Contacts of the helix formed by residues 215 - 232 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ALA* 3.8 17.8 - - + +
188A TYR* 3.4 32.3 - + + +
189A ARG* 3.6 24.0 - - + +
193A ASP* 3.1 44.4 + - + +
195A ASN 5.2 0.2 + - - -
198A HIS* 3.3 50.8 + + + +
214A LEU* 1.3 75.7 - - - +
216A GLY* 1.3 66.8 + - - +
217A LEU* 4.2 2.9 - - + +
218A CYS* 2.9 17.8 + - + +
219A THR* 3.4 7.3 + - - -
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Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A HIS* 6.3 0.2 - - - -
198A HIS* 4.8 2.6 - - - -
214A LEU 3.4 3.9 + - - -
215A HIS* 1.3 72.1 - - - +
217A LEU* 1.3 57.5 + - - +
218A CYS 3.2 0.5 + - - -
219A THR* 3.2 8.0 + - - -
220A PHE 3.0 22.2 + - - -
246A PHE* 3.3 31.5 - - - -
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 4.3 2.9 + - - -
62A VAL* 3.3 35.7 - - + -
63A ILE* 6.4 0.2 - - + -
66A GLN* 3.3 26.7 - - - +
69A MET* 6.2 0.7 - - + -
89A HIS* 3.9 24.2 + - + +
92A GLN* 3.8 22.2 - - + -
142A PHE* 4.8 3.1 - - + -
188A TYR* 3.4 21.7 + - + +
193A ASP* 5.8 0.9 - - - +
215A HIS* 3.1 2.4 - - + +
216A GLY* 1.3 76.1 - - - +
218A CYS* 1.3 56.4 - - - +
219A THR 3.5 0.2 - - - -
220A PHE* 3.1 17.1 - - + +
221A GLY* 2.9 22.7 + - - -
246A PHE* 3.9 13.4 - - + -
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Residues in contact with CYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLY 3.1 27.6 - - - -
34A VAL* 3.5 2.4 - - - +
184A GLN* 4.1 11.0 - - - -
188A TYR* 3.7 37.6 - - + -
214A LEU* 4.0 13.7 - - + -
215A HIS* 2.9 13.1 + - + +
217A LEU* 1.3 74.9 - - - +
219A THR* 1.3 67.2 + - - +
220A PHE 3.1 0.9 - - - -
221A GLY* 3.0 2.6 + - - -
222A PHE* 2.9 41.4 + - - -
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Residues in contact with THR 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 3.9 11.7 + - - +
215A HIS 3.4 8.7 + - - -
216A GLY* 3.2 9.6 + - - -
218A CYS* 1.3 77.3 - - - +
220A PHE* 1.3 64.6 + - - +
222A PHE* 3.1 5.4 + - - +
223A SER* 3.0 22.7 + - - -
250A VAL* 3.9 15.8 - - - +
256A LEU* 3.7 37.7 - - + -
271A THR* 4.1 4.9 - - + -
280A VAL* 3.9 16.2 - - + -
281A ILE* 3.7 19.1 - - + -
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Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 5.0 0.9 - - - -
59A THR* 3.5 25.1 - - + -
62A VAL* 3.7 19.1 - - + -
92A GLN* 4.1 17.9 - - + -
94A LEU* 5.2 0.9 - - + -
216A GLY 3.0 13.8 + - - +
217A LEU* 3.1 27.1 - - + +
219A THR* 1.3 76.2 - - - +
221A GLY* 1.3 64.3 + - - +
223A SER* 3.4 1.3 + - - -
224A ALA* 2.9 27.5 + - + +
242A VAL* 3.0 35.4 - - + -
244A ALA* 3.6 32.1 - - + -
246A PHE* 4.0 12.8 - + + -
269A PHE* 5.3 6.8 - + - -
281A ILE* 3.6 10.4 - - + +
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Residues in contact with GLY 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 3.8 10.5 - - - -
34A VAL* 3.2 28.9 - - - +
59A THR* 4.0 9.4 + - - -
217A LEU 2.9 13.9 + - - -
218A CYS 3.0 0.8 + - - -
220A PHE* 1.3 75.8 - - - +
222A PHE* 1.3 51.9 + - - +
224A ALA* 3.7 1.3 - - - +
225A ARG* 2.8 36.6 + - - +
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Residues in contact with PHE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.1 26.7 - - - +
35A GLY* 3.5 22.4 - - - -
178A ASP* 3.6 40.6 - - + -
179A THR 4.9 6.1 - - - -
180A THR* 4.5 10.1 - - - -
184A GLN* 3.7 27.1 - - + -
214A LEU* 5.2 0.9 - - + -
218A CYS* 2.9 42.6 + - - -
219A THR* 3.1 8.9 + - - +
221A GLY* 1.3 74.4 - - - +
223A SER* 1.3 66.7 + - - +
225A ARG* 2.8 17.6 + - - +
226A ARG* 2.9 17.9 + - - +
256A LEU* 3.6 21.8 - - + -
258A THR* 5.6 1.1 - - - +
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Residues in contact with SER 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A THR 3.0 10.3 + - - -
220A PHE 4.0 1.6 - - - -
222A PHE* 1.3 79.1 - - - +
224A ALA* 1.3 65.0 + - - +
226A ARG* 3.0 4.1 + - - +
227A VAL* 2.9 28.2 + - - +
256A LEU* 5.5 0.2 - - - +
258A THR* 2.9 29.2 + - - +
269A PHE* 3.5 27.4 - - - -
271A THR* 2.7 27.8 + - - +
281A ILE* 4.9 1.3 - - - -
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR* 3.5 30.3 - - + +
220A PHE* 2.9 21.6 + - + +
221A GLY 3.8 1.8 - - - +
223A SER* 1.3 77.1 - - - +
225A ARG* 1.3 63.7 + - - +
227A VAL* 3.3 8.7 + - - +
228A LEU* 3.0 23.4 + - - +
239A PHE* 3.9 17.1 - - + -
242A VAL* 5.0 5.2 - - + -
269A PHE* 4.9 7.9 - - + -
286A VAL* 6.0 0.9 - - - -
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Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 2.4 34.6 + - + -
35A GLY* 3.0 26.1 + - - -
36A ALA* 3.5 20.4 - - - +
43A ASP* 4.3 12.8 + - - +
46A PHE* 5.2 5.4 - - + -
57A LEU* 4.0 35.7 - - + -
59A THR* 5.7 0.2 + - - -
178A ASP* 3.2 24.0 + - - -
221A GLY 2.8 19.8 + - - +
222A PHE* 2.8 15.4 + - - +
224A ALA* 1.3 77.0 - - - +
226A ARG* 1.3 75.0 + - - +
228A LEU* 3.4 12.4 - - + +
229A GLN* 3.2 25.6 + - - +
234A ASN* 4.7 0.6 + - - +
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Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 3.3 41.0 - - + +
177A THR 3.0 24.7 + - - -
178A ASP* 2.6 32.1 + - - +
222A PHE 2.9 16.8 + - - +
223A SER* 3.5 8.1 - - - +
225A ARG* 1.3 88.1 - - - +
227A VAL* 1.3 67.0 + - - +
229A GLN* 2.5 40.2 + - - +
230A GLN* 2.8 27.4 + - - +
258A THR* 4.6 9.0 - - - +
260A MET* 4.3 7.4 - - + -
173E ASP* 4.3 7.3 + - - +
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A SER 2.9 19.4 + - - +
224A ALA* 3.6 7.6 - - - +
226A ARG* 1.3 75.3 - - - +
228A LEU* 1.3 59.6 + - - +
231A PHE* 2.9 30.4 + - + +
232A ALA* 4.0 0.9 + - - +
239A PHE* 5.3 0.2 - - + -
258A THR* 4.8 0.9 - - + -
260A MET* 3.8 27.1 - - + -
267A ILE* 3.8 22.2 - - + -
269A PHE* 4.2 18.6 - - + -
286A VAL* 3.1 42.4 - - + -
288A LEU* 5.2 3.1 - - + -
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.7 30.5 - - + -
57A LEU* 3.9 17.9 - - + -
58A PRO* 4.2 10.5 - - + -
224A ALA 3.0 12.8 + - - +
225A ARG* 3.4 11.2 - - - +
227A VAL* 1.3 77.5 - - - +
229A GLN* 1.3 55.8 - - - +
232A ALA* 3.2 27.7 + - + +
234A ASN* 3.1 25.4 + - - +
235A ASP 4.0 31.2 - - - +
236A VAL* 4.1 6.1 - - + +
239A PHE* 3.9 27.1 - - + -
288A LEU* 5.7 0.7 - - - -
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Residues in contact with GLN 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASP* 3.8 20.8 + - - +
42A LYS* 5.5 3.6 - - + +
43A ASP* 4.1 14.6 + - - -
176A LEU* 4.4 2.0 - - + +
225A ARG* 3.2 11.8 + - - +
226A ARG* 2.5 51.0 + - - +
228A LEU* 1.3 79.4 - - - +
230A GLN* 1.3 70.4 + - + +
233A ASP* 4.0 11.8 + - - +
234A ASN* 3.0 30.8 + - - +
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Residues in contact with GLN 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ALA* 3.8 13.6 - - + +
176A LEU* 3.6 27.0 - - + +
226A ARG 2.8 15.7 + - - +
229A GLN* 1.3 82.7 + - - +
231A PHE* 1.3 92.8 + - + +
232A ALA 3.7 0.2 - - - -
233A ASP 5.0 0.4 + - - -
260A MET* 4.2 7.2 - - + -
176E LEU* 3.8 2.7 - - - +
230E GLN* 2.8 42.1 + - - +
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Residues in contact with PHE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP* 4.6 10.1 - - + -
174A ALA* 4.3 13.0 - - + -
227A VAL 2.9 10.8 + - - +
230A GLN* 1.3 103.2 - - + +
232A ALA* 1.3 59.7 + - - +
233A ASP 3.9 0.4 - - - -
238A ARG* 3.9 9.6 + - - -
260A MET* 3.5 33.0 - - + -
262A LYS* 3.8 31.9 - - + -
267A ILE* 3.5 43.5 - - + -
288A LEU* 3.1 14.5 - - + +
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 3.2 24.6 + - + +
231A PHE* 1.3 79.5 - - - +
233A ASP* 1.3 72.0 + - - +
234A ASN 3.2 1.3 - - - -
235A ASP* 2.8 21.5 + - - +
238A ARG* 3.5 27.2 + - + +
288A 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
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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