Contacts of the helix formed by residues 215 - 232 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H ALA* 3.6 30.5 - - + +
188H TYR* 3.5 33.8 - + + +
189H ARG* 3.7 13.1 - - + +
193H ASP* 3.2 37.1 + - + +
198H HIS* 3.1 54.9 + + + +
214H LEU* 1.3 76.1 - - - +
216H GLY* 1.3 66.3 + - - +
217H LEU* 4.2 2.9 - - + +
218H CYS* 3.0 18.0 + - + +
219H THR* 3.4 7.3 + - - -
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Residues in contact with GLY 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H HIS* 5.9 4.8 - - - +
198H HIS* 4.8 2.6 - - - -
214H LEU 3.4 4.5 + - - -
215H HIS* 1.3 70.8 - - - +
217H LEU* 1.3 57.4 + - - +
218H CYS 3.2 0.3 + - - -
219H THR* 3.3 10.2 + - - -
220H PHE 3.0 21.8 + - - -
246H PHE* 3.3 32.2 - - - -
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Residues in contact with LEU 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H TYR* 4.4 2.4 + - - -
62H VAL* 3.4 25.1 - - + -
66H GLN* 3.3 28.9 - - - +
89H HIS* 3.6 30.2 + - + +
92H GLN* 3.5 32.1 - - + -
142H PHE* 4.6 2.9 - - + -
188H TYR* 3.4 23.0 + - + +
193H ASP* 5.8 0.9 - - - +
215H HIS* 3.2 2.3 - - + +
216H GLY* 1.3 75.6 - - - +
218H CYS* 1.3 57.4 + - - +
220H PHE* 3.2 16.2 - - + +
221H GLY* 2.9 21.5 + - - -
246H PHE* 3.9 8.2 - - + -
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Residues in contact with CYS 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H GLY 3.2 26.2 - - - -
34H VAL* 3.6 1.9 - - - +
184H GLN* 4.0 11.7 - - - -
188H TYR* 3.8 37.0 - - + -
214H LEU* 4.0 13.5 - - + -
215H HIS* 3.0 14.0 + - + +
217H LEU* 1.3 75.5 - - - +
219H THR* 1.3 65.2 - - - +
220H PHE 3.0 0.9 - - - -
221H GLY* 2.9 3.1 + - - -
222H PHE* 2.9 43.0 + - - -
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Residues in contact with THR 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H LEU* 4.0 10.6 + - - +
215H HIS 3.4 9.4 + - - -
216H GLY* 3.3 10.0 + - - -
218H CYS* 1.3 77.8 - - - +
220H PHE* 1.3 64.0 + - - +
222H PHE* 3.2 4.7 + - - +
223H SER* 3.0 23.4 + - - -
250H VAL* 3.8 16.2 - - - +
256H LEU* 3.7 37.2 - - + -
271H THR* 4.0 4.9 - - + -
280H VAL* 3.8 16.6 - - + -
281H ILE* 3.6 18.2 - - + -
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Residues in contact with PHE 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H TYR* 5.1 0.7 - - - -
59H THR* 3.7 23.3 - - + -
62H VAL* 3.7 21.5 - - + -
92H GLN* 4.0 20.6 - - + -
94H LEU* 5.1 1.1 - - + -
216H GLY 3.0 11.9 + - - +
217H LEU* 3.2 26.5 - - + +
219H THR* 1.3 80.6 - - - +
221H GLY* 1.3 64.6 + - - +
223H SER* 4.0 1.7 - - - -
224H ALA* 2.9 27.6 + - + +
242H VAL* 3.0 35.9 - - + -
244H ALA* 3.6 31.9 - - + -
246H PHE* 4.1 11.7 - + + -
269H PHE* 5.2 6.0 - + - -
281H ILE* 3.7 9.9 - - + -
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Residues in contact with GLY 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H TYR* 3.9 10.3 - - - -
34H VAL* 3.2 27.9 - - - +
59H THR* 4.1 9.8 + - - -
217H LEU 2.9 13.9 + - - -
218H CYS 2.9 0.8 + - - -
220H PHE* 1.3 76.5 - - - +
222H PHE* 1.3 52.2 + - - +
224H ALA* 3.7 1.7 - - - +
225H ARG* 2.8 36.8 + - - +
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Residues in contact with PHE 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H VAL 3.2 25.4 - - - -
35H GLY* 3.5 24.5 - - - -
178H ASP* 3.7 35.9 - - + -
179H THR 4.8 7.9 - - - -
180H THR* 4.6 8.5 - - - -
184H GLN* 3.7 31.9 - - + -
214H LEU* 5.2 0.7 - - + -
218H CYS* 2.9 36.1 + - - -
219H THR* 3.2 8.0 + - - +
221H GLY* 1.3 73.8 - - - +
223H SER* 1.3 65.6 + - - +
225H ARG* 2.8 23.0 + - - +
226H ARG* 3.0 17.8 + - - +
256H LEU* 3.6 22.7 - - + -
258H THR* 5.6 0.7 - - - +
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Residues in contact with SER 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219H THR 3.0 9.9 + - - -
220H PHE 4.0 1.8 - - - -
222H PHE* 1.3 78.5 - - - +
224H ALA* 1.3 63.8 + - - +
226H ARG* 3.0 3.9 + - - +
227H VAL* 2.8 29.0 + - - +
256H LEU* 5.5 0.2 - - - +
258H THR* 2.8 27.2 + - - +
269H PHE* 3.6 19.1 - - - -
271H THR* 2.6 35.6 + - - +
281H ILE* 4.9 1.1 - - - -
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Residues in contact with ALA 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H THR* 3.5 31.0 - - + +
220H PHE* 2.9 22.3 + - + +
221H GLY 3.7 2.2 - - - +
223H SER* 1.3 77.1 - - - +
225H ARG* 1.3 62.5 + - - +
227H VAL* 3.3 8.6 + - - +
228H LEU* 3.0 23.2 + - - +
239H PHE* 3.9 16.8 - - + -
242H VAL* 5.1 5.2 - - + -
269H PHE* 4.9 8.6 - - + -
286H VAL* 6.0 0.9 - - - -
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Residues in contact with ARG 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H VAL* 2.4 34.1 + - + -
35H GLY* 3.1 24.8 + - - -
36H ALA* 3.6 20.1 - - - +
43H ASP* 4.5 11.6 + - - +
46H PHE* 5.3 5.4 - - + -
57H LEU* 4.0 36.6 - - + -
178H ASP* 3.2 24.4 + - - -
221H GLY 2.8 15.1 + - - +
222H PHE* 2.8 25.1 + - - +
224H ALA* 1.3 77.6 - - - +
226H ARG* 1.3 71.9 + - - +
228H LEU* 3.3 12.2 - - + +
229H GLN* 3.1 26.0 + - - +
234H ASN* 4.6 0.8 + - - +
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Residues in contact with ARG 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H LEU* 3.3 39.6 - - + +
177H THR 3.0 24.0 + - - +
178H ASP* 2.6 31.0 + - - +
222H PHE 3.0 17.1 + - - +
223H SER* 3.5 9.9 - - - +
225H ARG* 1.3 84.5 - - - +
227H VAL* 1.3 62.1 + - - +
229H GLN* 2.4 42.8 + - - +
230H GLN* 2.8 32.1 + - - +
258H THR* 4.6 7.9 - - - +
260H MET* 4.4 7.2 - - + -
173I ASP* 4.4 6.5 + - - +
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Residues in contact with VAL 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223H SER 2.8 18.5 + - - +
224H ALA* 3.6 8.5 - - - +
226H ARG* 1.3 75.1 - - - +
228H LEU* 1.3 66.6 + - - +
231H PHE* 3.0 23.8 + - + +
232H ALA* 4.0 0.7 + - - +
239H PHE* 5.3 0.2 - - + -
258H THR* 4.8 1.3 - - + -
260H MET* 3.8 28.9 - - + -
267H ILE* 3.9 22.4 - - + -
269H PHE* 4.2 19.7 - - + -
286H VAL* 3.1 41.3 - - + -
288H LEU* 5.2 2.9 - - + -
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Residues in contact with LEU 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H PHE* 3.9 29.4 - - + -
57H LEU* 3.9 16.6 - - + -
58H PRO* 4.2 11.7 - - + -
224H ALA 3.0 12.7 + - - +
225H ARG* 3.3 11.9 - - + +
226H ARG 3.1 0.2 - - - -
227H VAL* 1.3 78.6 - - - +
229H GLN* 1.3 57.5 + - - +
232H ALA* 3.2 27.7 + - + +
234H ASN* 3.1 26.2 + - - +
235H ASP 3.9 31.9 - - - +
236H VAL* 4.0 4.9 - - + +
239H PHE* 4.0 27.1 - - + -
288H LEU* 5.7 0.4 - - - -
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Residues in contact with GLN 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H ASP* 4.0 18.5 + - - +
42H LYS* 5.6 3.0 - - - +
43H ASP* 4.2 13.3 + - - -
176H LEU* 4.4 1.5 - - + +
225H ARG* 3.1 11.2 + - + +
226H ARG* 2.4 50.3 + - - +
228H LEU* 1.3 78.9 - - - +
230H GLN* 1.3 71.7 + - + +
233H ASP* 3.9 12.5 + - - +
234H ASN* 2.9 30.9 + - - +
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Residues in contact with GLN 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H ALA* 3.8 12.9 - - + +
176H LEU* 3.7 26.9 - - + +
226H ARG 2.8 20.5 + - - +
229H GLN* 1.3 79.8 + - - +
231H PHE* 1.3 90.8 + - + +
232H ALA 3.7 0.4 + - - -
233H ASP 5.2 0.3 + - - -
260H MET* 4.1 8.5 - - + -
176I LEU* 3.9 2.8 - - - +
230I GLN* 2.9 41.9 + - - +
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Residues in contact with PHE 231 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H ASP* 4.7 10.8 - - + -
174H ALA* 4.4 11.9 - - + -
227H VAL 3.0 11.9 + - - +
230H GLN* 1.3 102.1 - - + +
232H ALA* 1.3 60.4 + - - +
233H ASP* 3.8 0.7 - - - -
238H ARG* 3.9 8.9 + - - -
260H MET* 3.5 32.8 - - + -
262H LYS* 3.7 33.9 - - + -
267H ILE* 3.6 42.4 - - + -
288H LEU* 3.1 13.6 - - + +
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Residues in contact with ALA 232 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228H LEU* 3.2 24.8 + - + +
231H PHE* 1.3 79.6 - - - +
233H ASP* 1.3 73.5 + - - +
234H ASN 3.3 0.9 - - - -
235H ASP* 2.9 19.5 + - - +
238H ARG* 3.5 28.1 + - + +
288H LEU* 3.9 25.4 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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