Contacts of the helix formed by residues 232 - 238 (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 ILE 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A TYR* 4.1 20.2 - - - +
229A MSE 3.2 20.8 + - + -
231A HIS* 1.3 86.0 - - + +
233A SER* 1.3 67.3 + - - +
234A GLY 3.1 2.7 - - - -
235A LEU* 3.8 24.0 - - + -
236A VAL* 2.9 44.4 + - + +
241A VAL* 4.6 7.6 - - + -
242A PRO 4.9 3.6 - - - +
244A PRO* 5.1 1.1 - - + -
258A THR* 3.4 2.2 - - - -
356A ASN* 4.8 9.0 - - + +
357A HIS* 4.3 8.5 - - + +
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Residues in contact with SER 233 (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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104A TYR* 2.8 31.4 + - - -
229A MSE 2.8 18.0 + - - -
230A ALA 3.3 11.4 + - - -
232A ILE* 1.3 75.1 - - - +
234A GLY* 1.3 60.7 + - - +
237A ALA* 3.0 19.1 + - - +
253A THR* 3.3 24.7 - - - -
254A THR 3.8 4.2 + - - -
256A HIS 4.1 1.6 + - - -
258A THR* 3.2 4.8 + - - -
259A LEU* 3.5 22.6 + - - +
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Residues in contact with GLY 234 (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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233A SER* 1.3 72.2 + - - +
235A LEU* 1.3 64.4 + - - -
236A VAL 3.1 1.8 - - - -
237A ALA* 3.2 2.1 + - - +
238A ALA* 2.9 25.6 + - - +
258A THR* 2.7 38.9 + - - -
259A LEU* 3.9 12.8 - - - -
324A PHE* 3.9 3.0 - - - -
328A GLN* 3.8 8.2 - - - +
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Residues in contact with LEU 235 (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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232A ILE* 3.2 16.1 + - + +
234A GLY* 1.3 74.8 - - - +
236A VAL* 1.3 61.8 + - - +
238A ALA 3.5 0.9 + - - -
239A GLY 3.2 2.8 + - - -
240A VAL* 3.2 39.8 + - + +
241A VAL* 3.6 19.9 + - + -
258A THR* 3.9 11.9 + - + -
328A GLN* 3.0 49.4 - - + +
331A VAL* 4.5 9.4 - - + -
332A LEU* 4.3 5.2 - - + -
356A ASN* 3.9 19.3 - - + -
357A HIS* 3.8 28.5 - - - +
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Residues in contact with VAL 236 (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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104A TYR* 4.1 19.0 - - + -
229A MSE 4.3 5.6 - - - -
232A ILE* 2.9 51.7 + - + +
233A SER 3.8 3.4 - - - +
235A LEU* 1.3 74.0 - - - +
237A ALA* 1.3 67.4 + - - +
238A ALA 3.1 1.6 - - - -
239A GLY* 2.9 15.1 + - - -
241A VAL* 3.7 16.4 - - + +
242A PRO 4.2 5.4 - - - +
243A SER* 3.8 33.6 - - - +
244A PRO* 4.0 9.4 - - + -
245A PHE* 4.8 0.4 - - + -
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Residues in contact with ALA 237 (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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103A ALA* 3.7 22.8 - - + +
104A TYR* 3.6 25.3 - - + +
105A HIS* 5.3 6.2 + - - -
233A SER 3.0 18.2 + - - +
234A GLY* 3.2 6.5 + - - +
236A VAL* 1.3 76.5 - - - +
238A ALA* 1.3 60.7 + - - +
239A GLY* 3.4 0.9 + - - -
259A LEU* 4.6 8.3 - - + -
316A LEU* 6.5 0.2 - - + -
319A ALA* 4.7 12.0 - - + +
324A PHE* 4.6 7.4 - - + -
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Residues in contact with ALA 238 (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 GLY 2.9 17.8 + - - +
235A LEU 3.8 2.7 - - - +
237A ALA* 1.3 77.9 - - - +
239A GLY* 1.3 57.6 + - - +
240A VAL* 3.2 7.2 + - + +
319A ALA 5.1 0.9 - - - -
324A PHE* 4.2 11.4 - - + -
325A LYS* 2.9 45.1 + - - +
328A GLN* 3.5 29.8 - - + -
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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