Contacts of the strand formed by residues 223 - 243 (chain C) in PDB entry 4IYC
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 THR 223 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASP* 3.6 6.8 - - - +
216C HIS* 4.6 0.5 - - - -
221C GLY* 3.3 9.8 - - - +
222C ASP* 1.4 82.4 - - + +
224C SER* 1.3 66.6 + - - +
270C GLU* 3.5 34.8 + - - +
271C VAL 3.0 14.1 - - - +
272C ASN* 3.9 20.4 - - + +
273C TRP* 4.0 2.2 - - - -
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Residues in contact with SER 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASP* 2.4 34.2 + - - -
89C VAL* 3.4 8.5 - - - +
216C HIS* 3.8 0.3 + - - -
223C THR* 1.3 70.6 + - - +
225C GLU* 1.3 60.5 + - - +
226C PHE* 3.7 22.8 - - - -
269C TYR 4.0 0.3 - - - +
270C GLU* 3.6 4.9 - - - +
271C VAL* 2.8 31.8 + - - +
273C TRP* 3.0 24.6 + - - -
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Residues in contact with GLU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C THR* 2.9 29.3 + - - -
85C ASN* 3.1 37.4 + - - +
224C SER* 1.3 73.6 - - - +
226C PHE* 1.3 61.8 + - - +
268C LYS* 4.4 27.2 - - + +
269C TYR 3.4 10.1 - - - +
270C GLU* 4.4 6.3 - - + +
281C LYS* 3.4 32.6 - - + -
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Residues in contact with PHE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 5.7 0.4 - - + -
46C LEU* 4.4 7.0 - - + -
48C LEU* 4.9 10.1 - - + -
82C LEU* 4.2 26.0 - - + -
83C LYS 3.5 4.9 - - - +
84C THR* 3.7 26.5 - - + -
89C VAL* 4.1 10.8 - - + -
214C VAL* 3.8 38.8 - - + -
224C SER* 3.7 28.0 - - - -
225C GLU* 1.3 74.1 - - - +
227C GLU* 1.3 58.9 + - - +
228C ILE* 5.2 2.7 - - + -
268C LYS* 3.5 3.0 - - - -
269C TYR* 2.7 51.7 + - + +
271C VAL* 4.0 28.7 - - + -
273C TRP* 4.4 4.7 - + - -
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Residues in contact with GLU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLY 3.8 0.7 - - - +
82C LEU* 3.3 5.5 - - - +
83C LYS* 2.9 67.0 + - + +
226C PHE* 1.3 70.4 - - - +
228C ILE* 1.3 60.0 + - - +
229C THR* 4.3 2.5 + - - +
266C THR* 3.5 30.1 - - + +
267C VAL 3.4 6.7 - - - +
268C LYS* 2.9 39.8 + - + +
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Residues in contact with ILE 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLN* 3.1 26.2 + - - +
31C ILE* 3.9 29.4 - - + -
33C PHE* 5.1 0.2 - - + -
48C LEU* 4.3 8.5 - - + -
50C MET* 4.3 9.2 - - + -
81C GLY 3.3 9.2 - - - +
82C LEU* 3.7 26.0 - - + -
226C PHE* 5.2 1.8 - - + -
227C GLU* 1.3 76.4 - - - +
229C THR* 1.3 63.6 + - - +
230C TYR* 3.5 25.1 - - + -
266C THR* 3.5 0.4 - - - -
267C VAL 2.8 34.6 + - - -
269C TYR* 3.8 25.1 - - + -
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Residues in contact with THR 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ASN* 3.4 2.5 - - + +
80C ILE* 3.4 2.9 - - - -
81C GLY* 2.9 39.9 + - - -
155C GLN* 5.6 3.6 - - - +
227C GLU* 5.0 2.1 + - - +
228C ILE* 1.3 69.9 + - - +
230C TYR* 1.3 68.2 + - - +
264C ASN* 3.2 43.7 - - + +
265C TYR 3.5 3.6 - - - +
266C THR* 3.1 31.3 + - - +
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Residues in contact with TYR 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 3.5 22.2 - - + +
28C THR 3.8 14.4 - - - -
29C GLN* 3.8 15.9 - - + -
31C ILE* 3.4 6.1 - - + +
50C MET* 3.0 17.5 - - + +
51C GLN 2.6 45.3 + - - -
53C PHE 4.8 0.4 - - - -
54C ILE* 3.7 21.1 - - + -
79C ASN 3.2 5.8 - - - -
80C ILE* 3.9 15.0 - - + -
208C PRO* 3.5 19.7 - - + -
228C ILE* 3.5 25.6 - - + -
229C THR* 1.3 82.1 - - - +
231C GLY* 1.3 54.8 + - - +
264C ASN* 3.9 3.1 - - - -
265C TYR* 2.7 37.9 + - - +
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Residues in contact with GLY 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 4.8 1.3 - - - -
54C ILE* 3.5 11.5 - - - +
78C TYR* 3.4 10.7 - - - -
79C ASN* 2.8 32.7 + - - +
230C TYR* 1.3 75.2 - - - +
232C ARG* 1.3 68.0 + - - +
263C ARG 3.4 8.7 - - - -
264C ASN* 3.1 15.8 + - - -
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Residues in contact with ARG 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LYS 5.5 0.2 + - - -
25C TRP* 2.8 35.7 + - - +
26C GLY 4.1 1.6 + - - -
27C VAL* 4.3 3.4 - - - +
54C ILE* 3.4 17.1 - - + +
55C ASN 2.8 28.4 + - - -
56C SER* 3.3 26.2 + - - +
57C LYS* 4.0 15.2 - - - +
75C PRO* 4.1 4.9 - - + -
77C GLN 3.3 8.5 - - - +
78C TYR* 3.8 17.7 - - + -
79C ASN* 3.8 2.5 - - - -
231C GLY* 1.3 77.3 - - - +
233C ASN* 1.3 66.6 + - - +
234C MET* 3.7 23.8 - - + +
262C ASN 3.5 0.2 + - - -
263C ARG* 2.8 66.4 + - + +
264C ASN* 3.3 1.4 + - - -
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Residues in contact with ASN 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C PRO 3.7 0.9 - - - -
76C PHE* 2.8 28.2 + - + +
77C GLN* 2.8 37.8 + - + +
79C ASN* 2.9 20.5 - - - +
232C ARG* 1.3 68.1 - - - +
234C MET* 1.3 61.0 + - - +
258C ASN* 3.6 27.1 + - - +
260C PHE 3.5 5.4 - - - +
261C VAL* 4.0 14.3 - - - +
262C ASN* 2.8 34.6 + - - +
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Residues in contact with MET 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C SER 3.4 18.2 - - - +
57C LYS* 3.5 20.9 - - + +
73C ARG* 3.8 31.6 - - + +
74C TRP* 3.4 17.9 - - - +
75C PRO* 3.7 18.8 - - - -
232C ARG* 3.7 23.8 - - + +
233C ASN* 1.3 71.9 - - - +
235C ASP* 1.4 55.7 + - - +
258C ASN 3.6 1.9 - - - -
259C ALA* 2.8 31.1 + - - +
260C PHE* 2.7 28.4 + - + +
263C ARG* 4.1 20.6 - - + -
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Residues in contact with ASP 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C MET 3.7 0.7 - - - +
73C ARG* 3.2 6.9 - - - +
74C TRP* 2.8 54.1 + - + +
76C PHE* 3.5 16.6 - - + +
233C ASN 4.0 0.6 + - - -
234C MET* 1.4 71.4 - - - +
236C VAL* 1.3 63.5 + - - +
237C THR 4.2 0.4 - - - -
255C ARG* 2.7 34.7 + - - -
256C ILE 3.7 3.4 - - - -
257C HIS* 3.1 20.5 + - - -
258C ASN* 2.6 31.8 + - - -
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Residues in contact with VAL 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C TYR* 3.4 27.6 - - - +
71C ALA* 4.1 5.2 - - + -
72C MET 3.5 6.5 - - - +
73C ARG* 4.2 8.1 - - + -
235C ASP* 1.3 79.0 - - - +
237C THR* 1.3 63.1 + - - +
238C HIS* 3.6 30.2 + - + +
254C SER 3.8 0.5 - - - +
255C ARG* 3.4 6.0 - - - -
256C ILE* 2.9 46.3 + - + +
259C ALA* 3.7 19.5 - - + -
260C PHE* 4.0 15.0 - - + -
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Residues in contact with THR 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ALA* 3.4 3.1 - - - -
72C MET* 2.9 34.9 + - - -
74C TRP* 3.2 24.5 + - - -
175C PRO 4.1 7.6 - - - +
177C LEU 4.0 19.3 + - - +
179C VAL* 4.0 13.9 - - + -
192C PHE* 3.4 25.9 - - + -
235C ASP 4.2 0.4 - - - -
236C VAL* 1.3 70.4 - - - +
238C HIS* 1.4 62.9 + - - +
254C SER 3.4 8.7 - - - +
255C ARG* 3.3 19.4 + - - -
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Residues in contact with HIS 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C TYR* 4.8 3.4 + - - -
63C TYR* 3.8 35.1 - + - -
69C ILE* 4.1 15.9 - - + -
70C LYS 3.5 2.9 - - - -
71C ALA* 3.6 22.3 - - + +
236C VAL* 3.6 15.3 + - + +
237C THR* 1.4 71.3 - - - +
239C ALA* 1.3 59.4 + - - +
240C THR* 4.0 4.0 + - - +
252C GLU 3.6 1.2 - - - +
253C GLY* 3.2 4.3 - - - -
254C SER* 2.9 54.1 + - - +
256C ILE* 3.6 35.0 - - + +
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Residues in contact with ALA 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ILE* 3.6 1.8 - - - -
70C LYS 2.8 28.3 + - - -
179C VAL* 3.9 11.0 - - + -
191C TYR* 3.3 38.6 - - + +
192C PHE* 3.7 21.8 - - + -
237C THR 3.9 1.2 + - - -
238C HIS* 1.3 72.3 - - - +
240C THR* 1.4 59.6 + - - +
251C LEU* 4.4 5.2 - - + -
252C GLU 3.3 6.7 - - - +
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Residues in contact with THR 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C HIS* 3.6 20.6 - - + +
69C ILE* 3.9 23.3 - - + +
238C HIS* 4.6 5.5 + - - +
239C ALA* 1.4 73.9 - - - +
241C ARG* 1.3 70.5 + - - +
242C ARG* 3.5 35.5 + - - +
251C LEU* 3.4 6.0 - - - -
252C GLU* 2.7 35.9 + - - -
254C SER* 5.7 3.6 - - - -
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Residues in contact with ARG 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ASP* 3.2 30.7 + - - -
68C HIS* 3.0 45.8 + - + +
183C PRO* 3.3 34.4 + - + -
184C TYR* 3.2 45.4 + - - +
185C SER 5.4 0.6 + - - +
191C TYR* 3.7 15.4 + - - +
240C THR* 1.3 78.0 - - - +
242C ARG* 1.3 75.2 + - - +
243C THR* 6.1 0.2 - - - -
249C SER* 4.4 1.3 - - - +
250C TYR 3.7 3.8 - - - -
251C LEU* 3.7 6.6 - - + +
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Residues in contact with ARG 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C THR* 3.5 35.7 - - - +
241C ARG* 1.3 79.6 + - - +
243C THR* 1.3 60.6 + - - +
244C ALA 4.2 0.2 - - - -
249C SER* 3.2 8.6 - - - -
250C TYR* 2.9 63.9 + - + +
252C GLU* 2.9 40.3 + - + +
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Residues in contact with THR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C TYR* 4.3 6.3 + - - -
242C ARG* 1.3 74.3 - - - +
244C ALA* 1.3 66.1 + - - +
247C GLY* 3.0 28.9 + - - -
248C ASN 3.3 3.5 + - - -
249C SER* 3.6 8.3 + - - -
250C TYR* 4.4 3.2 - - - -
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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