Contacts of the helix formed by residues 287 - 297 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C TYR* 4.9 10.9 + - - +
285C TYR 5.4 2.2 - - - +
286C TYR* 1.3 75.6 - - - +
288C LEU* 1.3 66.8 + - - +
289C GLU* 3.3 3.1 - - - -
290C SER* 3.1 21.6 + - - +
291C LEU* 3.2 39.2 + - + +
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Residues in contact with LEU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C LEU* 3.6 31.4 - - + -
224C TYR* 3.6 31.2 - - + +
249C HIS* 3.9 15.5 - - + +
250C VAL* 4.3 4.9 - - + -
269C TYR* 4.0 11.2 - - + -
270C ARG* 3.4 36.3 - - + +
286C TYR* 3.5 27.6 - - + +
287C GLU* 1.3 78.3 - - - +
289C GLU* 1.3 65.6 + - - +
290C SER 3.2 0.2 + - - -
291C LEU* 3.2 1.4 + - + +
292C ILE* 2.8 34.4 + - + +
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Residues in contact with GLU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C TYR* 3.2 40.5 + - + +
270C ARG 4.6 1.0 + - - -
271C LYS* 2.9 42.0 + - + +
286C TYR 5.5 0.6 - - - +
287C GLU* 3.3 1.1 - - - -
288C LEU* 1.3 76.0 - - - +
290C SER* 1.3 58.8 + - - +
293C ASN* 2.9 46.6 + - - +
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Residues in contact with SER 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C GLU* 3.1 16.8 + - - -
289C GLU* 1.3 82.1 - - - +
291C LEU* 1.3 63.4 + - - +
293C ASN* 4.3 2.2 - - - +
294C SER* 2.6 34.7 + - - -
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Residues in contact with LEU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ALA* 3.5 28.5 - - + +
131C LEU* 4.0 21.8 - - + -
224C TYR* 5.4 1.8 - - - +
287C GLU* 3.2 43.6 + - + +
288C LEU 4.0 3.1 - - - +
290C SER* 1.3 81.5 - - - +
292C ILE* 1.3 64.2 + - - +
294C SER* 3.7 4.1 - - - -
295C ALA* 2.9 18.9 + - - +
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Residues in contact with ILE 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ASN* 5.1 2.7 - - - +
126C ALA 5.3 0.9 - - - +
127C VAL* 4.7 8.1 - - + -
130C ALA* 3.7 16.8 - - + -
131C LEU* 4.4 13.7 - - + -
250C VAL* 4.2 16.2 - - + -
267C ILE* 3.8 40.4 - - + -
269C TYR* 3.7 39.3 - - + -
288C LEU* 2.8 25.5 + - + +
289C GLU 4.2 0.7 - - - +
291C LEU* 1.3 70.6 - - - +
293C ASN* 1.3 68.3 + - - +
295C ALA* 2.9 13.5 + - - +
296C VAL* 3.0 19.1 + - + +
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Residues in contact with ASN 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C TYR* 2.6 43.5 + - + -
113C VAL 4.5 1.9 + - - +
114C ASN* 2.6 35.6 + - - +
269C TYR* 3.4 22.9 + - - -
289C GLU* 2.9 34.7 + - - +
290C SER* 4.3 2.2 - - - +
292C ILE* 1.3 76.9 - - - +
294C SER* 1.3 58.7 + - - +
296C VAL 3.5 0.2 + - - -
297C PHE 3.0 16.9 + - - +
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Residues in contact with SER 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C SER* 2.6 25.1 + - - -
291C LEU* 3.7 4.3 - - - -
292C ILE 3.1 0.4 - - - -
293C ASN* 1.3 75.5 - - - +
295C ALA* 1.3 67.6 - - - +
297C PHE 3.0 14.2 - - - -
298C PRO* 3.5 6.6 - - - +
299C GLY* 3.0 22.9 + - - -
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ALA 3.4 16.8 - - - +
129C THR* 4.4 9.8 - - + +
130C ALA* 3.4 33.7 - - + +
291C LEU 2.9 5.4 + - - +
292C ILE* 2.9 9.8 + - - +
294C SER* 1.3 78.6 - - - +
296C VAL* 1.3 57.1 + - - +
299C GLY* 3.2 5.3 - - - -
300C LEU* 2.8 36.2 + - + +
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Residues in contact with VAL 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C TYR* 3.6 13.2 - - - +
114C ASN* 3.7 29.2 - - - +
116C GLN* 4.2 9.6 - - + +
117C PRO* 4.8 4.0 - - + -
126C ALA* 4.1 23.3 - - + -
267C ILE* 4.3 11.2 - - + -
292C ILE* 3.0 14.9 + - + +
293C ASN 3.7 0.2 - - - +
295C ALA* 1.3 75.5 - - - +
297C PHE* 1.3 62.3 + - + +
300C LEU* 4.6 2.5 - - - +
301C GLN* 2.9 53.9 + - + +
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Residues in contact with PHE 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C GLU* 3.1 57.7 - - + +
76C GLY* 3.9 9.0 - - - -
77C TYR* 4.2 20.3 - + + +
82C TYR* 3.3 34.8 - + - -
116C GLN* 4.9 5.4 - - - +
293C ASN 3.0 17.1 + - - +
294C SER* 3.0 10.9 + - - +
296C VAL* 1.3 81.0 - - + +
298C PRO* 1.3 84.4 - - + +
299C GLY 3.3 1.8 - - - +
301C GLN* 3.3 22.0 - - + -
302C GLY 3.8 7.4 - - - +
149D LEU* 4.5 7.0 - - + -
602D THF 4.0 6.1 - - - -
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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