Contacts of the helix formed by residues 232 - 248 (chain H) in PDB entry 1RFU
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 232 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18H TYR 3.8 5.8 - - - -
19H VAL* 3.3 20.0 - - - -
23H ALA* 4.1 3.5 - - - +
231H VAL* 1.3 74.9 - - - +
233H THR* 1.3 67.0 + - - +
234H GLY 3.2 2.2 - - - -
235H ASP* 3.2 8.0 + - - +
236H LEU* 2.9 21.8 + - - +
291H LEU* 4.1 5.6 - - - -
7401H PLP 2.8 19.7 + - - -
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Residues in contact with THR 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230H PHE* 3.7 28.6 + - + -
231H VAL 3.3 1.2 + - - -
232H GLY* 1.3 77.0 + - - +
234H GLY* 1.3 61.5 + - - +
236H LEU 2.9 2.4 + - - -
237H PHE* 2.9 19.9 + - - +
263H MET* 3.0 16.6 - - + +
267H LEU* 3.7 17.5 - - + -
291H LEU* 4.1 10.9 - - + +
7401H PLP 3.8 2.6 + - - -
7402H ADP 2.7 64.0 + - + +
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Residues in contact with GLY 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H ASP* 4.0 7.7 - - - +
148H THR* 5.4 0.5 + - - -
186H THR* 5.5 3.6 - - - -
233H THR* 1.3 72.3 - - - +
235H ASP* 1.3 58.3 + - - +
237H PHE* 2.8 26.2 - - - +
238H ALA* 3.1 8.3 + - - +
7401H PLP 3.1 1.2 + - - -
7402H ADP 2.7 49.4 + - - -
7403H ZN 4.0 0.7 - - - -
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Residues in contact with ASP 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H GLN* 3.2 24.3 + - - +
20H GLY* 3.9 25.3 + - - +
23H ALA* 4.5 2.9 - - + -
24H ALA* 4.4 5.1 - - + +
81H LEU* 5.6 0.5 - - - +
83H GLY* 4.9 0.5 - - - -
84H TYR 4.7 2.9 + - - -
113H ASP* 3.7 16.7 - - - +
115H VAL* 4.1 9.2 - - - +
232H GLY* 3.5 10.0 - - - +
234H GLY* 1.3 73.1 - - - +
236H LEU* 1.3 64.9 + - - +
238H ALA* 3.5 3.1 + - - +
239H ALA* 3.2 24.4 + - - +
7401H PLP 2.4 44.1 + - - +
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Residues in contact with LEU 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H ALA* 3.5 13.8 - - + +
27H PRO* 3.2 35.4 - - + -
232H GLY 2.9 12.2 + - - +
233H THR* 3.3 9.2 - - - +
235H ASP* 1.3 76.0 - - - +
237H PHE* 1.3 64.1 + - - +
239H ALA* 3.4 1.4 + - - +
240H MET* 3.0 47.3 + - + +
263H MET* 3.5 17.9 - - + -
266H VAL* 4.1 32.1 - - + -
291H LEU* 4.1 14.4 - - + -
293H MET* 4.2 10.3 - - + -
300H ILE* 4.6 1.8 - - + -
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Residues in contact with PHE 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H THR* 4.3 7.6 - - - -
184H VAL* 3.9 24.9 - - + -
186H THR* 3.3 31.0 - - + -
221H MET* 6.4 0.7 - - + -
233H THR 2.9 11.1 + - - +
234H GLY* 2.8 16.8 - - - +
236H LEU* 1.3 74.0 - - - +
238H ALA* 1.3 57.6 + - - -
240H MET* 3.0 4.5 + - - +
241H LEU* 2.5 57.2 + - + +
256H CYS* 5.9 3.4 - - + -
259H THR* 3.3 29.8 - - + +
260H VAL* 4.1 21.3 - - + -
263H MET* 3.9 18.8 - - + +
7402H ADP 4.4 15.5 - - - -
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Residues in contact with ALA 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H LEU* 4.2 20.4 - - + -
111H VAL* 4.5 4.4 - - + +
113H ASP* 4.5 9.9 - - + +
148H THR* 3.9 26.7 - - + +
234H GLY 3.1 6.3 + - - +
235H ASP* 4.0 6.3 - - - +
237H PHE* 1.3 82.9 - - - +
239H ALA* 1.3 53.7 + - - +
241H LEU* 2.9 9.5 + - - +
242H LEU* 2.5 38.8 + - - +
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Residues in contact with ALA 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H ALA* 3.7 36.8 - - + +
27H PRO* 4.6 5.8 - - + -
28H LEU* 2.9 27.9 - - + +
81H LEU* 3.8 15.3 - - + +
235H ASP 3.2 12.2 + - - +
236H LEU* 3.5 9.2 - - - +
238H ALA* 1.3 80.8 - - - +
240H MET* 1.3 62.7 + - - +
242H LEU* 3.1 7.6 + - - +
243H ALA 3.2 1.9 + - - -
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Residues in contact with MET 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H PRO* 4.0 17.5 - - + -
31H LEU* 4.6 8.1 - - + -
236H LEU* 3.0 40.2 + - + +
237H PHE* 3.0 5.6 + - - +
239H ALA* 1.3 75.3 - - - +
241H LEU* 1.3 62.5 + - - +
243H ALA* 2.7 24.5 + - - +
244H TRP* 3.0 26.1 + - - +
259H THR* 4.0 14.4 - - + +
262H ALA* 3.6 31.6 - - + -
263H MET* 3.4 23.1 - - - +
266H VAL* 5.5 0.2 - - + -
300H ILE* 4.2 22.0 - - + +
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Residues in contact with LEU 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H VAL* 5.5 0.9 - - + -
146H ILE* 4.1 18.2 - - + -
148H THR* 3.5 29.2 - - + -
182H THR* 5.9 0.7 - - + -
184H VAL* 4.4 11.4 - - + -
237H PHE* 2.5 39.5 + - + +
238H ALA* 3.2 9.4 - - - +
240H MET* 1.3 73.7 - - - +
242H LEU* 1.3 64.0 + - - +
243H ALA 2.9 0.9 + - - -
245H THR* 3.1 48.9 + - + +
252H LEU* 5.5 0.4 - - + -
255H ALA 4.7 3.4 - - - +
256H CYS* 4.6 18.8 - - - -
259H THR* 3.6 21.5 + - + +
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Residues in contact with LEU 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H VAL* 3.6 28.7 - - + -
28H LEU* 4.1 11.7 - - + -
33H PHE* 4.1 21.3 - - + -
79H TYR* 3.7 33.8 - - + -
80H VAL 4.8 0.2 - - - +
81H LEU* 4.2 16.4 - - + -
111H VAL* 3.9 24.4 - - + +
146H ILE* 6.0 0.4 - - - -
238H ALA 2.5 17.0 + - - +
239H ALA* 3.1 12.1 + - - +
241H LEU* 1.3 73.6 - - - +
243H ALA* 1.3 63.1 + - - +
245H THR* 3.7 8.8 + - - -
246H HIS* 3.5 13.9 - - - +
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Residues in contact with ALA 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H LEU* 4.3 2.7 - - + -
31H LEU* 3.5 31.6 - - + -
33H PHE* 3.6 28.0 - - + -
239H ALA 3.2 7.7 + - - +
240H MET 2.7 11.2 + - - +
242H LEU* 1.3 78.0 - - - +
244H TRP* 1.3 67.4 + - + +
246H HIS* 3.4 14.2 - - - +
247H LYS* 3.5 8.3 + - - +
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Residues in contact with TRP 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H LEU* 4.2 20.5 - - + +
240H MET* 3.0 25.4 + - - +
241H LEU 4.3 0.9 - - - +
243H ALA* 1.3 75.9 - - + +
245H THR* 1.3 54.8 + - - +
246H HIS 3.0 2.0 - - - -
247H LYS* 2.6 29.6 + - + +
248H HIS* 2.6 35.0 + + + -
255H ALA* 3.7 22.9 - - + +
258H LYS* 3.6 43.0 - - + +
259H THR* 3.1 37.3 - - - +
300H ILE 4.1 10.4 + - - -
301H GLU 4.0 13.9 - - - -
302H SER* 5.5 0.4 - - - -
303H PRO* 4.0 24.5 - - + +
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Residues in contact with THR 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H TYR* 5.5 2.9 - - - -
146H ILE* 3.9 24.9 - - + +
182H THR* 5.3 2.2 - - + -
205H GLN* 6.2 2.9 - - - +
241H LEU* 3.1 36.3 + - + +
242H LEU* 3.7 6.6 + - - -
244H TRP* 1.3 74.6 - - - +
246H HIS* 1.3 58.8 + - - +
248H HIS 3.7 10.8 - - - +
249H PRO* 2.9 35.3 - - - +
252H LEU* 4.9 11.9 - - + -
255H ALA* 3.6 18.4 - - + -
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Residues in contact with HIS 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H MET* 4.3 6.3 - - + -
3H GLU* 3.5 30.8 + - - -
5H CYS* 3.3 30.9 - - - -
33H PHE* 3.8 20.4 - + + -
79H TYR* 2.8 35.2 + + + +
242H LEU 3.5 11.2 + - - +
243H ALA 3.4 11.0 - - - +
244H TRP 3.0 0.2 - - - -
245H THR* 1.3 81.6 + - - +
247H LYS* 1.3 65.2 + - + +
249H PRO* 4.0 7.4 - - - +
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Residues in contact with LYS 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H MET* 6.3 2.5 - - + -
243H ALA 3.5 6.5 + - - +
244H TRP* 2.6 30.9 + - + +
246H HIS* 1.3 87.3 - - + +
248H HIS* 1.3 88.9 + - + +
249H PRO* 3.4 7.5 - - - +
258H LYS* 4.2 8.7 - - - +
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Residues in contact with HIS 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H GLN* 5.5 0.2 + - - -
244H TRP 2.6 18.3 + - - +
245H THR* 3.1 13.8 - - - +
247H LYS* 1.3 107.4 + - + +
249H PRO* 1.3 62.3 - - - +
250H ASN 3.1 6.4 + - - -
251H ASN* 3.1 40.8 + - + +
252H LEU 4.5 0.3 + - - -
254H VAL* 3.6 23.2 - - + +
255H ALA* 4.4 5.5 - - - +
258H LYS* 2.8 34.2 + - + -
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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