Contacts of the helix formed by residues 257 - 277 (chain B) in PDB entry 3M9M
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 ASN 257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B SER* 3.3 3.1 + - - +
256B ARG* 1.3 74.1 - - - +
258B LEU* 1.3 56.3 + - - +
259B GLU* 3.1 19.9 + - - +
260B GLU* 2.6 56.6 + - + +
261B ILE* 3.0 12.2 + - - +
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Residues in contact with LEU 258 (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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256B ARG 3.2 7.4 + - - -
257B ASN* 1.3 71.0 + - - +
259B GLU* 1.3 62.0 + - + +
261B ILE* 3.7 7.6 - - - +
262B LYS* 2.9 57.1 + - + +
316B VAL* 4.4 14.1 - - + +
319B LEU* 4.3 11.8 - - + +
320B GLN* 3.4 38.4 - - + +
323B LEU* 3.8 21.5 - - + -
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Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASN* 2.9 11.4 + - - +
258B LEU* 1.3 79.3 - - + +
260B GLU* 1.3 59.8 + - - +
261B ILE 3.2 0.2 - - - -
262B LYS* 2.8 40.4 + - - +
263B PRO* 3.1 23.2 - - - +
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Residues in contact with GLU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B MET* 4.7 2.5 - - - +
253B ARG* 2.4 40.0 + - - +
255B SER* 3.0 29.5 - - - +
257B ASN* 2.6 32.3 + - + +
259B GLU* 1.3 74.8 - - - +
261B ILE* 1.3 60.8 + - - +
263B PRO* 3.8 3.4 - - - +
264B TYR* 3.6 23.8 - - + -
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B MET* 4.0 15.7 - - - -
255B SER* 3.4 35.0 - - - +
256B ARG* 4.5 3.1 - - - +
257B ASN 3.0 22.2 + - - +
258B LEU* 3.7 7.2 - - - +
260B GLU* 1.3 79.2 - - - +
262B LYS* 1.3 65.6 + - - +
263B PRO 3.3 0.4 - - - -
264B TYR* 3.1 18.9 + - - +
265B LEU* 3.3 8.5 + - + -
319B LEU* 3.3 28.9 - - + -
323B LEU* 5.0 4.3 - - + -
330B ILE* 4.0 19.7 - - + -
333B ILE* 3.8 22.0 - - + -
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Residues in contact with LYS 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 2.9 31.3 + - + +
259B GLU* 2.8 36.3 + - - +
261B ILE* 1.3 75.4 - - - +
263B PRO* 1.3 63.4 - - + +
265B LEU* 3.3 8.8 + - + +
266B PHE* 2.9 65.5 + - + -
316B VAL* 3.8 28.9 - - + +
319B LEU* 4.9 3.5 - - + +
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Residues in contact with PRO 263 (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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259B GLU 3.1 22.7 - - - +
260B GLU* 3.8 6.5 - - - +
261B ILE 3.4 4.7 - - - -
262B LYS* 1.3 93.7 - - + +
264B TYR* 1.3 60.9 + - + +
266B PHE* 3.9 7.6 - - + +
267B ARG* 3.0 46.2 + - - +
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Residues in contact with TYR 264 (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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249B VAL* 3.6 20.3 - - + +
250B THR 4.1 4.7 - - - -
251B MET* 3.6 30.5 - - + -
252B LYS* 3.4 31.3 + - + +
260B GLU 3.6 23.8 - - - -
261B ILE 3.1 4.7 + - - +
263B PRO* 1.3 78.8 - - + +
265B LEU* 1.3 60.7 + - - +
267B ARG* 3.0 37.7 + - - +
268B ALA* 2.8 28.8 + - - +
333B ILE* 3.4 21.5 - - + -
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ILE 3.3 8.2 + - - +
262B LYS* 3.3 11.4 + - + +
264B TYR* 1.3 78.9 - - - +
266B PHE* 1.3 77.0 + - + +
268B ALA* 3.0 6.9 + - - +
269B ILE* 2.9 24.8 + - + +
286B VAL* 3.7 33.4 - - + -
315B SER* 3.3 36.6 - - - +
316B VAL* 4.6 4.7 - - + +
319B LEU* 4.5 13.2 - - + -
333B ILE* 3.9 21.8 - - + +
334B GLY 3.8 13.5 - - - +
335B VAL* 5.3 2.9 - - + -
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Residues in contact with PHE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LYS* 2.9 54.4 + - + +
263B PRO* 4.0 7.0 - - + +
265B LEU* 1.3 88.1 - - + +
267B ARG* 1.3 61.2 + - - +
269B ILE* 3.5 9.5 + - + +
270B GLU* 3.2 29.0 + - - +
312B TYR* 3.6 60.8 + + + +
315B SER* 4.3 0.4 - - - -
316B VAL* 3.8 16.6 - - + -
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Residues in contact with ARG 267 (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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249B VAL* 5.0 7.5 - - + +
263B PRO* 3.0 35.7 + - - +
264B TYR* 3.0 57.4 + - - +
266B PHE* 1.3 77.9 - - - +
268B ALA* 1.3 58.2 + - - +
270B GLU* 3.7 6.7 + - + +
271B GLU* 3.0 42.1 + - + +
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Residues in contact with ALA 268 (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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247B ARG* 3.3 33.2 - - + +
249B VAL* 3.8 15.0 - - + -
264B TYR 2.8 12.1 + - - +
265B LEU* 3.0 8.2 + - - +
267B ARG* 1.3 76.3 - - - +
269B ILE* 1.3 55.8 + - - +
271B GLU* 3.2 3.1 + - - +
272B SER* 2.7 38.1 + - - -
333B ILE 4.5 0.7 - - - +
334B GLY* 4.2 12.6 - - - -
335B VAL* 4.2 2.9 - - + +
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Residues in contact with ILE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU* 2.9 20.0 + - + +
266B PHE* 3.7 16.4 - - + +
267B ARG 3.4 0.2 - - - -
268B ALA* 1.3 75.2 - - - +
270B GLU* 1.3 67.0 + - - +
272B SER* 2.8 18.8 + - - -
273B TYR* 2.9 36.4 + - + -
284B ILE* 5.0 0.7 - - + -
308B LYS* 4.5 0.4 - - + -
311B ALA* 3.4 33.2 - - + +
312B TYR* 4.0 26.7 - - + -
315B SER* 3.4 17.7 - - - +
335B VAL* 4.1 20.9 - - + -
337B PHE* 4.5 1.6 - - + -
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Residues in contact with GLU 270 (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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266B PHE 3.2 14.1 + - - +
267B ARG* 3.7 9.0 - - + +
268B ALA 3.3 0.2 - - - -
269B ILE* 1.3 81.5 - - - +
271B GLU* 1.3 64.7 + - + +
273B TYR* 3.0 12.5 + - - +
274B TYR* 3.2 11.3 + - - +
308B LYS* 2.6 35.2 + - - +
312B TYR* 2.3 39.2 + - - +
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Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ARG* 2.8 42.0 + - + -
249B VAL* 5.3 2.5 - - - -
267B ARG* 3.0 30.0 - - + +
268B ALA* 3.2 5.1 + - - +
270B GLU* 1.3 77.2 - - + +
272B SER* 1.3 63.0 + - - +
274B TYR* 3.2 19.3 + - - +
275B LYS* 3.3 21.3 + - - +
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 4.3 2.6 - - - +
246B GLY* 4.7 4.5 - - - -
247B ARG* 3.5 19.0 + - - +
268B ALA 2.7 20.4 + - - -
269B ILE 2.8 11.6 + - - -
271B GLU* 1.3 77.6 - - - +
273B TYR* 1.3 55.6 + - - +
275B LYS* 3.4 10.3 + - - +
276B LEU* 3.2 29.8 + - - +
335B VAL* 3.1 16.3 - - - +
337B PHE* 3.4 26.5 - - - -
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Residues in contact with TYR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ILE* 2.9 18.0 + - + +
270B GLU 3.0 8.0 + - - +
272B SER* 1.3 74.1 - - - +
274B TYR* 1.3 66.1 + - - +
275B LYS 3.2 0.4 - - - -
276B LEU* 3.9 23.7 - - + +
277B ASP* 3.5 15.4 + - - -
279B ARG 5.6 1.3 - - - -
281B PRO* 4.3 4.1 - - + +
306B ILE* 2.4 47.1 + - - +
307B SER* 5.0 0.7 - - - -
308B LYS* 3.6 46.7 + - + +
311B ALA* 3.8 8.5 - - + -
337B PHE* 3.6 28.5 - + - -
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Residues in contact with TYR 274 (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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270B GLU 3.2 10.7 + - - +
271B GLU* 3.2 15.7 + - - +
273B TYR* 1.3 77.9 - - - +
275B LYS* 1.3 69.4 + - + +
277B ASP* 3.7 12.1 + - - +
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Residues in contact with LYS 275 (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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245B ILE* 3.7 22.9 - - + -
246B GLY 3.3 21.6 + - - +
247B ARG* 4.3 14.3 - - - +
271B GLU* 3.3 16.3 + - - +
272B SER* 3.5 9.0 - - - +
273B TYR 3.2 0.2 - - - -
274B TYR* 1.3 80.0 - - + +
276B LEU* 1.3 69.1 + - - +
277B ASP* 2.8 11.1 + - - +
279B ARG* 3.5 10.5 + - - -
6T T 3.7 23.2 + - - -
7T T 4.7 9.3 + - - +
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 4.0 10.5 - - + +
272B SER 3.2 15.9 + - - +
273B TYR* 3.9 33.2 - - + +
275B LYS* 1.3 76.6 - - - +
277B ASP* 1.3 70.6 + - - +
279B ARG* 3.0 47.9 + - + +
281B PRO* 3.9 26.2 - - + -
337B PHE* 4.1 20.6 - - + -
340B PHE* 3.4 37.7 - - + -
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Residues in contact with ASP 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B TYR 3.5 8.9 + - - -
274B TYR 3.7 11.0 - - - +
275B LYS 2.8 13.3 + - - +
276B LEU* 1.3 83.1 - - - +
278B LYS* 1.3 84.9 + - - +
279B ARG* 3.1 4.5 + - - +
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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