Contacts of the helix formed by residues 215 - 232 (chain G) in PDB entry 1S9C
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 HIS 215 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G ALA* 3.6 30.5 - - + +
188G TYR* 3.4 33.9 - + + +
189G ARG* 3.5 13.1 - - + +
193G ASP* 3.2 42.2 + - + +
195G ASN 5.1 0.2 + - - -
198G HIS* 3.2 52.6 - + + +
214G LEU* 1.3 75.8 - - - +
216G GLY* 1.3 67.1 + - - +
217G LEU* 4.2 3.1 - - + +
218G CYS* 2.9 17.1 + - + +
219G THR* 3.4 7.1 + - - -
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Residues in contact with GLY 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G HIS* 5.7 3.1 + - - -
198G HIS* 4.7 2.8 - - - -
214G LEU 3.4 4.5 + - - -
215G HIS* 1.3 71.6 - - - +
217G LEU* 1.3 61.8 + - - +
218G CYS 3.2 0.3 + - - -
219G THR* 3.3 9.2 + - - -
220G PHE 3.1 17.0 + - - -
246G PHE* 3.2 31.4 - - - -
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Residues in contact with LEU 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G TYR* 4.3 2.9 + - - -
62G VAL* 3.3 26.5 - - + -
66G GLN* 3.3 30.5 - - - +
69G MET* 4.9 1.3 - - + -
89G HIS* 3.4 29.2 + - + +
92G GLN* 3.5 31.0 - - + -
142G PHE* 4.4 4.0 - - + -
188G TYR* 3.3 23.3 + - + +
193G ASP* 5.7 0.9 - - - +
215G HIS* 3.2 2.5 - - + +
216G GLY* 1.3 74.3 - - - +
218G CYS* 1.3 57.0 + - - +
220G PHE* 3.1 17.0 - - + +
221G GLY* 2.9 20.8 + - - -
246G PHE* 3.9 7.4 - - + -
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Residues in contact with CYS 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G GLY 3.3 26.9 - - - -
34G VAL* 3.6 2.6 - - - +
184G GLN* 4.0 2.7 - - - -
188G TYR* 3.7 33.2 - - + -
214G LEU* 3.9 26.2 - - + -
215G HIS* 2.9 13.3 + - + +
217G LEU* 1.3 74.7 - - - +
219G THR* 1.3 66.9 + - - +
220G PHE 3.0 0.7 - - - -
221G GLY* 3.0 2.9 + - - -
222G PHE* 3.0 41.4 + - - -
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Residues in contact with THR 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G LEU* 3.9 11.2 + - - +
215G HIS 3.4 9.7 + - - -
216G GLY* 3.3 10.6 + - - -
218G CYS* 1.3 76.5 - - - +
220G PHE* 1.3 63.5 + - - +
222G PHE* 3.0 5.9 + - - +
223G SER* 3.0 22.5 + - - -
250G VAL* 3.9 15.3 - - + +
256G LEU* 3.7 38.4 - - + -
271G THR* 4.1 4.3 - - + -
280G VAL* 3.9 15.9 - - + -
281G ILE* 3.7 19.1 - - + -
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Residues in contact with PHE 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G TYR* 5.0 0.9 - - - -
59G THR* 3.6 17.9 - - + -
62G VAL* 3.6 28.0 - - + -
92G GLN* 4.0 21.8 - - + -
94G LEU* 5.1 1.1 - - + -
216G GLY 3.1 11.7 + - - +
217G LEU* 3.1 26.9 - - + +
219G THR* 1.3 78.6 - - - +
221G GLY* 1.3 65.2 + - - +
223G SER* 3.5 1.5 + - - +
224G ALA* 2.9 28.0 + - + +
242G VAL* 3.1 34.8 - - + -
244G ALA* 3.6 30.7 - - + -
246G PHE* 4.1 11.7 - + + -
269G PHE* 5.4 5.9 - + - -
281G ILE* 3.7 10.7 - - + +
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Residues in contact with GLY 221 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G TYR* 3.8 10.8 - - - -
34G VAL* 3.3 26.7 - - - +
59G THR* 4.0 10.5 + - - -
217G LEU 2.9 13.9 + - - -
218G CYS 3.0 0.8 + - - -
220G PHE* 1.3 76.2 - - - +
222G PHE* 1.3 53.3 + - - +
224G ALA* 3.7 1.3 - - - +
225G ARG* 2.8 36.0 + - - +
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Residues in contact with PHE 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G VAL 3.1 25.6 - - - -
35G GLY* 3.5 24.7 - - - -
178G ASP* 3.6 37.0 - - + -
179G THR 4.8 7.6 - - - -
180G THR* 4.5 8.7 - - - -
184G GLN* 3.7 30.3 - - + -
214G LEU* 5.2 0.9 - - + -
218G CYS* 3.0 37.4 + - - -
219G THR* 3.0 8.7 + - - +
221G GLY* 1.3 74.3 - - - +
223G SER* 1.3 65.7 + - - +
225G ARG* 2.9 22.4 + - - +
226G ARG* 2.9 17.8 + - - +
256G LEU* 3.6 21.3 - - + -
258G THR* 5.6 0.7 - - - +
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Residues in contact with SER 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G THR 3.0 8.9 + - - -
220G PHE 4.1 2.0 - - - -
222G PHE* 1.3 79.5 - - - +
224G ALA* 1.3 64.0 + - - +
226G ARG* 3.0 5.1 + - - +
227G VAL* 2.9 26.9 + - - +
256G LEU* 5.6 0.3 - - - +
258G THR* 2.7 29.0 + - - +
269G PHE* 3.6 26.2 - - - -
271G THR* 2.7 28.4 + - - +
281G ILE* 4.6 1.7 - - - +
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Residues in contact with ALA 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G THR* 3.5 30.7 - - + +
220G PHE* 2.9 21.7 + - + +
221G GLY 3.7 2.0 - - - +
223G SER* 1.3 76.3 - - - +
225G ARG* 1.3 62.4 - - - +
227G VAL* 3.3 9.1 + - - +
228G LEU* 3.0 23.7 + - - +
239G PHE* 3.9 17.1 - - + -
242G VAL* 5.1 5.4 - - + -
269G PHE* 5.0 8.2 - - + -
286G VAL* 6.0 0.9 - - - -
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Residues in contact with ARG 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G VAL* 2.5 34.6 + - + -
35G GLY* 3.2 24.0 + - - -
36G ALA* 3.6 20.1 - - - +
43G ASP* 4.5 12.0 + - - +
46G PHE* 5.3 4.9 - - + -
57G LEU* 4.0 36.8 - - + -
59G THR* 5.6 0.2 + - - -
178G ASP* 3.2 24.4 + - - -
221G GLY 2.8 19.7 + - - +
222G PHE* 3.2 18.5 - - - +
224G ALA* 1.3 77.2 - - - +
226G ARG* 1.3 73.5 + - - +
228G LEU* 3.4 12.0 - - + +
229G GLN* 3.2 26.5 + - - +
234G ASN* 5.9 0.7 - - - +
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Residues in contact with ARG 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D ASP 4.5 5.1 + - - -
176G LEU* 3.3 40.9 - - + +
177G THR 3.0 25.3 + - - +
178G ASP* 2.6 33.8 + - - +
222G PHE 2.9 18.4 + - - +
223G SER* 3.0 9.8 + - - +
225G ARG* 1.3 86.0 - - - +
227G VAL* 1.3 61.2 + - - +
229G GLN* 2.5 40.6 + - - +
230G GLN* 2.8 33.2 + - - +
258G THR* 4.7 7.6 - - - +
260G MET* 4.4 8.1 - - + -
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Residues in contact with VAL 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223G SER 2.9 20.0 + - - +
224G ALA* 3.6 8.3 - - - +
226G ARG* 1.3 75.0 - - - +
228G LEU* 1.3 59.2 + - - +
231G PHE* 2.9 31.3 + - + +
232G ALA* 3.9 0.7 + - - +
258G THR* 4.8 0.4 - - + -
260G MET* 3.7 29.6 - - + -
267G ILE* 3.8 22.9 - - + -
269G PHE* 4.3 18.4 - - + -
286G VAL* 3.1 41.7 - - + -
288G LEU* 5.2 3.1 - - + -
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Residues in contact with LEU 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G PHE* 3.8 29.6 - - + -
57G LEU* 3.9 16.8 - - + -
58G PRO* 4.2 11.9 - - + -
224G ALA 3.0 13.4 + - - +
225G ARG* 3.4 11.7 - - + +
226G ARG 3.1 0.2 - - - -
227G VAL* 1.3 77.5 - - - +
229G GLN* 1.3 57.4 + - - +
232G ALA* 3.2 27.5 + - + +
234G ASN* 3.1 25.7 + - - +
235G ASP 3.9 31.2 - - - +
236G VAL* 4.1 5.2 - - + +
239G PHE* 4.0 26.4 - - + -
288G LEU* 5.7 0.9 - - - -
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Residues in contact with GLN 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G ASP* 4.1 17.3 + - - +
42G LYS* 5.7 3.0 - - + +
43G ASP* 4.3 12.9 + - - -
176G LEU* 4.3 1.4 - - + +
225G ARG* 3.2 11.3 + - - +
226G ARG* 2.5 50.8 + - - +
228G LEU* 1.3 79.1 - - - +
230G GLN* 1.3 71.8 + - + +
233G ASP* 4.0 12.0 + - - -
234G ASN* 3.0 31.2 + - - +
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Residues in contact with GLN 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LEU* 3.9 2.9 - - - +
230D GLN* 3.2 36.8 + - - +
174G ALA* 3.6 19.1 - - + +
176G LEU* 3.8 23.1 - - + +
226G ARG 2.8 16.2 + - - +
229G GLN* 1.3 83.4 + - - +
231G PHE* 1.3 92.8 + - + +
232G ALA 3.7 0.4 - - - -
233G ASP 5.1 0.5 + - - -
260G MET* 4.1 8.1 - - + -
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Residues in contact with PHE 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173G ASP* 4.6 11.2 - - + -
174G ALA* 4.4 12.1 - - + -
227G VAL 2.9 12.5 + - - +
230G GLN* 1.3 105.1 - - + +
232G ALA* 1.3 58.7 - - - +
233G ASP* 5.9 0.4 - - - -
238G ARG* 4.0 9.0 + - - -
260G MET* 3.6 33.9 - - + -
262G LYS* 3.7 33.4 - - + -
267G ILE* 3.5 41.5 - - + -
288G LEU* 3.2 13.9 - - + +
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Residues in contact with ALA 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G LEU* 3.2 26.1 + - + +
231G PHE* 1.3 79.0 - - - +
233G ASP* 1.3 74.6 + - - +
234G ASN 3.2 1.6 - - - -
235G ASP* 2.9 19.4 + - - +
238G ARG* 3.6 27.9 + - + +
288G LEU* 4.0 24.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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