Contacts of the strand formed by residues 265 - 285 (chain C) in PDB entry 3M4D
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 TRP 265 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ALA 4.2 4.0 - - - -
74C ASN* 3.5 12.6 - - - -
191C TYR* 3.4 14.2 - - - -
197C MET* 3.5 18.4 - - + +
199C THR 3.4 10.5 - - - +
200C ARG 2.8 25.2 + - - +
202C GLY 2.8 12.1 + - - -
204C MET* 2.8 47.4 - - + +
206C ALA* 3.4 36.1 - - + -
209C ASN* 3.1 21.1 - - - +
258C LEU* 4.2 8.5 - - + -
259C HIS* 3.4 26.9 - - - -
260C TRP* 3.4 42.7 - + + -
264C ASN* 1.3 87.0 + - - +
266C LYS* 1.3 60.6 + - - +
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Residues in contact with LYS 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C TRP* 3.8 30.5 - - + -
189C PRO 3.8 22.4 + - - -
190C VAL 3.8 8.7 + - - +
191C TYR 3.3 16.8 - - - -
192C GLY* 3.7 4.3 - - - +
197C MET* 3.8 3.4 - - - -
257C GLN 3.8 0.2 - - - +
258C LEU* 3.5 1.8 - - - -
259C HIS* 3.1 62.4 + - + +
261C THR* 3.9 16.6 - - + -
265C TRP* 1.3 76.8 - - - +
267C GLY* 1.3 62.2 + - - +
268C THR* 5.5 0.4 - - + -
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Residues in contact with GLY 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C TRP* 3.6 1.6 - - - -
191C TYR 3.0 10.1 + - - -
192C GLY* 3.5 5.2 - - - -
193C ASN 2.8 40.5 + - - -
197C MET* 3.6 3.2 - - - +
256C TYR* 4.1 1.8 - - - -
257C GLN 3.1 9.4 - - - -
258C LEU* 3.7 9.6 - - - -
266C LYS* 1.3 73.1 - - - +
268C THR* 1.3 69.3 + - - +
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Residues in contact with THR 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C TRP* 4.2 21.3 - - + -
193C ASN* 4.4 2.9 + - - -
255C ASP 3.5 1.4 - - - +
256C TYR* 3.4 6.5 - - - -
257C GLN* 2.8 52.8 + - - +
259C HIS* 4.9 16.4 - - + +
266C LYS* 5.5 0.4 - - + -
267C GLY* 1.3 82.3 - - - +
269C ASN* 1.3 61.5 + - - +
270C THR* 4.3 3.4 + - - -
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Residues in contact with ASN 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C TRP* 3.0 30.1 + - - -
184C ARG* 3.7 30.3 + - - +
187C TRP* 5.8 0.2 - - - -
193C ASN* 3.9 23.6 - - - +
195C LEU* 5.3 1.3 - - - -
254C ASP* 3.0 27.9 + - - +
255C ASP 3.4 7.3 - - - +
256C TYR* 3.8 10.1 - - + +
268C THR* 1.3 76.6 - - - +
270C THR* 1.3 64.9 + - - +
271C LYS* 4.0 6.1 + - - +
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Residues in contact with THR 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C ASP* 3.4 4.2 - - - +
255C ASP* 2.9 48.0 + - - +
257C GLN* 4.3 12.3 + - - -
268C THR* 5.3 2.8 + - - -
269C ASN* 1.3 75.6 + - - +
271C LYS* 1.3 71.4 + - - +
273C LYS* 4.2 19.4 + - + +
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Residues in contact with LYS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ARG* 3.6 45.8 - - - +
185C ASP* 2.7 36.1 + - - -
254C ASP* 3.6 10.3 - - - +
269C ASN* 4.0 8.7 + - - +
270C THR* 1.3 78.1 - - - +
272C ASP* 1.3 74.3 + - - +
273C LYS* 3.2 2.3 + - - -
198D LYS* 5.9 3.2 - - - +
212D ASP* 4.5 13.3 + - - +
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Residues in contact with ASP 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C SER* 3.8 1.0 + - - -
184C ARG* 3.2 22.8 + - - -
252C VAL* 3.5 27.6 - - + +
253C ARG 3.7 6.3 - - - -
254C ASP* 2.9 9.5 + - - +
271C LYS* 1.3 77.0 - - - +
273C LYS* 1.3 63.3 + - - +
274C TRP* 3.3 4.6 - - - -
275C THR* 5.1 3.5 + - - +
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Residues in contact with LYS 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 5.3 1.3 - - - -
253C ARG 2.9 7.0 + - - +
255C ASP* 3.8 29.9 + - + +
270C THR* 4.3 17.5 - - + +
271C LYS 3.2 3.0 + - - -
272C ASP* 1.3 76.9 - - - +
274C TRP* 1.3 108.3 + - + +
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Residues in contact with TRP 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TYR* 3.4 50.0 - + - -
79C ALA* 3.6 12.8 - - + -
251C ARG 4.6 0.2 - - - -
252C VAL* 3.4 4.0 - - - +
253C ARG* 2.8 81.6 + - + +
254C ASP 3.6 18.4 - - - -
255C ASP* 3.7 15.0 - - + -
272C ASP 4.8 1.1 - - - -
273C LYS* 1.3 114.9 - - + +
275C THR* 1.3 64.6 + - - +
276C ASP* 4.3 0.4 - - - +
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Residues in contact with THR 275 (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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250C GLU* 3.6 25.4 - - + +
251C ARG 3.4 8.3 - - - +
252C VAL* 4.1 17.3 - - + +
272C ASP* 5.1 4.3 + - - +
274C TRP* 1.3 79.0 + - - +
276C ASP* 1.3 71.8 + - - +
277C ARG* 3.8 8.6 + - + +
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Residues in contact with ASP 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ASN* 3.5 18.7 - - - +
34C MET* 3.5 5.5 - - + +
64C GLN* 4.4 0.6 + - - -
250C GLU* 3.2 7.1 - - - +
251C ARG* 2.7 76.2 + - + +
253C ARG* 2.8 38.7 + - - -
274C TRP* 4.8 0.2 - - - +
275C THR* 1.3 76.1 - - - +
277C ARG* 1.3 59.0 + - - +
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Residues in contact with ARG 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ASN* 3.6 14.2 + - - -
87C GLN* 5.7 1.4 + - - -
89C GLN* 5.9 2.4 - - - +
248C ILE* 3.7 30.5 - - + +
250C GLU* 3.6 32.1 + - + +
275C THR* 3.8 10.0 + - + +
276C ASP* 1.3 72.6 - - - +
278C SER* 1.3 61.9 + - - +
279C SER* 3.7 21.5 + - - +
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Residues in contact with SER 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASP* 2.8 29.3 + - - +
32C ASN* 3.9 1.1 - - - +
34C MET* 3.6 25.1 - - - -
36C LYS* 2.7 35.1 + - - -
248C ILE* 3.3 3.0 - - - -
249C TYR 2.8 36.2 + - - -
277C ARG* 1.3 73.6 - - - +
279C SER* 1.3 59.7 + - - +
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Residues in contact with SER 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 4.2 3.7 + - - -
246C ASP* 4.4 11.3 + - - +
247C VAL 3.4 4.8 + - - -
248C ILE* 3.7 19.0 - - - +
277C ARG* 3.7 27.8 + - - +
278C SER* 1.3 75.3 + - - +
280C GLU* 1.3 66.9 + - - +
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Residues in contact with GLU 280 (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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27C THR* 2.8 36.2 + - - +
36C LYS* 3.9 13.2 + - - +
246C ASP* 3.4 5.0 - - - -
247C VAL 2.9 32.7 + - - +
279C SER* 1.3 79.4 + - - +
281C ARG* 1.3 71.3 + - - +
282C TYR* 3.3 29.2 + - + +
293C ASN* 2.5 36.4 + - + +
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Residues in contact with ARG 281 (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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91C PRO* 4.2 11.8 - - - +
244C ASN* 3.7 38.3 - - - +
245C ILE* 3.6 5.2 + - - +
246C ASP* 2.6 44.5 + - - +
280C GLU* 1.3 76.3 - - - +
282C TYR* 1.3 79.3 + - - +
283C LYS* 6.2 0.2 - - + -
293C ASN* 3.9 21.7 - - - +
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Residues in contact with TYR 282 (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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25C LEU* 3.8 31.2 + - + -
27C THR* 4.3 5.6 + - - -
36C LYS* 5.2 8.3 + - - +
38C VAL* 3.6 23.9 - - + +
243C THR 3.9 0.2 - - - +
244C ASN* 3.5 4.3 - - - -
245C ILE* 2.8 36.4 + - + +
247C VAL* 3.6 35.0 - - + +
280C GLU* 3.3 42.4 + - + +
281C ARG* 1.3 79.5 - - - +
283C LYS* 1.3 60.3 + - - +
291C MET* 3.5 27.6 - - + -
292C THR 3.3 9.6 - - - +
293C ASN* 3.7 23.3 - - + +
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Residues in contact with LYS 283 (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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94C GLU* 5.4 0.2 + - - -
240C LYS* 4.9 6.1 - - - +
242C GLN* 3.2 34.0 + - + +
243C THR 3.7 10.6 - - - +
244C ASN* 2.7 40.9 + - - +
281C ARG* 6.2 0.2 - - + -
282C TYR* 1.3 73.9 - - - +
284C ILE* 1.3 78.5 + - - +
285C ASP* 4.0 4.2 - - + +
290C GLU 3.8 1.0 - - - +
291C MET* 3.2 6.1 - - - +
292C THR* 2.8 46.1 + - - +
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Residues in contact with ILE 284 (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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42C PHE* 3.7 22.9 - - + -
53C LEU* 3.6 19.7 - - + -
55C ILE* 4.5 0.4 - - + -
232C ILE* 4.4 11.0 - - + -
242C GLN* 3.2 5.9 - - - -
243C THR* 2.7 57.3 + - + +
245C ILE* 3.8 26.7 - - + -
283C LYS* 1.3 76.0 - - - +
285C ASP* 1.3 60.9 + - - +
286C TRP* 3.7 29.4 + - + +
290C GLU 3.9 2.7 - - - -
291C MET* 3.7 23.6 - - + -
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Residues in contact with ASP 285 (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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42C PHE* 3.8 1.0 - - - -
241C GLN 3.9 6.2 - - - +
242C GLN* 4.5 13.5 - - + +
283C LYS* 4.0 5.1 + - + +
284C ILE* 1.3 73.4 - - - +
286C TRP* 1.3 56.8 + - - +
287C GLU* 3.0 23.4 + - - +
288C LYS* 3.0 33.3 + - - +
289C GLU* 2.8 30.3 + - - -
290C GLU* 3.0 27.3 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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