Contacts of the helix formed by residues 215 - 232 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K ALA* 3.6 30.6 - - - -
188K TYR* 3.4 32.4 - + + +
189K ARG* 3.5 12.9 - - + +
193K ASP* 3.2 44.1 + - + +
195K ASN 5.1 0.2 + - - -
198K HIS* 3.3 51.1 + + + +
214K LEU* 1.3 75.8 - - - +
216K GLY* 1.3 66.7 + - - +
217K LEU* 4.2 2.5 - - + +
218K CYS* 3.0 16.3 + - + +
219K THR* 3.4 7.3 + - - -
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Residues in contact with GLY 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89K HIS* 5.5 6.5 + - - +
198K HIS* 4.7 3.0 - - - -
214K LEU 3.4 3.7 + - - -
215K HIS* 1.3 72.0 - - - +
217K LEU* 1.3 57.4 + - - +
218K CYS 3.2 0.3 + - - -
219K THR* 3.3 9.7 + - - -
220K PHE 3.0 21.8 + - - -
246K PHE* 3.3 32.8 - - - -
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Residues in contact with LEU 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K TYR* 4.3 2.6 + - - -
62K VAL* 3.3 27.6 - - + -
66K GLN* 3.4 26.9 - - - +
89K HIS* 3.3 37.3 + - + +
92K GLN* 3.6 25.8 - - + -
142K PHE* 4.6 2.9 - - + -
188K TYR* 3.3 23.5 + - + +
193K ASP* 5.8 1.1 - - - +
215K HIS* 3.2 2.3 - - + +
216K GLY* 1.3 75.3 - - - +
218K CYS* 1.3 56.4 + - - +
220K PHE* 3.2 15.6 - - + +
221K GLY* 2.9 22.3 + - - -
246K PHE* 3.8 7.8 - - + -
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Residues in contact with CYS 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K GLY 3.2 27.1 - - - -
34K VAL* 3.6 2.2 - - - +
184K GLN* 4.0 2.2 - - - -
188K TYR* 3.7 34.3 - - + -
214K LEU* 4.0 24.9 - - + -
215K HIS* 3.0 12.7 + - + +
217K LEU* 1.3 75.3 - - - +
219K THR* 1.3 66.7 + - - +
220K PHE 3.1 0.9 - - - -
221K GLY* 3.0 2.6 + - - -
222K PHE* 2.9 42.4 + - - -
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Residues in contact with THR 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214K LEU* 3.9 11.1 + - - +
215K HIS 3.4 8.7 + - - -
216K GLY* 3.3 9.5 + - - -
218K CYS* 1.3 76.5 - - - +
220K PHE* 1.3 63.9 + - - +
222K PHE* 3.0 5.4 + - - +
223K SER* 3.0 23.0 + - - -
250K VAL* 3.8 16.5 - - + +
256K LEU* 3.7 36.1 - - + -
271K THR* 4.0 5.8 - - + -
280K VAL* 3.8 16.8 - - + -
281K ILE* 3.6 18.8 - - + -
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Residues in contact with PHE 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K TYR* 5.1 0.7 - - - -
59K THR* 3.6 24.9 - - + -
62K VAL* 3.8 19.7 - - + -
92K GLN* 3.9 22.2 - - + -
94K LEU* 5.1 1.6 - - + -
216K GLY 3.0 13.9 + - - +
217K LEU* 3.2 26.2 - - + +
219K THR* 1.3 76.2 - - - +
221K GLY* 1.3 60.8 + - - +
223K SER* 3.5 2.1 + - - -
224K ALA* 2.9 32.9 + - + +
242K VAL* 3.0 35.4 - - + -
244K ALA* 3.6 31.2 - - + -
246K PHE* 4.1 12.3 - + + -
269K PHE* 5.2 5.9 - + - -
281K ILE* 3.6 10.2 - - + +
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Residues in contact with GLY 221 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K TYR* 3.8 9.9 - - - -
34K VAL* 3.2 27.3 - - - +
59K THR* 4.0 9.6 + - - -
217K LEU 2.9 14.1 + - - -
218K CYS 3.0 0.8 + - - -
220K PHE* 1.3 75.0 - - - +
222K PHE* 1.3 58.8 + - - +
224K ALA* 3.8 2.0 - - - +
225K ARG* 2.8 32.7 + - - +
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Residues in contact with PHE 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K VAL 3.1 26.4 + - - -
35K GLY* 3.4 24.2 - - - -
178K ASP* 3.7 35.2 - - + -
179K THR 4.9 6.5 - - - -
180K THR* 4.5 9.9 - - - -
184K GLN* 3.6 31.6 - - + -
214K LEU* 5.1 0.7 - - + -
218K CYS* 2.9 37.3 + - - -
219K THR* 3.2 7.9 - - - +
221K GLY* 1.3 74.7 - - - +
223K SER* 1.3 59.5 + - - +
225K ARG* 2.8 28.5 + - - +
226K ARG* 3.0 17.6 + - - +
256K LEU* 3.6 22.0 - - + -
258K THR* 5.6 0.9 - - - +
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Residues in contact with SER 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219K THR 3.0 11.0 + - - -
220K PHE 4.1 1.6 - - - -
222K PHE* 1.3 78.5 - - - +
224K ALA* 1.3 64.8 + - - +
226K ARG* 3.1 4.9 + - - +
227K VAL* 2.9 27.6 + - - +
258K THR* 2.7 28.7 + - - +
269K PHE* 3.5 26.2 - - - -
271K THR* 2.7 28.1 + - - +
281K ILE* 5.0 1.1 - - - -
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Residues in contact with ALA 224 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K THR* 3.6 29.8 - - + +
220K PHE* 2.9 22.6 + - + +
221K GLY 3.8 2.2 - - - +
223K SER* 1.3 78.1 - - - +
225K ARG* 1.3 62.8 + - - +
227K VAL* 3.2 8.2 + - - +
228K LEU* 3.0 22.5 + - - +
239K PHE* 3.9 17.8 - - + -
242K VAL* 5.1 4.5 - - + -
269K PHE* 4.9 8.2 - - + -
286K VAL* 6.0 1.1 - - - -
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Residues in contact with ARG 225 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K VAL* 2.4 34.6 + - + -
35K GLY* 2.9 27.4 + - - -
36K ALA* 3.4 21.2 - - - +
43K ASP* 4.3 12.4 + - - +
46K PHE* 5.3 5.4 - - + -
57K LEU* 4.0 37.2 - - + -
178K ASP* 3.2 24.0 + - - -
221K GLY 2.8 15.4 + - - +
222K PHE* 3.1 22.9 - - - +
224K ALA* 1.3 78.0 - - - +
226K ARG* 1.3 71.2 + - - +
228K LEU* 3.3 11.6 - - + +
229K GLN* 3.1 25.4 + - - +
234K ASN* 4.6 1.2 + - - +
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Residues in contact with ARG 226 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173J ASP* 4.3 7.3 + - - +
176K LEU* 3.2 40.4 - - + +
177K THR 3.0 25.9 + - - +
178K ASP* 2.5 32.5 + - - +
222K PHE 3.0 17.1 + - - +
223K SER* 3.1 10.1 + - - +
225K ARG* 1.3 87.0 - - - +
227K VAL* 1.3 60.6 + - - +
229K GLN* 2.5 40.3 + - - +
230K GLN* 2.8 33.7 + - - +
258K THR* 4.7 7.4 - - + +
260K MET* 4.3 8.1 - - + -
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Residues in contact with VAL 227 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223K SER 2.9 19.7 + - - +
224K ALA* 3.6 8.1 - - - +
226K ARG* 1.3 74.3 - - - +
228K LEU* 1.3 65.2 + - - +
231K PHE* 2.9 25.7 + - + +
232K ALA* 4.0 1.0 + - - +
258K THR* 4.8 0.9 - - + -
260K MET* 3.7 28.5 - - + -
267K ILE* 3.8 23.8 - - + -
269K PHE* 4.2 18.2 - - + -
286K VAL* 3.1 40.6 - - + -
288K LEU* 5.2 2.7 - - + -
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Residues in contact with LEU 228 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K PHE* 3.7 31.2 - - + -
57K LEU* 3.9 16.6 - - + -
58K PRO* 4.3 10.5 - - + -
224K ALA 3.0 13.2 + - - +
225K ARG* 3.3 11.0 - - - +
227K VAL* 1.3 77.3 - - - +
229K GLN* 1.3 57.0 + - - +
232K ALA* 3.2 28.5 + - + +
234K ASN* 3.1 24.4 + - - +
235K ASP 3.9 32.3 - - - +
236K VAL* 4.1 5.4 - - + +
239K PHE* 4.0 26.2 - - + -
288K LEU* 5.7 0.7 - - - -
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Residues in contact with GLN 229 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K ASP* 3.8 20.7 + - - +
42K LYS* 5.5 2.8 - - + +
43K ASP* 4.0 15.0 + - - -
176K LEU* 4.3 1.8 - - + +
225K ARG* 3.1 11.4 + - - +
226K ARG* 2.5 51.2 + - - +
228K LEU* 1.3 79.1 - - - +
230K GLN* 1.3 70.2 + - + +
233K ASP* 3.9 12.5 + - - -
234K ASN* 3.0 29.6 + - - +
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Residues in contact with GLN 230 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J LEU* 3.9 3.2 - - - +
230J GLN* 3.0 41.1 + - - +
174K ALA* 3.7 13.8 - - + +
176K LEU* 3.5 26.2 - - + +
226K ARG 2.8 21.3 + - - +
229K GLN* 1.3 80.1 + - - +
231K PHE* 1.3 91.5 + - + +
232K ALA 3.7 0.2 - - - -
233K ASP 4.9 0.6 + - - -
260K MET* 4.2 7.0 - - + -
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Residues in contact with PHE 231 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173K ASP* 4.6 11.0 - - + -
174K ALA* 4.3 12.6 - - + -
227K VAL 2.9 12.1 + - - +
230K GLN* 1.3 105.5 - - + +
232K ALA* 1.3 59.9 + - - +
233K ASP* 3.8 0.7 - - - -
238K ARG* 3.9 9.6 + - - -
260K MET* 3.5 33.0 - - + -
262K LYS* 3.7 33.4 - - + -
267K ILE* 3.6 41.3 - - + -
288K LEU* 3.2 13.7 - - + +
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Residues in contact with ALA 232 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228K LEU* 3.2 25.2 + - + +
231K PHE* 1.3 79.7 - - - +
233K ASP* 1.3 72.4 + - - +
234K ASN 3.2 1.3 - - - -
235K ASP* 2.8 21.8 + - - +
238K ARG* 3.6 27.4 + - + +
288K LEU* 3.9 25.8 - - + -
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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