Contacts of the strand formed by residues 265 - 285 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA 3.4 13.7 - - - -
74B ASN* 3.8 2.9 - - - -
191B TYR* 3.4 13.3 - - - -
197B MET* 3.7 15.1 - - + +
199B THR 3.4 11.2 - - - +
200B ARG 2.9 20.5 + - - +
202B GLY 2.9 26.0 + - - -
203B SER* 5.5 0.2 - - - -
204B MET* 3.0 35.8 - - + +
206B ALA* 3.3 38.8 - - + -
209B ASN* 3.0 20.4 - - - +
258B LEU* 4.2 9.6 - - + -
259B HIS* 3.6 26.9 - - - -
260B TRP* 3.5 34.2 - + + -
264B ASN* 1.3 90.9 + - - +
266B LYS* 1.3 61.1 + - - +
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TRP* 3.6 34.3 - - + -
189B PRO 4.0 20.2 + - - -
190B VAL 4.0 6.5 - - - +
191B TYR 3.2 18.2 - - - +
192B GLY* 3.7 5.4 - - - +
197B MET* 4.0 2.2 - - - -
257B GLN 3.7 0.2 - - - +
258B LEU* 3.5 3.3 - - - -
259B HIS* 3.1 64.9 + - + +
261B THR* 4.1 14.4 - - + -
265B TRP* 1.3 77.5 - - - +
267B GLY* 1.3 60.3 + - - +
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Residues in contact with GLY 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TRP* 3.6 3.3 - - - -
191B TYR 2.8 13.1 + - - -
192B GLY* 3.6 5.5 - - - -
193B ASN* 2.7 41.6 + - - -
197B MET* 3.7 3.2 - - - +
256B TYR* 4.0 1.3 - - - -
257B GLN 3.2 8.7 - - - -
258B LEU* 3.8 9.6 - - - -
266B LYS* 1.3 73.6 - - - +
268B THR* 1.3 65.0 + - - -
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Residues in contact with THR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TRP* 4.2 17.8 - - + -
193B ASN* 4.3 2.7 + - - -
255B ASP 3.6 1.6 - - - +
256B TYR* 3.3 7.5 - - - -
257B GLN* 2.8 43.6 + - - +
259B HIS* 4.8 13.1 + - - -
266B LYS* 5.4 0.2 - - - +
267B GLY* 1.3 78.5 + - - -
269B ASN* 1.3 72.5 + - - +
270B THR* 4.7 10.5 - - + -
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Residues in contact with ASN 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TRP* 3.0 34.9 + - - -
184B ARG* 3.9 23.6 + - - +
193B ASN* 4.0 23.8 - - - +
195B LEU* 5.2 1.6 - - + -
254B ASP* 2.9 27.8 + - - +
255B ASP 3.4 7.5 - - - +
256B TYR* 3.8 10.8 - - + +
268B THR* 1.3 81.3 - - - +
270B THR* 1.3 68.4 + - - +
271B LYS* 4.2 5.4 + - - +
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Residues in contact with THR 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ASP* 3.4 2.9 - - - +
255B ASP* 2.8 61.3 + - - +
257B GLN* 4.9 11.0 - - - +
268B THR* 4.7 11.7 - - + -
269B ASN* 1.3 79.2 - - - +
271B LYS* 1.3 65.2 + - - +
273B LYS* 3.9 12.5 + - - +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ARG* 3.6 49.3 - - - +
185B ASP* 2.7 35.9 + - - -
254B ASP* 3.5 10.1 - - - +
269B ASN* 4.2 6.5 - - - +
270B THR* 1.3 74.3 - - - +
272B ASP* 1.3 76.7 + - - +
273B LYS* 3.1 3.2 + - - -
212C ASP* 5.3 8.3 + - - +
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Residues in contact with ASP 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B SER* 3.8 0.3 + - - -
184B ARG* 3.2 23.1 + - - -
252B VAL* 3.3 27.3 - - + +
253B ARG 3.6 6.7 - - - -
254B ASP* 2.9 8.3 + - - -
271B LYS* 1.3 76.3 - - - +
273B LYS* 1.3 64.3 + - - +
274B TRP* 3.3 5.1 + - - +
275B THR* 5.0 3.8 + - - +
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Residues in contact with LYS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ARG 2.9 6.8 + - - +
255B ASP* 3.7 39.0 + - + +
257B GLN* 5.6 0.8 - - - +
270B THR* 3.9 11.8 + - - +
271B LYS 3.1 3.8 + - - +
272B ASP* 1.3 76.7 - - - +
274B TRP* 1.3 101.5 + - + +
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Residues in contact with TRP 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 3.6 44.2 - + - -
79B ALA* 3.4 22.7 - - + -
251B ARG 4.6 0.2 - - - -
252B VAL* 3.5 4.0 - - - +
253B ARG* 2.8 82.2 + - + +
254B ASP 3.7 12.1 - - - -
255B ASP* 3.9 14.6 - - + -
272B ASP 4.7 1.1 - - - -
273B LYS* 1.3 112.6 - - + +
275B THR* 1.3 64.6 + - - +
276B ASP* 4.3 0.7 - - - +
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Residues in contact with THR 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B GLU* 3.7 34.8 - - + +
251B ARG 3.5 3.8 - - - +
252B VAL* 4.2 14.2 - - + +
272B ASP* 5.0 4.3 + - - +
274B TRP* 1.3 79.2 + - - +
276B ASP* 1.3 66.2 + - - +
277B ARG* 3.9 13.5 + - + +
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Residues in contact with ASP 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASN* 3.5 15.6 - - - +
34B MET* 3.4 5.2 - - + +
64B GLN* 4.2 0.7 + - - -
250B GLU* 3.3 5.4 - - - +
251B ARG* 2.7 84.2 + - - +
253B ARG* 2.8 40.2 + - - -
274B TRP* 4.7 0.2 - - - +
275B THR* 1.3 76.6 + - - +
277B ARG* 1.3 60.0 + - - +
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Residues in contact with ARG 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ASN* 3.2 17.4 + - - -
87B GLN* 3.8 18.8 + - - +
248B ILE* 4.3 24.4 - - + +
249B TYR 3.7 2.2 - - - -
250B GLU* 2.7 34.9 + - + +
275B THR* 3.9 12.2 + - + +
276B ASP* 1.3 72.1 - - - +
278B SER* 1.3 61.4 + - - +
279B SER* 4.2 2.8 + - - -
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 2.6 30.2 + - - +
32B ASN* 4.0 0.9 - - - +
34B MET* 3.6 24.7 - - - -
36B LYS* 2.9 32.6 + - - -
247B VAL 3.7 1.2 - - - +
248B ILE* 3.4 4.2 - - - -
249B TYR 2.9 32.3 + - - -
277B ARG* 1.3 73.8 - - - +
279B SER* 1.3 59.5 + - - +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LYS* 4.0 2.2 + - - -
246B ASP* 5.0 5.5 - - - +
247B VAL 3.4 7.0 + - - -
248B ILE* 4.2 17.2 - - - +
277B ARG* 4.2 3.9 + - - -
278B SER* 1.3 74.7 + - - +
280B GLU* 1.3 73.2 + - - +
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B THR* 3.6 20.8 + - - +
36B LYS* 3.4 22.8 + - - +
245B ILE 3.8 0.5 - - - +
246B ASP* 3.4 3.8 - - - +
247B VAL* 2.7 41.1 + - + +
279B SER* 1.3 80.0 + - - +
281B ARG* 1.3 65.3 + - - +
282B TYR* 3.6 35.1 - - + +
293B ASN* 2.7 31.3 + - - +
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Residues in contact with ARG 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B PRO* 4.3 10.7 - - - +
244B ASN* 3.8 37.6 - - + +
245B ILE 3.6 0.9 - - - +
246B ASP* 2.7 41.9 + - - +
280B GLU* 1.3 75.8 - - - +
282B TYR* 1.3 72.0 + - - +
283B LYS* 5.7 0.7 - - + -
293B ASN* 3.7 20.4 - - - +
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Residues in contact with TYR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 3.9 27.6 + - + -
27B THR* 4.6 4.5 + - - -
36B LYS* 5.1 12.5 + - - +
38B VAL* 3.5 24.4 + - + +
243B THR 3.7 0.5 - - - +
244B ASN* 3.4 5.0 - - - +
245B ILE* 2.9 37.9 + - + +
247B VAL* 3.7 39.1 - - + +
249B TYR* 6.1 0.7 - - - -
280B GLU* 3.6 26.4 - - + +
281B ARG* 1.3 77.8 - - - +
283B LYS* 1.3 60.2 + - - +
284B ILE 4.0 0.2 - - - -
291B MET* 3.6 28.5 - - + -
292B THR 3.3 7.6 - - - +
293B ASN* 3.4 34.0 + - + -
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Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B GLN* 4.3 27.0 - - + +
243B THR 3.7 3.1 - - - +
244B ASN* 4.1 15.0 - - - +
281B ARG* 4.4 0.6 + - + -
282B TYR* 1.3 71.9 - - - +
284B ILE* 1.3 68.0 + - - +
285B ASP* 3.9 8.2 + - + +
290B GLU 3.8 1.2 - - - +
291B MET* 3.3 5.9 - - - -
292B THR* 2.8 49.7 + - - +
293B ASN* 5.1 0.2 - - - +
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 3.7 27.4 - - + -
53B LEU* 3.5 26.0 - - + -
55B ILE* 4.6 3.6 - - + -
90B LEU* 5.1 2.0 - - + -
232B ILE* 5.4 3.1 - - + -
241B GLN 3.9 0.2 - - - +
242B GLN* 3.2 6.4 - - - +
243B THR* 2.6 62.6 + - + +
245B ILE* 4.0 25.8 - - + -
283B LYS* 1.3 77.3 - - - +
285B ASP* 1.3 62.6 + - - +
286B TRP* 3.6 25.2 + - + +
290B GLU 3.9 2.5 - - - -
291B MET* 4.2 14.4 - - + +
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Residues in contact with ASP 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE* 3.8 1.0 - - - -
241B GLN 3.8 6.2 - - - +
242B GLN* 4.6 13.7 - - + +
283B LYS* 3.9 9.2 + - + -
284B ILE* 1.3 74.2 - - - +
286B TRP* 1.3 58.3 + - - +
287B GLU* 2.9 24.0 + - - +
288B LYS* 2.9 35.3 + - - +
289B GLU* 2.8 29.8 + - - -
290B GLU* 3.0 28.8 + - + +
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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