Contacts of the helix formed by residues 252 - 267 (chain F) in PDB entry 5MG3
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 SER 252 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519D ASP* 2.7 27.8 + - - -
522D VAL* 4.9 0.6 - - - +
209F TYR 3.6 18.4 - - - -
210F SER 4.4 0.9 - - - -
212F ASN* 3.0 23.9 + - - -
213F ASP* 5.2 2.9 - - - -
249F LEU 5.2 0.2 - - - -
250F ILE 3.4 0.6 + - - -
251F THR* 1.4 71.6 - - - +
253F GLY* 1.3 58.7 + - - +
254F THR* 3.3 2.4 + - - -
255F THR* 3.1 17.3 - - - -
256F LEU* 3.0 28.6 + - - +
281F VAL* 4.1 10.9 - - - +
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Residues in contact with GLY 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D PHE* 3.6 17.8 - - - -
249F LEU 4.5 4.0 + - - -
250F ILE 3.0 17.0 + - - -
251F THR 3.1 2.0 + - - -
252F SER* 1.3 79.8 - - - +
254F THR* 1.3 54.8 + - - +
256F LEU* 3.4 10.8 + - - +
257F MET* 3.0 31.4 + - - +
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Residues in contact with THR 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D SER* 3.1 44.5 + - - +
467D PHE* 3.7 23.9 - - + -
468D MET* 5.0 3.1 - - + -
518D VAL* 3.8 17.6 + - + +
519D ASP* 2.5 22.1 + - - -
522D VAL* 3.3 35.5 - - + +
252F SER 4.3 2.8 + - - -
253F GLY* 1.3 71.9 - - - +
255F THR* 1.3 63.4 - - - -
257F MET* 3.4 4.4 + - - +
258F VAL* 3.4 9.5 + - - +
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Residues in contact with THR 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515D ALA* 3.3 44.0 - - + +
518D VAL* 4.3 1.1 - - + -
519D ASP* 2.7 29.0 + - - +
209F TYR* 3.8 9.2 - - + +
252F SER* 3.1 18.0 + - - -
254F THR* 1.3 74.6 - - - +
256F LEU* 1.4 65.7 + - - +
258F VAL* 3.1 17.8 + - + +
259F ILE* 3.2 22.1 + - + +
281F VAL* 3.6 13.3 - - - +
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Residues in contact with LEU 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252F SER 3.0 20.9 + - - +
253F GLY* 3.5 8.3 - - - +
255F THR* 1.4 76.3 - - - +
257F MET* 1.4 64.0 + - + +
259F ILE* 3.3 4.0 + - + -
260F LEU* 3.0 49.4 + - + +
278F LEU* 4.2 25.4 - - + +
281F VAL* 3.4 29.8 - - + +
282F SER* 6.0 3.1 - - - -
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Residues in contact with MET 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D GLY 4.5 2.2 - - - -
463D VAL* 3.6 42.2 - - + +
464D SER* 4.3 1.8 - - - +
467D PHE* 4.2 27.1 - - + +
470D ILE* 6.1 4.9 - - + -
471D PHE* 5.1 7.2 - - + -
253F GLY 3.0 18.3 + - - +
254F THR 3.6 8.5 - - - +
255F THR 3.3 0.6 - - - -
256F LEU* 1.4 76.5 - - - +
258F VAL* 1.4 61.1 + - - +
260F LEU* 3.4 19.4 + - + +
261F MET* 3.4 26.9 + - - +
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Residues in contact with VAL 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456D ALA 4.6 3.3 - - - +
457D CYS* 5.6 0.4 - - - -
460D GLY* 3.6 18.3 - - - +
464D SER* 3.0 23.6 - - - +
511D VAL* 3.9 29.6 - - + +
514D LEU* 3.9 33.0 - - + -
515D ALA* 5.3 0.9 - - + -
518D VAL* 4.3 10.1 - - + -
254F THR 3.5 7.2 - - - +
255F THR* 3.1 13.2 + - + +
257F MET* 1.4 75.7 - - - +
259F ILE* 1.4 60.3 + - + +
261F MET* 3.2 6.8 + - - +
262F LEU* 3.2 19.7 + - + +
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Residues in contact with ILE 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511D VAL* 4.9 7.6 - - + -
206F VAL* 5.6 1.8 - - + -
255F THR* 3.2 22.7 + - + +
256F LEU* 3.3 5.4 + - + +
258F VAL* 1.4 74.7 - - + +
260F LEU* 1.3 59.9 - - - +
262F LEU* 3.4 11.3 - - + +
263F TYR* 2.8 28.1 + - - +
274F SER* 4.0 6.4 - - - +
277F MET* 3.3 56.8 - - + +
278F LEU* 3.4 24.5 - - + +
281F VAL* 3.9 23.1 - - + -
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Residues in contact with LEU 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F LEU* 3.0 41.4 + - + +
257F MET* 3.7 21.5 - - - +
258F VAL 3.3 0.2 - - - -
259F ILE* 1.3 78.8 - - - +
261F MET* 1.4 66.9 + - + +
263F TYR* 3.3 14.2 + - + +
264F LEU* 2.9 29.5 + - - +
278F LEU* 3.7 29.6 - - + -
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Residues in contact with MET 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456D ALA* 3.9 9.3 - - - +
459D ALA* 3.6 23.6 - - + -
460D GLY* 3.5 17.7 - - - +
463D VAL* 3.6 37.9 - - + -
257F MET* 3.4 11.8 + - - +
258F VAL 3.2 6.6 + - - +
260F LEU* 1.4 86.2 - - + +
262F LEU* 1.3 61.7 + - - +
264F LEU* 3.5 16.5 + - + -
265F PHE* 3.4 42.2 + - - -
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Residues in contact with LEU 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452D GLN 5.0 0.4 - - - +
453D GLY* 4.2 7.0 - - - +
456D ALA* 3.5 26.5 - - + +
504D MET* 4.2 21.3 - - + -
511D VAL* 4.1 29.8 - - + -
258F VAL* 3.2 13.2 + - + +
259F ILE* 3.4 12.6 - - - +
261F MET* 1.3 74.1 - - - +
263F TYR* 1.3 56.9 + - - +
266F GLY* 2.9 30.7 + - - -
270F LEU* 5.0 8.1 - - + -
273F PHE* 4.2 24.5 - - + -
274F SER* 4.0 12.5 + - - +
277F MET* 5.0 12.8 - - + -
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Residues in contact with TYR 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259F ILE 2.8 20.7 + - - +
260F LEU* 3.3 14.3 + - + +
262F LEU* 1.3 72.9 - - - +
264F LEU* 1.4 59.9 + - + +
267F GLY* 3.3 22.6 + - - +
271F GLU* 4.9 24.7 + - + +
274F SER* 3.5 29.7 + - - -
275F LEU* 5.4 6.7 - - + -
278F LEU* 3.7 27.1 - - + -
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Residues in contact with LEU 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260F LEU 2.9 17.3 + - - +
261F MET* 3.5 23.1 + - + +
262F LEU 3.4 0.6 - - - -
263F TYR* 1.4 75.5 - - + +
265F PHE* 1.3 92.5 + - + +
267F GLY* 3.9 8.3 + - - -
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Residues in contact with PHE 265 (chain F).
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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440D THR* 4.9 7.0 - - + -
441D ILE* 4.6 8.3 - - + +
452D GLN* 2.9 43.5 + - + +
455D GLU* 4.3 25.1 - - + -
456D ALA* 5.0 1.6 - - - +
459D ALA* 4.6 11.7 - - + -
261F MET* 3.4 34.4 + - - +
264F LEU* 1.3 108.3 - - + +
266F GLY* 1.3 59.9 + - - +
267F GLY 3.3 1.3 - - - -
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Residues in contact with GLY 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452D GLN* 3.4 10.1 + - - -
262F LEU 2.9 19.6 + - - -
263F TYR 4.2 0.4 - - - -
265F PHE* 1.3 76.7 - - - +
267F GLY* 1.3 65.4 + - - +
268F PRO* 3.5 0.5 - - - +
269F VAL* 3.4 13.7 - - - +
270F LEU* 3.1 41.3 + - - -
274F SER* 5.2 0.7 - - - -
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Residues in contact with GLY 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F SER* 4.9 0.7 - - - -
263F TYR* 3.3 20.1 + - - +
264F LEU 3.9 6.7 + - - -
265F PHE 3.3 3.0 - - - -
266F GLY* 1.3 73.9 - - - +
268F PRO* 1.4 73.2 - - - +
271F GLU* 3.2 23.3 + - - +
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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