Contacts of the strand formed by residues 223 - 243 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASP* 3.6 7.4 - - - +
216B HIS* 4.5 0.2 - - - -
221B GLY* 3.3 7.8 - - - +
222B ASP* 1.3 83.4 - - + +
224B SER* 1.3 67.5 + - - +
270B GLU* 3.5 34.7 + - - +
271B VAL 3.0 12.8 - - - +
272B ASN* 4.1 11.4 - - + +
273B TRP* 4.1 2.0 - - - -
279B LYS* 3.9 8.3 - - - +
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Residues in contact with SER 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASP* 2.5 29.2 + - - -
89B VAL* 3.4 8.1 - - - +
216B HIS* 3.5 0.7 + - - -
223B THR* 1.3 71.1 + - - +
225B GLU* 1.3 64.7 + - - +
226B PHE* 3.9 24.4 - - - -
269B TYR 3.9 0.3 - - - +
270B GLU* 3.6 3.8 - - - -
271B VAL* 3.0 32.0 + - - +
273B TRP* 2.8 27.1 + - - -
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Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS 4.6 0.2 - - - -
84B THR* 2.5 34.8 + - - -
85B ASN* 3.7 30.7 + - - +
224B SER* 1.3 75.0 - - - +
226B PHE* 1.4 61.5 + - - +
268B LYS* 3.6 31.2 + - - +
269B TYR 3.5 12.2 - - - +
270B GLU* 3.8 8.4 - - + +
281B LYS* 3.2 54.1 + - - +
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Residues in contact with PHE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 5.7 0.2 - + - -
46B LEU* 3.9 19.3 - - + -
48B LEU* 4.9 9.6 - - + -
82B LEU* 4.4 23.3 - - + -
83B LYS 3.4 5.8 - - - +
84B THR* 3.6 25.4 - - + -
89B VAL* 4.0 9.9 - - + -
214B VAL* 3.7 34.5 - - + -
224B SER* 3.9 27.6 - - - -
225B GLU* 1.4 77.2 - - - +
227B GLU* 1.3 59.4 + - - +
228B ILE* 4.9 2.2 - - + -
267B VAL 3.7 0.9 - - - +
268B LYS* 3.5 3.9 - - - +
269B TYR* 2.8 50.1 + - + +
271B VAL* 3.8 23.6 - - + -
273B TRP* 4.2 6.7 - + - -
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLY 3.7 1.0 - - - +
82B LEU* 3.4 6.4 - - - -
83B LYS* 2.9 63.3 + - + +
226B PHE* 1.3 72.4 - - - +
228B ILE* 1.3 61.0 + - - +
229B THR* 4.2 4.2 + - - +
266B THR* 3.6 28.1 - - + +
267B VAL 3.4 6.1 - - - +
268B LYS* 4.1 32.5 + - + +
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLN* 2.9 27.7 + - - +
31B ILE* 3.8 29.6 - - + -
48B LEU* 4.2 7.4 - - + -
50B MET* 4.2 10.3 - - + -
81B GLY 3.4 9.9 - - - +
82B LEU* 3.8 26.0 - - + -
226B PHE* 4.9 2.5 - - + +
227B GLU* 1.3 76.2 - - - +
229B THR* 1.3 63.6 + - - +
230B TYR* 3.4 31.0 - - + -
267B VAL 2.7 28.6 + - - -
269B TYR* 3.7 25.4 - - + -
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Residues in contact with THR 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASN* 3.6 1.7 - - + +
80B ILE* 3.4 5.7 - - - -
81B GLY* 2.9 39.8 + - - -
155B GLN* 5.6 3.8 - - - +
227B GLU* 4.9 4.0 + - - +
228B ILE* 1.3 71.0 + - - +
230B TYR* 1.3 63.9 + - - +
264B ASN* 3.2 42.4 - - + +
265B TYR 3.5 3.4 - - - -
266B THR* 3.3 29.8 + - - +
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Residues in contact with TYR 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 3.5 24.1 - - + +
28B THR 3.6 20.0 - - - -
29B GLN* 3.7 15.7 - - + +
31B ILE* 3.3 12.0 - - + +
50B MET* 3.1 12.8 - - + +
51B GLN 2.5 45.1 + - - -
54B ILE* 4.0 15.9 - - + -
79B ASN 3.3 5.4 - - - -
80B ILE* 4.1 15.7 - - + -
208B PRO* 3.6 17.9 - - + -
228B ILE* 3.4 22.4 - - + -
229B THR* 1.3 81.9 - - - +
231B GLY* 1.3 57.0 + - - +
264B ASN* 3.8 3.6 - - - -
265B TYR* 2.7 35.5 + - - -
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Residues in contact with GLY 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 4.8 1.6 - - - -
54B ILE* 3.9 13.9 - - - +
78B TYR* 3.4 13.3 - - - +
79B ASN 3.0 27.9 + - - +
230B TYR* 1.3 74.9 - - - +
232B ARG* 1.4 67.4 + - - +
263B ARG 3.3 8.5 - - - -
264B ASN* 3.0 14.2 + - - -
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Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LYS 5.4 0.8 + - - -
25B TRP* 2.8 36.1 + - - +
26B GLY 4.1 1.2 + - - -
27B VAL* 4.4 1.8 - - - +
54B ILE* 3.4 21.6 - - + +
55B ASN 3.0 28.8 + - - -
56B SER* 3.4 11.2 + - - +
57B LYS* 3.8 18.4 - - - +
75B PRO* 4.4 1.3 - - + -
77B GLN 3.4 8.5 - - - +
78B TYR* 3.9 11.7 - - + -
79B ASN* 3.6 2.4 - - - +
231B GLY* 1.4 78.7 - - - +
233B ASN* 1.4 67.2 + - - +
234B MET* 3.2 34.5 - - + +
262B ASN 3.5 0.3 + - - -
263B ARG* 2.8 61.4 + - + +
264B ASN* 3.2 1.8 + - - -
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Residues in contact with ASN 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PRO* 3.5 2.8 - - - +
76B PHE* 2.7 32.5 + - + -
77B GLN* 2.8 40.3 + - + +
79B ASN* 2.9 29.8 + - - +
232B ARG* 1.4 67.2 - - - +
234B MET* 1.3 56.1 + - - +
258B ASN* 3.6 24.8 + - - +
260B PHE 3.4 4.9 - - - +
261B VAL* 4.0 13.6 - - - +
262B ASN* 3.0 20.6 + - - +
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Residues in contact with MET 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER 3.5 9.9 - - - +
57B LYS* 4.7 7.0 - - - +
73B ARG* 3.9 28.7 - - + +
74B TRP* 3.4 14.8 - - - -
75B PRO* 3.4 20.6 - - + -
232B ARG* 3.2 47.8 - - + +
233B ASN* 1.3 72.5 - - - +
235B ASP* 1.3 63.3 + - - +
258B ASN* 3.6 1.4 - - - -
259B ALA* 2.8 26.3 + - - +
260B PHE* 2.8 30.6 + - + +
263B ARG* 4.2 15.3 - - + -
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Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG* 3.2 4.0 - - - +
74B TRP* 2.8 55.1 + - + +
76B PHE* 3.5 18.0 - - + +
233B ASN 4.2 0.8 + - - -
234B MET* 1.3 74.5 - - - +
236B VAL* 1.4 63.1 + - - +
237B THR 4.1 0.2 - - - -
255B ARG* 2.8 28.1 + - - -
256B ILE 3.7 3.1 - - - -
257B HIS* 2.8 30.6 + - - -
258B ASN* 2.7 29.3 + - - +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR* 3.4 27.1 - - - +
71B ALA* 4.0 4.7 - - + -
72B MET 3.3 7.2 - - - +
73B ARG* 4.3 8.5 - - + -
235B ASP* 1.4 74.5 - - - +
237B THR* 1.3 63.9 + - - +
238B HIS* 3.7 31.4 + - + +
254B SER 3.8 0.2 - - - +
255B ARG* 3.4 6.0 - - - -
256B ILE* 2.9 43.4 + - + +
259B ALA* 3.7 22.0 - - + +
260B PHE* 4.1 14.6 - - + -
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Residues in contact with THR 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA* 3.4 4.5 - - - +
72B MET* 2.7 39.3 + - - -
74B TRP* 3.1 22.2 + - - -
175B PRO 4.3 10.3 - - - +
177B LEU 3.9 20.9 + - - +
179B VAL* 4.4 9.4 - - + -
192B PHE* 3.5 24.2 - - + -
235B ASP 4.1 0.6 - - - -
236B VAL* 1.3 71.0 - - - +
238B HIS* 1.3 63.6 + - - +
254B SER 3.4 7.6 - - - +
255B ARG* 3.5 19.1 + - - -
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Residues in contact with HIS 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR* 4.9 4.0 + - - -
63B TYR* 3.8 35.5 - + - -
69B ILE* 4.4 12.1 - - + -
70B LYS 3.8 2.0 - - - -
71B ALA* 3.5 23.8 - - + +
236B VAL* 3.7 14.3 + - + +
237B THR* 1.3 72.1 - - - +
239B ALA* 1.3 59.8 + - - +
240B THR* 4.0 3.3 + - - +
252B GLU 3.5 1.9 - - - +
253B GLY* 3.2 4.3 - - - -
254B SER* 2.7 59.5 + - - +
256B ILE* 3.6 34.5 - - + +
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 3.4 4.9 - - - +
70B LYS 2.9 31.0 + - - +
179B VAL* 4.8 6.3 - - + -
191B TYR* 3.7 32.3 - - + +
192B PHE* 3.7 24.7 - - + -
237B THR 3.9 1.6 + - - -
238B HIS* 1.3 71.3 - - - +
240B THR* 1.3 59.9 + - - +
251B LEU* 4.3 9.2 - - + -
252B GLU 3.6 6.3 - - - +
253B GLY* 4.5 0.9 - - - -
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Residues in contact with THR 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B HIS* 3.6 12.3 - - + +
69B ILE* 3.6 33.3 - - + +
238B HIS* 4.5 5.4 + - - +
239B ALA* 1.3 73.3 - - - +
241B ARG* 1.4 74.6 + - - +
242B ARG* 3.5 33.0 - - - +
251B LEU* 3.4 5.5 - - - -
252B GLU 2.9 35.6 + - - +
254B SER* 5.6 2.6 + - - -
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP* 4.2 13.7 + - - +
68B HIS* 2.9 58.5 + - + +
183B PRO* 3.2 43.0 + - + +
184B TYR* 4.7 9.5 + - - +
185B SER 5.2 1.0 + - - -
191B TYR* 3.5 16.7 + - - +
240B THR* 1.4 77.4 - - - +
242B ARG* 1.3 69.4 + - - +
249B SER* 4.2 15.9 - - - -
250B TYR 3.6 5.4 - - - +
251B LEU* 3.9 6.3 - - + +
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Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B THR* 3.5 33.0 - - - +
241B ARG* 1.3 83.8 + - - +
243B THR* 1.3 63.0 + - - +
249B SER* 2.9 7.9 - - - -
250B TYR* 2.8 61.6 + - + +
252B GLU* 3.2 40.2 + - + +
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Residues in contact with THR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ARG* 1.3 76.1 - - - +
244B ALA* 1.3 68.6 + - - +
247B GLY* 4.7 7.8 + - - -
248B ASN 3.4 9.0 + - - -
249B SER* 4.3 7.5 + - - +
250B TYR* 4.2 7.4 + - - -
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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) + - + + + + + -
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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