Contacts of the helix formed by residues 228 - 238 (chain A) in PDB entry 1EAG
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 GLN 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A LEU 3.4 2.4 + - - -
227A GLN* 1.3 70.6 - - - +
229A ASP* 1.3 56.9 + - - +
231A ALA* 4.2 2.2 - - - -
232A ASP* 2.8 57.9 + - - +
252A TYR* 5.3 4.4 + - - -
300A VAL* 3.4 31.0 - - + +
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Residues in contact with ASP 229 (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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211A ASP* 5.4 1.7 - - - +
227A GLN* 3.0 33.1 + - - +
228A GLN* 1.3 74.1 - - - +
230A LEU* 1.3 74.7 + - - +
232A ASP* 4.2 4.5 + - - +
233A GLN* 2.9 29.1 + - - +
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Residues in contact with LEU 230 (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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208A ILE* 4.6 1.4 - - + +
209A ASN 3.8 22.4 - - - +
210A THR* 3.8 33.0 - - + +
211A ASP* 4.4 9.2 - - + +
213A VAL* 4.1 17.7 - - + -
226A LEU* 4.5 15.7 - - + -
227A GLN* 2.8 33.0 + - + +
229A ASP* 1.3 92.1 - - - +
231A ALA* 1.3 68.7 + - - +
232A ASP 3.1 2.2 - - - -
233A GLN* 3.0 27.3 + - - +
234A ILE* 3.3 16.6 + - - +
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Residues in contact with ALA 231 (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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226A LEU* 3.6 30.4 - - + +
227A GLN 3.0 7.6 + - - +
228A GLN 3.9 0.9 - - - +
230A LEU* 1.3 77.9 - - - +
232A ASP* 1.3 57.5 + - - +
234A ILE* 3.2 8.0 + - - +
235A ILE* 3.0 36.4 + - + +
298A PHE* 4.7 7.1 - - + -
299A ASP 4.0 9.0 - - - +
300A VAL* 3.7 24.2 - - + -
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Residues in contact with ASP 232 (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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228A GLN* 2.8 48.7 + - - +
229A ASP* 4.6 4.6 - - - +
230A LEU 3.1 0.2 - - - -
231A ALA* 1.3 78.0 - - - +
233A GLN* 1.3 60.9 + - + +
235A ILE* 3.9 11.1 - - - +
236A LYS* 3.2 23.7 + - - +
252A TYR* 4.4 7.1 + - - -
300A VAL* 4.2 9.7 - - - +
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Residues in contact with GLN 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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206A LYS* 5.8 0.3 - - - +
208A ILE* 3.4 33.0 - - + +
209A ASN 4.3 6.0 + - - +
229A ASP* 2.9 27.7 + - - +
230A LEU* 3.0 21.3 + - - +
232A ASP* 1.3 76.2 - - + +
234A ILE* 1.3 61.2 - - - +
236A LYS* 3.3 13.2 - - - +
237A ALA* 3.2 20.4 + - - +
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Residues in contact with ILE 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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201A VAL* 4.3 22.0 - - + -
203A VAL* 4.6 4.9 - - + -
208A ILE* 3.7 30.5 - - + -
210A THR* 4.6 3.4 - - + -
226A LEU* 3.9 16.4 - - + -
230A LEU 3.3 14.5 + - - +
231A ALA 3.2 6.1 + - - +
233A GLN* 1.3 74.6 - - - +
235A ILE* 1.3 66.2 + - - +
237A ALA* 3.2 11.3 + - - +
238A PHE* 3.1 44.1 + - + -
298A PHE* 3.8 41.1 - - + -
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Residues in contact with ILE 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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231A ALA* 3.0 29.7 + - + +
232A ASP* 3.9 10.5 - - - +
234A ILE* 1.3 75.9 - - + +
236A LYS* 1.3 58.4 + - - +
238A PHE* 3.1 4.0 + - - +
239A ASN 2.9 8.8 + - - -
240A GLY* 2.8 40.7 + - - +
252A TYR* 3.7 53.6 - - + -
296A LEU* 3.8 22.2 - - + -
298A PHE* 4.3 15.5 - - + +
300A VAL* 4.2 14.6 - - + -
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Residues in contact with LYS 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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232A ASP 3.2 16.4 + - - +
233A GLN* 3.3 12.6 - - - +
235A ILE* 1.3 81.0 - - - +
237A ALA* 1.3 56.8 + - - +
239A ASN* 2.9 27.1 + - - +
240A GLY 4.7 2.0 - - - +
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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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203A VAL* 4.0 23.5 - - + +
204A SER* 4.7 6.1 + - - -
206A LYS* 4.0 29.9 + - + +
208A ILE* 3.9 18.4 - - + -
233A GLN 3.2 9.9 + - - +
234A ILE 3.2 10.1 + - - +
236A LYS* 1.3 77.9 - - - +
238A PHE* 1.3 56.6 + - - +
239A ASN* 3.2 7.5 + - - -
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Residues in contact with PHE 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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203A VAL* 3.8 22.0 - - + -
234A ILE* 3.1 46.7 + - + -
235A ILE 3.1 7.7 + - - +
237A ALA* 1.3 75.7 - - - +
239A ASN* 1.3 71.4 + - - +
240A GLY 4.2 0.2 - - - +
254A VAL* 3.5 22.4 - - + +
258A LEU* 4.0 36.8 - - + +
262A VAL* 3.8 28.7 - - + -
276A ALA* 5.1 3.1 - - + -
279A PHE* 4.3 16.2 - + + -
296A LEU* 3.7 23.8 - - + -
298A PHE* 4.2 10.1 - + + -
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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