Contacts of the helix formed by residues 215 - 232 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185L ALA* 3.7 18.5 - - - +
188L TYR* 3.3 32.8 - + + +
189L ARG* 3.5 23.7 - - + +
193L ASP* 3.1 46.5 + - + +
198L HIS* 3.3 50.2 + + + +
214L LEU* 1.3 76.5 - - - +
216L GLY* 1.3 66.7 + - - +
217L LEU* 4.2 2.9 - - + +
218L CYS* 2.9 17.9 + - + +
219L THR* 3.4 7.3 + - - -
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Residues in contact with GLY 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198L HIS* 4.7 2.8 - - - -
214L LEU 3.4 5.1 + - - -
215L HIS* 1.3 71.4 - - - +
217L LEU* 1.3 61.5 + - - +
218L CYS 3.1 0.5 + - - -
219L THR* 3.3 9.6 + - - -
220L PHE 3.0 17.7 + - - -
246L PHE* 3.3 31.2 - - - -
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Residues in contact with LEU 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 4.3 2.9 + - - -
62L VAL* 3.3 35.7 - - + -
63L ILE* 6.2 0.2 - - + -
66L GLN* 3.1 32.1 - - + +
89L HIS* 4.2 20.0 - - + +
92L GLN* 4.0 14.8 - - + -
142L PHE* 5.2 1.8 - - + -
188L TYR* 3.3 23.2 + - + +
193L ASP* 5.9 0.2 - - - +
215L HIS* 3.2 2.1 - - + +
216L GLY* 1.3 75.1 - - - +
218L CYS* 1.3 56.2 + - - +
220L PHE* 3.2 16.9 - - + +
221L GLY* 2.9 22.0 + - - -
246L PHE* 3.8 19.5 - - + -
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Residues in contact with CYS 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L GLY 3.2 27.6 - - - -
34L VAL* 3.6 1.6 - - - +
184L GLN* 4.0 1.8 - - - -
188L TYR* 3.7 38.5 - - + -
214L LEU* 4.0 22.7 - - + -
215L HIS* 2.9 12.5 + - + +
217L LEU* 1.3 75.9 - - - +
219L THR* 1.3 66.4 + - - +
220L PHE 3.0 1.1 - - - -
221L GLY* 2.9 3.1 + - - -
222L PHE* 2.9 41.3 + - - -
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Residues in contact with THR 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214L LEU* 3.9 14.6 + - - +
215L HIS 3.4 8.7 + - - -
216L GLY* 3.3 9.3 + - - -
218L CYS* 1.3 76.5 - - - +
220L PHE* 1.3 62.6 + - - +
222L PHE* 3.1 4.0 + - - +
223L SER* 3.0 24.6 + - - -
250L VAL* 3.9 12.9 - - + +
256L LEU* 3.7 37.2 - - + -
271L THR* 4.0 4.7 - - + -
280L VAL* 3.9 16.2 - - + -
281L ILE* 3.7 18.8 - - + -
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Residues in contact with PHE 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 5.0 0.9 - - - -
59L THR* 3.6 18.4 - - + -
62L VAL* 3.6 27.1 - - + -
92L GLN* 4.2 18.6 - - + -
94L LEU* 5.3 0.9 - - + -
216L GLY 3.0 12.1 + - - +
217L LEU* 3.2 26.9 - - + +
219L THR* 1.3 79.4 - - - +
221L GLY* 1.3 57.0 + - - +
223L SER* 4.0 1.7 - - - -
224L ALA* 2.9 32.9 + - + +
242L VAL* 3.0 36.8 - - + -
244L ALA* 3.6 31.9 - - + -
246L PHE* 4.1 11.7 - + + -
269L PHE* 5.2 6.5 - + - -
281L ILE* 3.6 10.0 - - + +
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Residues in contact with GLY 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 3.8 10.3 - - - -
34L VAL* 3.2 27.2 - - - +
59L THR* 4.0 8.8 + - - -
217L LEU 2.9 10.4 + - - -
218L CYS 2.9 4.2 + - - -
220L PHE* 1.3 75.2 - - - +
222L PHE* 1.3 55.1 + - - +
224L ALA* 3.7 1.5 - - - +
225L ARG* 2.8 36.6 + - - +
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Residues in contact with PHE 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L VAL* 3.3 24.4 - - - +
35L GLY* 3.6 19.1 - - - -
178L ASP* 3.7 35.0 - - + -
179L THR 4.9 7.0 - - - -
180L THR* 4.5 9.9 - - - -
184L GLN* 3.6 37.7 - - + -
214L LEU* 5.1 1.1 - - + -
218L CYS* 2.9 38.7 + - - -
219L THR* 3.2 7.9 - - - +
221L GLY* 1.3 74.1 - - - +
223L SER* 1.3 65.9 + - - +
225L ARG* 2.9 22.6 + - - +
226L ARG* 2.9 17.7 + - - +
256L LEU* 3.6 22.4 - - + -
258L THR* 5.6 0.7 - - - +
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Residues in contact with SER 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219L THR 3.0 10.0 + - - -
220L PHE 4.1 1.6 - - - -
222L PHE* 1.3 78.9 - - - +
224L ALA* 1.3 63.3 + - - +
226L ARG* 3.0 5.2 + - - +
227L VAL* 2.9 28.8 + - - +
256L LEU* 5.5 0.2 - - - +
258L THR* 2.7 28.6 + - - +
269L PHE* 3.6 18.8 - - - -
271L THR* 2.6 35.2 + - - +
281L ILE* 5.0 1.1 - - - -
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Residues in contact with ALA 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L THR* 3.5 30.1 - - + +
220L PHE* 2.9 23.1 + - + +
221L GLY 3.7 2.0 - - - +
223L SER* 1.3 75.3 - - - +
225L ARG* 1.3 62.8 + - - +
227L VAL* 3.3 9.3 + - - +
228L LEU* 3.0 23.0 + - - +
239L PHE* 3.9 17.7 - - + -
242L VAL* 5.1 4.7 - - + -
269L PHE* 4.9 9.0 - - + -
286L VAL* 6.0 1.1 - - - -
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Residues in contact with ARG 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L VAL* 2.3 44.1 + - + -
35L GLY* 3.0 26.0 + - - -
36L ALA* 3.4 21.4 - - - +
43L ASP* 4.5 11.0 + - - +
46L PHE* 5.4 4.5 - - + -
57L LEU* 4.1 28.0 - - + -
178L ASP* 3.1 24.5 + - - -
221L GLY 2.8 22.8 + - - +
222L PHE* 3.2 19.0 - - - +
224L ALA* 1.3 72.9 - - - +
226L ARG* 1.3 75.3 + - - +
228L LEU* 3.4 11.6 - - + +
229L GLN* 3.2 26.4 + - - +
234L ASN* 4.7 1.2 + - - +
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Residues in contact with ARG 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176L LEU* 3.2 41.1 - - + +
177L THR 2.9 25.5 + - - +
178L ASP* 2.5 32.0 + - - +
222L PHE 2.9 18.6 + - - +
223L SER* 3.4 9.6 - - - +
225L ARG* 1.3 86.3 - - - +
227L VAL* 1.3 66.8 + - - +
229L GLN* 2.5 41.2 + - - +
230L GLN* 2.8 26.3 + - - +
258L THR* 4.6 7.6 - - - +
260L MET* 4.3 7.6 - - + -
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Residues in contact with VAL 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L SER 2.9 19.5 + - - +
224L ALA* 3.6 8.7 - - - +
226L ARG* 1.3 75.4 - - - +
228L LEU* 1.3 62.6 + - - +
231L PHE* 2.9 25.4 + - + +
232L ALA* 4.0 1.0 + - - +
258L THR* 4.8 0.9 - - + -
260L MET* 3.7 27.8 - - + -
267L ILE* 3.8 23.1 - - + -
269L PHE* 4.2 19.1 - - + -
286L VAL* 3.1 42.4 - - + -
288L LEU* 5.2 2.5 - - + -
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Residues in contact with LEU 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46L PHE* 3.8 29.4 - - + -
57L LEU* 3.9 17.0 - - + -
58L PRO* 4.3 10.5 - - + -
224L ALA 3.0 13.8 + - - +
225L ARG* 3.4 11.7 - - + +
226L ARG 3.1 0.2 - - - -
227L VAL* 1.3 77.6 - - - +
229L GLN* 1.3 58.4 + - - +
232L ALA* 3.2 26.8 + - + +
234L ASN* 3.1 26.5 + - - +
235L ASP 3.9 31.6 - - - +
236L VAL* 4.1 4.9 - - + +
239L PHE* 4.0 26.9 - - + -
288L LEU* 5.7 0.7 - - - -
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Residues in contact with GLN 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L ASP* 3.9 19.8 + - - +
42L LYS* 5.8 1.0 - - - +
43L ASP* 4.3 13.3 + - - -
176L LEU* 4.2 1.7 - - + +
225L ARG* 3.2 12.4 + - - +
226L ARG* 2.5 50.1 + - - +
228L LEU* 1.3 80.0 - - - +
230L GLN* 1.3 71.4 + - + +
233L ASP* 4.0 12.2 + - - +
234L ASN* 2.9 30.1 + - - +
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Residues in contact with GLN 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L ALA* 3.6 14.7 - - + +
176L LEU* 3.4 38.6 - - + +
226L ARG 2.8 17.0 + - - +
229L GLN* 1.3 83.5 + - - +
231L PHE* 1.3 91.8 + - + +
232L ALA 3.7 0.2 - - - -
233L ASP 4.9 0.8 + - - -
260L MET* 4.2 4.9 - - + -
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Residues in contact with PHE 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173L ASP* 4.5 11.2 - - + -
174L ALA* 4.3 14.8 - - + -
227L VAL 2.9 11.9 + - - +
230L GLN* 1.3 104.2 - - + +
232L ALA* 1.3 60.5 + - - +
233L ASP* 3.8 0.4 - - - -
238L ARG* 3.9 9.8 + - - -
260L MET* 3.6 31.6 - - + -
262L LYS* 3.8 33.0 - - + -
267L ILE* 3.6 42.6 - - + -
288L LEU* 3.2 13.2 - - + +
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Residues in contact with ALA 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227L VAL 4.0 0.2 + - - -
228L LEU* 3.2 25.4 + - + +
231L PHE* 1.3 80.1 - - - +
233L ASP* 1.3 73.1 + - - +
234L ASN 3.3 1.6 - - - -
235L ASP* 2.9 20.6 + - - +
238L ARG* 3.5 28.1 + - + +
288L LEU* 3.9 25.1 - - + -
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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