Contacts of the helix formed by residues 249 - 258 (chain B) in PDB entry 1DIZ
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 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B GLY 4.1 7.4 - - - +
248B MET* 1.3 71.9 - - - +
250B PRO* 1.3 70.4 - - + +
251B ALA* 4.8 1.7 - - - +
252B GLN* 2.7 46.6 + - - +
253B ILE* 2.9 29.7 + - - +
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Residues in contact with PRO 250 (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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236B PRO* 3.4 40.2 - - - +
237B ASP* 4.4 9.6 - - + -
242B LYS* 3.2 33.0 - - + +
248B MET 3.9 1.1 - - - +
249B THR* 1.3 84.0 - - + +
251B ALA* 1.3 56.2 + - - +
252B GLN 2.7 14.3 + - - -
253B ILE* 3.0 15.6 + - + +
254B ARG 3.6 0.7 + - - -
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Residues in contact with ALA 251 (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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217B ARG* 5.4 9.6 - - - +
236B PRO* 5.3 1.3 - - - -
249B THR* 3.7 1.9 + - - +
250B PRO* 1.3 78.8 - - - +
252B GLN* 1.3 56.9 + - - +
254B ARG* 3.8 20.5 - - - +
255B ARG* 4.0 14.8 + - - +
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Residues in contact with GLN 252 (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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248B MET* 3.0 24.3 - - + +
249B THR* 2.7 55.3 + - - +
250B PRO 2.7 2.2 + - - -
251B ALA* 1.3 77.0 - - - +
253B ILE* 1.3 52.3 + - - +
254B ARG 2.7 14.7 + - - -
255B ARG* 2.8 36.0 + - - +
256B TYR* 3.7 5.5 + - - +
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Residues in contact with ILE 253 (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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234B PHE* 4.2 16.6 - - + -
236B PRO* 3.9 23.1 - - + +
241B ILE* 4.1 12.8 - - + +
242B LYS* 4.2 6.1 - - - -
245B PHE* 3.4 60.3 - - + -
248B MET* 3.9 21.5 - - + +
249B THR 2.9 21.4 + - - +
250B PRO* 3.5 8.5 - - + +
252B GLN* 1.3 74.3 - - - +
254B ARG* 1.3 56.0 + - - +
256B TYR* 3.3 3.4 + - - +
257B ALA* 3.0 26.8 + - + +
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Residues in contact with ARG 254 (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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203B GLU* 5.7 7.7 - - - +
206B MET* 5.8 4.4 - - - +
217B ARG* 4.4 27.0 - - - +
221B ASN* 4.6 9.4 + - - +
234B PHE* 4.5 16.3 + - - +
236B PRO* 4.1 31.3 - - + +
250B PRO 3.6 4.2 + - - +
251B ALA* 3.8 22.0 - - - +
252B GLN 2.7 1.0 + - - -
253B ILE* 1.3 80.0 - - - +
255B ARG* 1.3 61.6 + - + +
256B TYR 3.3 0.7 + - - -
257B ALA* 3.3 15.5 + - + +
258B GLU* 3.6 13.9 + - - +
264B ARG* 5.8 0.9 + - - -
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Residues in contact with ARG 255 (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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251B ALA 4.4 9.4 + - - +
252B GLN* 2.8 41.3 + - - +
254B ARG* 1.3 73.9 - - + +
256B TYR* 1.3 60.2 + - - +
258B GLU* 3.4 32.4 - - - +
259B ARG 5.0 0.3 + - - -
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Residues in contact with TYR 256 (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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245B PHE* 3.8 20.4 - + - -
248B MET* 4.6 13.7 - - + -
252B GLN 3.7 2.3 + - - +
253B ILE* 3.3 15.0 + - - +
254B ARG 3.2 0.2 - - - -
255B ARG* 1.3 78.0 - - - +
257B ALA* 1.3 63.6 + - - +
258B GLU 3.2 2.5 + - - -
259B ARG* 3.0 66.3 + - - +
260B TRP* 3.6 26.3 - + - -
277B TRP* 4.2 6.5 - + - -
279B PRO* 3.4 20.9 - - + +
280B ASP* 2.8 35.8 + - - +
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Residues in contact with ALA 257 (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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234B PHE* 3.9 34.3 - - + -
253B ILE 3.0 15.7 + - - +
254B ARG* 3.3 9.1 + - + +
256B TYR* 1.3 77.5 - - - +
258B GLU* 1.3 64.0 + - - +
260B TRP* 2.9 37.6 + - + -
264B ARG* 3.5 17.9 - - - +
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Residues in contact with GLU 258 (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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254B ARG 3.6 10.7 + - - +
255B ARG* 3.4 28.5 - - - +
256B TYR 3.2 0.2 - - - -
257B ALA* 1.3 77.2 - - - +
259B ARG* 1.3 64.2 + - - +
260B TRP 2.8 1.9 + - - -
261B LYS* 2.9 22.3 + - + +
264B ARG* 4.5 19.5 - - - +
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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