Contacts of the helix formed by residues 257 - 266 (chain M) in PDB entry 5MS0
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 ALA 257 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252M VAL 2.5 13.9 + - - -
253M GLY* 4.1 0.4 - - - -
254M MET 3.4 29.6 - - - +
255M ARG 3.5 1.1 - - - +
256M GLY* 1.3 76.7 + - - +
258M ARG* 1.3 54.2 + - - +
259M VAL 3.4 1.6 - - - -
260M GLN* 3.4 10.5 - - + +
261M ALA* 2.7 34.7 + - - +
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Residues in contact with ARG 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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212M GLU* 5.1 18.5 - - + +
213M VAL* 6.3 2.2 - - + -
250M ALA 5.5 1.3 - - - +
251M CYS* 3.4 21.5 - - - +
252M VAL 2.9 6.5 + - - +
253M GLY* 4.9 2.2 - - - +
257M ALA* 1.3 79.3 - - - +
259M VAL* 1.3 57.4 + - - +
261M ALA* 3.9 5.1 - - - +
262M VAL* 2.9 33.0 + - - +
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Residues in contact with VAL 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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251M CYS 4.2 8.8 + - - +
252M VAL* 4.3 2.7 + - - -
256M GLY 5.4 2.2 - - - +
257M ALA 4.3 0.2 - - - +
258M ARG* 1.3 77.9 - - - +
260M GLN* 1.3 50.3 + - - +
262M VAL* 4.8 3.4 - - - -
263M SER* 2.6 39.3 + - - +
271M ILE* 4.0 27.6 - - + +
16R A 4.6 24.9 - - + +
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Residues in contact with GLN 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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256M GLY* 4.5 9.1 - - - -
257M ALA* 3.2 21.0 + - + +
258M ARG 3.1 0.6 - - - -
259M VAL* 1.3 78.1 - - - +
261M ALA* 1.3 60.0 + - - +
263M SER* 3.6 4.4 - - - -
264M THR* 2.9 30.0 + - - -
16R A 4.7 7.4 + - - +
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Residues in contact with ALA 261 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94E ALA* 4.2 25.4 - - + -
95E GLY* 5.2 5.4 - - - +
257M ALA 2.7 20.0 + - - +
258M ARG* 4.0 4.5 - - - +
260M GLN* 1.3 71.4 - - - +
262M VAL* 1.3 59.0 + - - +
264M THR* 3.4 5.1 + - - -
265M GLU* 2.9 27.4 + - - +
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Residues in contact with VAL 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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205M LEU 5.8 0.9 - - - +
208M LEU* 4.7 24.0 - - + +
209M PHE* 5.5 1.8 - - - +
212M GLU* 5.5 5.8 - - + -
258M ARG 2.9 17.9 + - - +
259M VAL* 4.8 2.9 - - - +
261M ALA* 1.3 73.6 - - - +
263M SER* 1.3 64.9 + - - +
265M GLU* 3.4 9.5 + - - +
266M LEU* 3.3 21.7 + - - +
269M GLU* 5.1 0.3 - - - +
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Residues in contact with SER 263 (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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259M VAL 2.6 26.9 + - - -
260M GLN* 3.6 7.4 - - - -
262M VAL* 1.3 76.5 - - - +
264M THR* 1.3 57.6 + - - +
266M LEU 3.1 16.1 + - - -
267M GLY 2.9 20.6 + - - +
269M GLU* 3.3 31.5 + - - -
271M ILE* 5.7 1.1 - - - -
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Residues in contact with THR 264 (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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260M GLN 2.9 17.8 + - - -
261M ALA* 4.0 4.5 - - - -
263M SER* 1.3 72.8 - - - +
265M GLU* 1.3 64.3 + - - +
267M GLY* 3.8 13.6 + - - -
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Residues in contact with GLU 265 (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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208M LEU* 6.1 4.0 - - + -
261M ALA 2.9 14.3 + - - +
262M VAL* 3.5 14.6 - - - +
263M SER 3.2 0.4 - - - -
264M THR* 1.3 79.0 - - - +
266M LEU* 1.3 58.2 + - + +
267M GLY 3.5 1.1 + - - -
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Residues in contact with LEU 266 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199M ARG 5.8 3.8 - - - +
230M PRO 4.2 15.5 - - - +
231M GLY* 4.7 2.4 - - - -
262M VAL 3.3 10.4 + - - +
263M SER 3.1 6.7 + - - -
265M GLU* 1.3 79.1 - - + +
267M GLY* 1.3 60.0 + - - +
268M GLY 3.5 2.6 + - - -
269M GLU* 3.5 21.7 + - + +
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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