18.8 - - - +
114B ASN* 3.5 30.5 - - - +
116B GLN* 4.1 10.3 - - + +
117B PRO* 4.6 4.0 - - + -
126B ALA* 4.1 22.7 - - + -
267B ILE* 4.2 12.1 - - + -
292B ILE* 3.0 13.8 + - + +
293B ASN 3.7 0.7 - - - +
295B ALA* 1.3 77.4 - - - +
297B PHE* 1.3 59.2 + - + +
300B LEU* 3.7 1.7 - - - -
301B GLN* 2.7 57.7 + - - +
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Residues in contact with PHE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 4.2 4.7 - - + -
600A THF 4.2 14.4 - + - +
75B GLU* 3.2 61.0 - - + +
76B GLY* 4.4 4.3 - - - -
77B TYR* 3.9 19.8 - + + +
82B TYR* 4.1 20.0 - + - -
116B GLN* 4.8 5.4 - - - +
293B ASN 3.1 11.3 + - - +
294B SER* 3.1 13.1 + - - +
296B VAL* 1.3 86.3 - - + +
298B PRO* 1.3 86.6 - - + +
299B GLY 3.3 0.7 - - - +
301B GLN* 2.9 26.9 - - + -
302B GLY 3.3 13.0 - - - +
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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