Contacts of the helix formed by residues 225 - 235 (chain A) in PDB entry 3PEP
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 THR 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A GLY 3.8 1.2 + - - -
224A PRO* 1.3 69.5 - - - +
226A SER* 1.3 61.2 + - - +
228A ILE* 3.9 7.6 - - - +
229A ALA* 3.1 26.9 + - - +
288A GLY* 3.9 20.0 - - - -
289A MET* 4.0 6.0 + - - +
290A ASP* 3.0 20.5 + - - +
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Residues in contact with SER 226 (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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224A PRO* 2.9 8.7 + - - +
225A THR* 1.3 77.8 + - - +
227A ALA* 1.3 65.7 + - - -
229A ALA* 3.0 15.8 + - - +
230A ASN* 3.4 10.4 + - - +
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Residues in contact with ALA 227 (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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205A ALA* 4.6 13.6 - - + +
224A PRO* 3.2 11.4 + - + +
226A SER* 1.3 78.7 - - - +
228A ILE* 1.3 61.7 + - - +
230A ASN* 3.2 12.8 + - - +
231A ILE* 3.0 25.0 + - - +
299A TRP* 3.4 35.7 - - + -
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Residues in contact with ILE 228 (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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221A LEU* 5.2 0.2 - - + -
222A THR 4.3 1.6 - - - -
223A GLY* 3.5 36.6 - - - +
224A PRO 2.9 22.2 + - - +
225A THR* 4.2 2.7 - - - +
227A ALA* 1.3 73.8 - - - +
229A ALA* 1.3 65.8 + - - +
230A ASN 3.0 2.0 - - - -
231A ILE* 2.9 8.1 + - + +
232A GLN* 2.9 45.9 + - + +
286A PHE* 4.2 26.2 - - + -
287A GLU 3.5 8.5 - - - +
288A GLY* 3.7 19.5 - - - +
299A TRP* 4.2 13.0 - - + -
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Residues in contact with ALA 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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225A THR 3.1 17.9 + - - +
226A SER* 3.0 7.5 + - - +
228A ILE* 1.3 73.9 - - - +
230A ASN* 1.3 62.9 + - - +
232A GLN* 3.2 11.9 + - - +
233A SER* 3.1 26.0 + - - -
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Residues in contact with ASN 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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204A ILE* 2.6 35.0 + - - +
226A SER 3.4 8.7 + - - +
227A ALA* 3.2 16.4 + - - +
229A ALA* 1.3 78.0 - - - +
231A ILE* 1.3 63.1 + - - +
233A SER* 5.2 0.7 - - - -
234A ASP* 2.7 38.3 + - - +
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Residues in contact with ILE 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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197A ILE* 4.5 12.1 - - + -
204A ILE* 4.5 17.0 - - + -
205A ALA* 4.3 19.5 - - + -
227A ALA 3.0 14.2 + - - +
228A ILE* 2.9 19.7 + - + +
230A ASN* 1.3 75.1 - - - +
232A GLN* 1.3 66.4 + - - +
234A ASP* 2.9 16.5 + - + +
235A ILE* 3.0 23.7 + - + +
258A ILE* 4.6 3.6 - - + -
286A PHE* 3.9 54.5 - - + -
299A TRP* 4.4 8.7 - - + -
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Residues in contact with GLN 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 ILE* 2.9 30.7 + - + +
229A ALA* 3.2 9.8 + - - +
231A ILE* 1.3 76.2 - - - +
233A SER* 1.3 61.7 + - - +
235A ILE* 3.5 7.0 - - - +
236A GLY 3.2 3.6 + - - -
237A ALA* 2.7 30.4 + - + +
245A MET* 3.6 35.8 - - + +
284A SER* 3.2 28.7 + - - -
286A PHE* 2.8 41.9 + - - +
287A GLU* 4.6 1.0 - - - +
288A GLY 5.2 0.4 - - - +
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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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229A ALA 3.1 13.8 + - - -
230A ASN* 5.2 0.7 - - - -
232A GLN* 1.3 74.5 - - - +
234A ASP* 1.3 67.0 + - - +
236A GLY* 3.1 12.7 + - - +
237A ALA 4.0 13.4 + - - -
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Residues in contact with ASP 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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199A MET* 4.5 19.4 - - - +
202A GLU* 5.6 0.9 - - - +
204A ILE* 3.9 22.1 - - + +
230A ASN* 2.7 31.1 + - - +
231A ILE* 2.9 12.0 + - - +
233A SER* 1.3 79.7 - - - +
235A ILE* 1.3 62.0 + - + +
236A GLY* 3.3 0.9 + - - -
255A LEU* 4.1 8.8 - - - +
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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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199A MET* 4.8 10.5 - - + -
231A ILE* 3.0 23.8 + - + +
232A GLN* 3.5 20.6 - - - +
234A ASP* 1.3 76.4 - - + +
236A GLY* 1.3 57.8 + - - +
247A ILE* 3.5 36.9 - - + +
251A SER* 4.6 4.0 + - - -
255A LEU* 3.6 32.1 - - + +
258A ILE* 6.0 0.9 - - + -
274A TYR* 3.6 33.9 - - + +
284A SER* 3.7 19.1 - - - -
286A PHE* 3.9 17.5 - - + -
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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