Contacts of the helix formed by residues 249 - 262 (chain M) in PDB entry 5D4D
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 LYS 249 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236M ILE* 4.0 0.4 - - - -
239M PHE* 4.8 0.2 - - - -
247M PRO* 2.7 34.8 + - - +
248M PRO* 1.3 71.9 - - - +
250M ARG* 1.3 62.8 + - - +
251M ASP* 3.4 29.4 - - - +
252M LYS* 4.0 13.1 - - + +
253M ALA* 2.9 31.0 + - - +
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Residues in contact with ARG 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232M GLU* 3.0 54.7 + - - +
235M LEU* 5.0 3.1 - - + -
236M ILE* 3.8 19.4 - - + +
248M PRO 3.8 1.8 + - - -
249M LYS* 1.3 75.9 - - - +
251M ASP* 1.3 58.8 + - - +
253M ALA* 3.9 0.7 - - - +
254M VAL* 2.9 60.1 + - + +
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Residues in contact with ASP 251 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249M LYS* 3.6 27.5 - - - +
250M ARG* 1.3 79.3 - - - +
252M LYS* 1.3 79.1 + - - +
254M VAL* 3.9 5.3 - - - +
255M ALA* 2.9 28.6 + - - +
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Residues in contact with LYS 252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239M PHE* 3.9 17.4 - - + -
243M ARG* 4.4 2.0 - - - +
246M ASP* 2.4 32.8 + - - -
247M PRO* 4.6 17.5 - - + +
249M LYS* 3.5 19.5 + - + +
250M ARG 3.3 0.4 - - - -
251M ASP* 1.3 87.7 + - - +
253M ALA* 1.3 58.8 + - - +
255M ALA* 3.4 7.6 + - + +
256M TYR* 2.9 27.7 + - - +
8S G 5.2 9.0 - - - -
9S G 4.1 12.4 + - - -
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Residues in contact with ALA 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M LEU* 3.5 22.7 - - + +
236M ILE* 4.5 5.2 - - + -
239M PHE* 3.5 38.3 - - + -
249M LYS 2.9 19.1 + - - +
250M ARG 4.0 0.4 - - - +
252M LYS* 1.3 75.8 - - - +
254M VAL* 1.3 58.9 + - - +
256M TYR* 3.7 0.5 - - - +
257M VAL* 2.9 35.4 + - + +
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Residues in contact with VAL 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M LEU* 3.9 17.5 - - + -
250M ARG* 2.9 47.2 + - - +
251M ASP* 4.0 5.6 - - - +
253M ALA* 1.3 72.5 - - - +
255M ALA* 1.3 61.5 + - - +
258M TYR* 2.9 37.8 + - + +
293M PHE* 4.9 13.5 - - + -
298M PHE* 3.7 28.6 - - + -
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Residues in contact with ALA 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251M ASP 2.9 19.5 + - - +
252M LYS* 3.4 9.2 - - + +
253M ALA 3.3 0.2 - - - -
254M VAL* 1.3 78.4 - - - +
256M TYR* 1.3 56.2 + - - +
258M TYR* 4.1 7.5 - - - +
259M GLY* 2.9 24.9 + - - -
266M ARG* 4.9 3.8 + - - -
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Residues in contact with TYR 256 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187M ASN* 4.5 5.2 + - - +
238M LEU* 5.9 0.2 - - + -
239M PHE* 3.6 25.4 - + + -
242M LEU* 3.7 43.5 + - + +
243M ARG* 3.5 34.2 - - - +
252M LYS 2.9 15.9 + - - +
253M ALA 3.7 2.2 - - - +
254M VAL 3.2 0.2 - - - -
255M ALA* 1.3 74.9 - - - +
257M VAL* 1.3 69.9 + - + +
259M GLY* 3.2 1.1 + - - -
260M LEU* 2.9 50.8 + - + +
10S A 4.1 22.4 - + - -
11S G 4.1 20.0 + - - -
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Residues in contact with VAL 257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M LEU* 5.6 7.9 - - + -
199M VAL* 5.1 5.8 - - + -
200M LEU* 6.1 1.6 - - + -
235M LEU* 3.8 28.9 - - + +
238M LEU* 4.3 22.7 - - + -
239M PHE* 5.7 2.2 - - + +
242M LEU* 5.9 0.2 - - + -
253M ALA* 2.9 23.3 + - + +
256M TYR* 1.3 82.2 - - + +
258M TYR* 1.3 57.8 + - - +
260M LEU* 4.7 4.3 - - + -
261M ILE* 2.9 47.0 + - + +
298M PHE* 3.8 16.8 - - + -
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Residues in contact with TYR 258 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254M VAL* 2.9 24.2 + - + +
255M ALA* 4.1 6.7 - - - +
257M VAL* 1.3 76.3 - - - +
259M GLY* 1.3 60.9 + - - +
262M ALA* 3.1 20.3 + - + -
263M ASP* 2.5 76.8 + - + -
264M PRO* 4.3 6.0 - - + +
293M PHE* 3.7 35.0 - + + -
298M PHE* 3.7 15.7 - + + -
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Residues in contact with GLY 259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255M ALA 2.9 19.2 + - - -
256M TYR* 3.2 1.3 + - - -
258M TYR* 1.3 82.5 - - - +
260M LEU* 1.3 60.8 + - - +
263M ASP* 3.9 12.5 + - - +
266M ARG* 3.2 51.1 - - - +
267M TYR 4.5 0.3 + - - -
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Residues in contact with LEU 260 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169M GLY* 5.2 0.2 - - - -
170M PRO* 3.6 34.0 - - + +
186M VAL* 4.1 20.0 - - + -
187M ASN* 3.9 12.6 - - - +
242M LEU* 4.2 10.1 - - + -
256M TYR* 2.9 44.6 + - + +
257M VAL* 4.3 3.1 - - + +
259M GLY* 1.3 77.4 - - - +
261M ILE* 1.3 74.7 + - + +
266M ARG* 5.0 3.6 - - - +
267M TYR* 3.6 24.1 - - - +
11S G 4.8 18.8 + - + +
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Residues in contact with ILE 261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170M PRO* 5.8 2.2 - - + -
172M ILE* 3.7 29.4 - - + -
184M MET* 5.0 3.8 - - + -
186M VAL* 5.2 1.8 - - + -
196M LEU* 4.6 16.2 - - + -
200M LEU* 5.5 4.9 - - + -
257M VAL* 2.9 38.7 + - + +
260M LEU* 1.3 93.5 - - + +
262M ALA* 1.3 62.8 + - + +
267M TYR* 5.0 6.2 - - + -
289M THR* 4.8 0.3 - - - -
290M LEU* 4.2 13.3 + - + +
291M ALA* 3.6 28.6 + - + -
298M PHE* 4.9 4.5 - - + -
303M PHE* 3.7 24.5 - - + -
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Residues in contact with ALA 262 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258M TYR* 3.1 33.9 + - + +
260M LEU 3.5 1.8 + - - -
261M ILE* 1.3 87.2 - - + +
263M ASP* 1.3 67.7 - - - +
264M PRO* 3.2 6.7 - - - +
267M TYR* 5.2 0.4 - - - -
289M THR* 3.2 23.9 + - - +
291M ALA 3.3 19.7 - - - +
293M PHE 4.7 4.9 - - - +
298M PHE* 4.4 8.1 - - + -
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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