Contacts of the helix formed by residues 246 - 258 (chain B) in PDB entry 5DTM
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 GLY 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242B ASN 4.4 1.8 + - - -
243B PHE 4.7 2.8 + - - -
244B ALA 3.5 2.6 - - - -
245B PHE* 1.3 82.2 - - - +
247B PRO* 1.4 75.1 - - - +
248B GLU 3.1 4.6 + - - -
249B VAL 3.4 0.5 + - - -
250B ASP* 3.2 22.4 + - - +
270B LYS* 5.5 6.3 - - - +
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Residues in contact with PRO 247 (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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246B GLY* 1.4 81.2 - - - +
248B GLU* 1.3 57.2 + - - +
249B VAL 3.6 0.2 - - - -
250B ASP* 3.5 14.5 - - + +
251B HIS* 3.1 28.4 + - - +
270B LYS* 6.2 0.9 - - - +
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Residues in contact with GLU 248 (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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224B LEU* 6.1 0.9 - - - +
245B PHE 6.0 0.2 - - - +
246B GLY 3.1 1.8 + - - -
247B PRO* 1.3 75.0 - - - +
249B VAL* 1.4 72.4 + - + +
251B HIS* 3.5 7.7 + - - +
252B GLN* 3.4 31.9 + - + +
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Residues in contact with VAL 249 (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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223B PHE* 4.4 19.3 - - + -
224B LEU* 4.4 16.6 - - + +
245B PHE* 3.6 48.4 + - + +
246B GLY 3.4 1.6 + - - -
248B GLU* 1.4 80.7 - - + +
250B ASP* 1.3 64.4 + - - +
252B GLN* 3.2 9.8 + - - +
253B LEU* 3.0 23.1 + - + +
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Residues in contact with ASP 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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242B ASN* 4.8 4.8 + - - +
245B PHE* 4.9 4.4 - - + +
246B GLY 3.2 19.9 + - - +
247B PRO* 3.5 14.8 - - + +
249B VAL* 1.3 76.5 - - - +
251B HIS* 1.3 61.5 + - - +
253B LEU* 3.3 8.8 + - - +
254B LYS* 3.1 54.0 + - - +
271B PRO 5.0 2.1 - - - +
272B PHE* 3.2 33.6 - - + -
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Residues in contact with HIS 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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247B PRO 3.1 15.1 + - - +
248B GLU* 3.5 7.6 - - - +
249B VAL 3.2 0.2 - - - -
250B ASP* 1.3 81.4 - - - +
252B GLN* 1.3 83.2 - - - +
254B LYS* 3.5 14.8 + - - +
255B GLU* 3.4 25.2 + - - +
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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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224B LEU* 3.7 27.6 - - + -
229B ARG* 4.6 1.9 + - - -
248B GLU* 3.4 21.6 + - - +
249B VAL* 3.2 8.4 + - - +
251B HIS* 1.3 93.9 - - - +
253B LEU* 1.3 62.2 + - - +
255B GLU* 3.3 14.8 + - - +
256B ARG* 2.9 56.8 + - - +
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Residues in contact with LEU 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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162B LEU* 3.8 22.0 - - + -
223B PHE* 3.7 27.4 - - + -
224B LEU* 4.4 4.7 - - + -
232B ILE* 4.7 7.2 - - + -
240B VAL* 4.3 6.7 - - + -
245B PHE* 4.0 32.1 - - + -
249B VAL* 3.0 16.3 + - + +
250B ASP* 3.5 9.0 - - - +
251B HIS 3.3 0.2 - - - -
252B GLN* 1.3 73.2 - - - +
254B LYS* 1.3 54.1 + - - +
256B ARG* 3.0 7.2 + - + +
257B PHE* 2.8 55.2 + - + -
272B PHE* 4.0 22.0 - - + -
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Residues in contact with LYS 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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250B ASP* 3.1 45.1 + - - +
251B HIS* 3.6 16.0 + - - +
252B GLN 3.4 0.2 - - - -
253B LEU* 1.3 74.1 - - - +
255B GLU* 1.3 55.4 + - - +
257B PHE* 3.4 7.9 + - - -
258B ALA* 3.0 25.5 + - - +
272B PHE* 3.2 35.8 + - + -
287B ILE* 3.3 39.6 - - + +
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Residues in contact with GLU 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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229B ARG* 2.8 33.4 + - - +
251B HIS* 3.4 15.4 + - + +
252B GLN* 3.3 23.4 + - - +
253B LEU 3.2 0.4 - - - -
254B LYS* 1.3 78.5 - - - +
256B ARG* 1.3 67.6 + - - +
258B ALA* 3.5 18.0 + - - +
259B ASN* 3.6 13.1 + - - +
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Residues in contact with ARG 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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223B PHE 4.7 1.2 + - - -
224B LEU* 2.7 52.1 + - + +
226B GLU* 5.2 0.2 + - - -
229B ARG* 3.4 58.6 - - + +
232B ILE* 3.8 42.7 - - + +
233B ALA 4.7 1.7 + - - -
252B GLN* 2.9 56.5 + - - +
253B LEU* 3.0 12.6 + - + +
255B GLU* 1.3 84.5 + - - +
257B PHE* 1.4 61.0 + - + +
259B ASN* 3.3 23.0 + - - +
260B MET* 4.1 2.1 + - - +
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Residues in contact with PHE 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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162B LEU* 4.2 10.1 - - + -
232B ILE* 4.0 10.3 - - + -
238B ILE* 4.0 21.8 - - + -
240B VAL* 4.3 3.4 - - + -
253B LEU* 2.8 44.6 + - + +
254B LYS* 3.8 9.4 - - - +
256B ARG* 1.4 71.7 - - - +
258B ALA* 1.4 56.4 + - - +
259B ASN 3.1 0.7 - - - -
260B MET* 3.0 43.3 + - - +
266B ILE* 3.9 35.2 - - + -
272B PHE* 3.6 45.5 - + + -
287B ILE* 4.5 1.1 - - + -
291B MET* 4.4 12.1 - - + -
317B ILE* 3.6 11.8 - - - +
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Residues in contact with ALA 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 LYS 3.0 15.6 + - - +
255B GLU* 3.6 12.3 - - - +
256B ARG 3.2 1.2 - - - -
257B PHE* 1.4 74.0 - - - +
259B ASN* 1.3 56.3 + - - +
260B MET 3.4 0.4 - - - -
287B ILE* 4.1 9.2 - - + +
290B ILE* 3.8 18.6 - - + +
319B ARG* 2.8 24.0 + - - -
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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