Contacts of the strand formed by residues 265 - 285 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ALA 3.5 13.0 - - - -
74D ASN* 4.0 2.9 - - - -
191D TYR* 3.4 14.2 - - - -
197D MET* 3.6 12.7 - - + +
199D THR 3.4 13.7 - - - +
200D ARG 2.8 25.6 + - - +
202D GLY 2.9 24.0 + - - -
203D SER 5.3 0.2 - - - -
204D MET* 3.4 29.3 - - + +
206D ALA* 3.3 39.5 - - + -
209D ASN* 3.2 30.8 - - + +
258D LEU* 4.4 7.0 - - + -
259D HIS* 3.6 26.7 - - - -
260D TRP* 3.7 37.4 - + + -
264D ASN* 1.3 88.3 + - - +
266D LYS* 1.3 60.3 + - - +
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Residues in contact with LYS 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D TRP* 3.6 33.5 - - + -
189D PRO 4.1 19.1 + - - -
190D VAL 3.9 7.9 - - - +
191D TYR 3.2 18.6 - - - -
192D GLY* 3.7 4.5 - - - +
197D MET* 3.9 1.6 - - - -
257D GLN 3.8 0.2 - - - +
258D LEU* 3.6 2.0 - - - -
259D HIS* 3.0 66.0 + - + +
261D THR* 3.7 16.2 - - + -
265D TRP* 1.3 77.6 - - - +
267D GLY* 1.3 61.0 + - - +
268D THR* 5.5 0.7 - - - +
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Residues in contact with GLY 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D TRP* 3.6 7.8 - - - -
191D TYR 2.8 12.9 + - - -
192D GLY* 3.6 1.4 - - - -
193D ASN 2.8 40.3 + - - -
197D MET* 3.5 4.0 - - - +
256D TYR* 4.0 1.8 - - - -
257D GLN 3.2 7.6 - - - -
258D LEU* 3.8 10.1 - - - -
266D LYS* 1.3 75.2 - - - +
268D THR* 1.3 66.3 + - - -
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Residues in contact with THR 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D TRP* 4.2 17.1 - - + -
193D ASN* 4.6 2.7 - - - -
255D ASP 3.6 1.0 - - - +
256D TYR* 3.2 8.6 - - - -
257D GLN* 2.7 51.5 + - + +
259D HIS* 5.0 10.7 + - - -
266D LYS* 5.5 0.3 - - - +
267D GLY* 1.3 78.0 + - - -
269D ASN* 1.3 71.4 + - - +
270D THR* 4.6 7.9 - - - +
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Residues in contact with ASN 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D TRP* 2.9 34.9 + - - -
184D ARG* 3.9 22.7 + - - +
187D TRP* 5.7 0.4 - - - -
193D ASN* 4.1 20.7 - - - +
195D LEU* 5.2 1.3 - - + -
254D ASP* 3.0 26.8 + - - +
255D ASP 3.3 10.1 - - - +
256D TYR* 3.8 12.5 - - + +
268D THR* 1.3 81.5 - - - +
270D THR* 1.3 65.7 + - - +
271D LYS* 4.1 5.9 + - - +
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Residues in contact with THR 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D ASP* 3.3 6.8 - - - +
255D ASP* 2.8 46.9 + - - +
257D GLN* 4.7 8.8 + - - -
268D THR* 4.6 8.3 - - - +
269D ASN* 1.3 76.3 + - - +
271D LYS* 1.3 69.2 + - - +
273D LYS* 4.2 23.0 + - + +
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Residues in contact with LYS 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ARG* 3.5 46.6 - - - +
185D ASP* 2.8 35.1 + - - -
254D ASP* 3.5 10.3 - - - +
269D ASN* 4.1 6.9 + - - +
270D THR* 1.3 76.4 - - - +
272D ASP* 1.3 76.4 + - - +
273D LYS* 3.2 5.0 + - - -
212E ASP* 4.4 13.1 + - - +
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Residues in contact with ASP 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D SER* 3.8 0.9 + - - -
83D ALA* 6.1 0.2 - - - +
184D ARG* 3.1 22.9 + - - -
252D VAL* 3.4 27.5 - - + +
253D ARG 3.6 7.0 - - - -
254D ASP* 2.9 9.0 + - - +
271D LYS* 1.3 77.2 - - - +
273D LYS* 1.3 64.2 + - - +
274D TRP* 3.3 5.7 + - - +
275D THR* 4.9 3.4 + - - +
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Residues in contact with LYS 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D TYR* 5.8 0.2 - - - -
253D ARG 2.9 5.8 + - - +
255D ASP* 3.6 36.9 + - + +
257D GLN* 5.9 0.8 - - - +
270D THR* 4.2 20.0 + - + +
271D LYS 3.2 3.8 + - - -
272D ASP* 1.3 77.1 - - - +
274D TRP* 1.3 104.3 + - + +
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Residues in contact with TRP 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D TYR* 3.7 42.0 - + - -
79D ALA* 3.5 21.3 - - + -
252D VAL* 3.5 2.9 - - - +
253D ARG* 2.7 83.6 + - + +
254D ASP 3.8 11.2 - - - -
255D ASP* 3.9 15.5 - - + -
272D ASP 4.7 0.9 - - - -
273D LYS* 1.3 114.8 - - + +
275D THR* 1.3 65.9 + - - +
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Residues in contact with THR 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D GLU* 3.4 37.7 - - + +
251D ARG 3.4 5.2 - - - +
252D VAL* 4.1 14.7 - - + +
272D ASP* 4.9 4.7 + - - +
274D TRP* 1.3 78.8 + - - +
276D ASP* 1.3 68.4 + - - +
277D ARG* 4.1 10.4 + - + +
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Residues in contact with ASP 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ASN* 3.4 21.6 - - - +
34D MET* 3.6 4.9 - - + +
64D GLN* 4.2 0.9 + - - -
250D GLU* 3.2 6.9 - - - +
251D ARG* 2.8 70.3 + - - +
253D ARG* 2.8 45.5 + - - -
274D TRP* 4.9 0.2 - - - +
275D THR* 1.3 77.0 - - - +
277D ARG* 1.3 61.1 + - - +
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Residues in contact with ARG 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ASN* 3.2 16.6 + - - +
87D GLN* 3.5 25.9 + - - +
248D ILE* 4.3 22.2 - - + +
249D TYR 3.7 2.5 - - - -
250D GLU* 2.7 33.9 + - + +
275D THR* 4.1 9.0 + - + -
276D ASP* 1.3 75.5 - - - +
278D SER* 1.3 61.9 + - - +
279D SER* 4.2 2.1 + - - +
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Residues in contact with SER 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ASP* 2.7 29.1 + - - +
32D ASN* 4.1 0.7 - - - -
34D MET* 3.6 24.2 - - - -
36D LYS* 2.8 33.8 + - - -
247D VAL 3.6 1.4 - - - +
248D ILE* 3.3 4.7 - - - +
249D TYR 2.9 32.3 + - - -
277D ARG* 1.3 73.8 - - - +
279D SER* 1.3 59.3 + - - +
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Residues in contact with SER 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LYS* 4.0 1.1 + - - -
246D ASP* 4.8 6.8 - - - +
247D VAL 3.4 6.5 + - - -
248D ILE* 3.9 19.5 - - - +
277D ARG* 4.2 2.1 + - - -
278D SER* 1.3 75.7 + - - +
280D GLU* 1.3 75.3 + - - +
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Residues in contact with GLU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D THR* 4.0 19.0 + - - +
36D LYS* 3.3 23.8 + - - +
245D ILE 3.8 0.5 - - - +
246D ASP* 3.4 3.7 - - - -
247D VAL* 2.8 38.6 + - + +
279D SER* 1.3 81.2 + - - +
281D ARG* 1.3 66.6 + - - +
282D TYR* 3.8 35.4 - - + +
293D ASN* 3.4 27.6 + - - +
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Residues in contact with ARG 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D PRO* 3.9 13.9 - - - +
244D ASN* 3.9 35.5 + - + +
245D ILE 3.6 1.1 - - - +
246D ASP* 2.7 43.4 + - - +
280D GLU* 1.3 75.8 - - - +
282D TYR* 1.3 72.1 + - - +
283D LYS* 5.0 7.0 - - + +
293D ASN* 3.8 20.1 - - - +
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Residues in contact with TYR 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 3.8 28.0 + - + -
27D THR* 4.6 4.5 + - - -
36D LYS* 5.0 12.0 + - - +
38D VAL* 3.5 24.3 + - + +
243D THR 3.9 0.2 - - - +
244D ASN* 3.5 4.3 - - - -
245D ILE* 2.9 37.1 + - + +
247D VAL* 3.6 40.1 - - + +
280D GLU* 3.8 25.4 - - + +
281D ARG* 1.3 77.1 - - - +
283D LYS* 1.3 63.8 + - - +
291D MET* 3.6 28.0 - - + -
292D THR 3.2 8.1 - - - +
293D ASN* 3.4 33.7 + - + -
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Residues in contact with LYS 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D THR 3.8 3.4 - - - -
244D ASN* 3.7 23.1 + - - +
281D ARG* 5.0 9.0 - - + +
282D TYR* 1.3 76.7 - - - +
284D ILE* 1.3 63.0 + - - +
285D ASP 4.0 0.4 + - - -
290D GLU 3.8 1.2 - - - +
291D MET* 3.2 5.9 - - - -
292D THR* 2.8 49.0 + - - +
293D ASN* 5.7 1.8 - - - -
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Residues in contact with ILE 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 3.7 22.0 - - + -
53D LEU* 3.4 25.1 - - + -
55D ILE* 4.5 0.9 - - + -
232D ILE* 4.2 13.7 - - + -
242D GLN* 3.3 6.3 - - - +
243D THR* 2.7 57.8 + - + +
245D ILE* 3.9 25.8 - - + -
283D LYS* 1.3 75.8 - - - +
285D ASP* 1.3 60.2 + - - +
286D TRP* 3.7 28.8 + - + +
290D GLU 3.8 2.9 - - - -
291D MET* 4.2 14.4 - - + +
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Residues in contact with ASP 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 3.8 0.9 - - - -
241D GLN 3.9 5.8 - - - +
242D GLN* 4.4 16.7 - - + +
283D LYS 4.0 1.0 + - - +
284D ILE* 1.3 73.9 - - - +
286D TRP* 1.3 53.8 + - - +
287D GLU* 2.9 23.1 + - - +
288D LYS* 2.9 31.6 + - - +
289D GLU* 2.8 34.7 + - - -
290D GLU* 2.9 32.9 + - + +
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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