Contacts of the helix formed by residues 264 - 279 (chain B) in PDB entry 1M7X
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 SER 264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B TRP 3.9 1.0 + - - -
263B LEU* 1.3 74.2 - - - +
265B TYR* 1.3 53.4 + - - +
266B ARG* 3.4 12.5 + - - +
267B GLU* 2.9 38.5 + - - +
268B LEU* 2.7 33.8 + - - +
312B PHE* 3.1 20.2 - - - +
317B ASP* 6.0 0.2 - - - -
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Residues in contact with TYR 265 (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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250B LEU* 4.0 19.3 - - + -
264B SER* 1.3 70.8 - - - +
266B ARG* 1.3 58.2 + - - +
268B LEU* 3.4 5.1 + - + -
269B ALA* 2.8 30.7 + - - +
289B ILE* 4.7 3.9 + - + +
308B PRO* 4.0 5.9 - - + +
309B THR* 2.6 42.4 + - - +
312B PHE* 2.8 42.7 + + + +
313B GLY 3.6 17.0 - - - -
314B THR 3.7 7.2 - - - -
317B ASP* 3.3 27.6 - - + +
318B PHE* 3.4 50.3 - + + -
320B TYR* 5.2 0.2 - - - -
321B PHE* 3.7 12.3 - + + +
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Residues in contact with ARG 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B SER* 3.1 10.3 - - - +
265B TYR* 1.3 76.8 - - - +
267B GLU* 1.3 64.0 + - + +
269B ALA* 3.2 5.2 + - - +
270B ASP* 3.1 30.0 + - - +
316B ASP* 3.9 10.5 + - - +
317B ASP* 3.3 36.5 + - - +
320B TYR* 3.3 63.3 - - + +
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Residues in contact with GLU 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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256B HIS* 2.9 37.1 + - - -
263B LEU* 3.3 13.8 - - + -
264B SER* 2.9 39.4 + - - +
266B ARG* 1.3 78.7 - - + +
268B LEU* 1.3 58.4 + - - +
270B ASP* 2.9 22.8 + - - +
271B GLN* 2.9 25.7 + - - +
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Residues in contact with LEU 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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250B LEU* 3.9 47.1 - - + +
253B TRP* 4.0 28.3 - - + -
254B ARG 5.5 0.4 - - - +
263B LEU* 3.7 31.9 - - + +
264B SER 2.7 25.5 + - - +
265B TYR* 3.7 7.4 - - - +
267B GLU* 1.3 72.5 - - - +
269B ALA* 1.3 58.7 + - - +
272B LEU* 2.8 44.5 + - + +
273B VAL 3.3 2.6 + - - -
312B PHE* 4.6 4.7 - - + -
321B PHE* 3.7 17.4 - - + -
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B TYR 2.8 18.4 + - - +
266B ARG 3.4 6.5 - - - +
267B GLU 3.1 0.2 - - - -
268B LEU* 1.3 76.9 - - - +
270B ASP* 1.3 62.1 + - - +
271B GLN 3.5 0.2 - - - -
273B VAL* 3.6 12.2 - - - +
274B PRO* 3.5 16.0 - - - +
320B TYR* 4.0 16.2 - - + -
321B PHE* 3.6 15.9 - - + -
324B ALA* 3.6 28.2 - - + +
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Residues in contact with ASP 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A GLU* 5.5 2.8 - - - +
266B ARG* 3.1 16.7 + - - +
267B GLU* 2.9 10.6 + - - +
269B ALA* 1.3 84.0 - - - +
271B GLN* 1.3 64.2 + - + +
274B PRO* 3.3 18.1 - - - +
320B TYR* 4.4 14.8 + - - -
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Residues in contact with GLN 271 (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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727A ALA* 3.4 36.1 - - + +
728A GLU* 4.7 6.5 + - - +
253B TRP* 3.9 12.9 - - + -
254B ARG* 3.7 18.6 + - - +
256B HIS* 5.4 0.2 + - - -
263B LEU* 3.6 28.1 - - + +
267B GLU* 2.9 25.0 + - - +
270B ASP* 1.3 87.6 - - + +
272B LEU* 1.3 61.1 + - - +
274B PRO* 3.5 3.4 - - - +
275B TYR* 3.1 30.1 + - - +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 4.1 18.2 - - + -
248B VAL* 4.0 15.3 - - + -
250B LEU* 3.6 30.7 - - + -
253B TRP* 3.5 44.8 - - + +
268B LEU* 2.8 30.1 + - + +
271B GLN* 1.3 72.4 - - - +
273B VAL* 1.3 58.7 + - - +
275B TYR* 3.1 2.6 + - + +
276B ALA* 2.9 27.9 + - - +
284B LEU* 4.4 15.9 - - + -
321B PHE* 3.8 15.9 - - + -
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Residues in contact with VAL 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LEU 3.3 1.2 + - - -
269B ALA* 3.6 16.2 - - - +
272B LEU* 1.3 75.9 - - - +
274B PRO* 1.3 71.0 - - + +
276B ALA* 3.5 0.6 + - - -
277B LYS* 3.0 26.3 + - - +
284B LEU* 4.5 4.3 - - + -
321B PHE* 4.0 26.0 - - + +
324B ALA 3.8 4.5 - - - +
325B ALA* 3.7 32.5 - - + +
328B ALA* 3.1 33.9 - - + -
330B LEU* 3.8 10.5 - - + +
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Residues in contact with PRO 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A HIS* 3.3 24.8 - - + +
269B ALA 3.5 11.7 - - - +
270B ASP* 3.3 20.0 - - - +
271B GLN* 3.5 14.6 - - - +
273B VAL* 1.3 97.9 - - + +
275B TYR* 1.3 55.0 + - - +
277B LYS* 3.7 6.7 - - + +
278B TRP* 2.9 24.9 + - - +
328B ALA* 5.7 0.2 - - + -
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Residues in contact with TYR 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 3.7 19.1 - + - -
253B TRP* 3.7 20.6 - + + -
254B ARG* 4.7 6.3 - - - +
271B GLN 3.1 21.3 + - - +
272B LEU 3.1 3.8 + - - +
274B PRO* 1.3 77.5 - - - +
276B ALA* 1.3 59.1 + - - +
278B TRP* 3.1 9.7 + + + +
279B MET* 2.9 53.6 + - + +
571B GLU* 2.6 37.6 + - - +
586B TRP* 3.6 17.2 - + - -
600B GLN* 2.9 32.2 + - - -
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 4.1 11.4 - - + -
272B LEU* 2.9 18.9 + - + +
275B TYR* 1.3 78.3 - - - +
277B LYS* 1.3 62.1 + - - +
279B MET 3.5 0.2 + - - -
280B GLY 3.4 3.8 + - - -
281B PHE* 3.1 43.9 + - + +
283B HIS 5.6 0.2 - - - +
284B LEU* 4.1 21.5 - - + -
330B LEU* 4.0 17.9 - - + -
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Residues in contact with LYS 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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612A HIS* 3.8 44.5 + - + +
614A LYS* 5.4 5.9 - - - +
273B VAL 3.0 19.9 + - - +
274B PRO* 3.7 5.4 - - + +
276B ALA* 1.3 76.6 - - - +
278B TRP* 1.3 63.8 + - - +
280B GLY* 3.2 12.3 + - - -
281B PHE 4.6 1.8 - - - +
328B ALA* 3.2 38.3 - - + +
330B LEU* 4.1 17.0 - - + +
608B LEU* 5.8 0.7 - - - +
611B ARG* 5.2 2.1 + - - -
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Residues in contact with TRP 278 (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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605A ASP* 5.3 0.4 - - - -
608A LEU* 3.3 28.5 - - + -
609A THR* 4.0 24.7 - - + -
612A HIS* 3.6 35.6 - + + +
613A HIS* 5.7 1.1 - + - -
678A ILE 5.8 3.1 - - - -
274B PRO 2.9 19.6 + - - +
275B TYR* 3.1 9.6 + + - +
277B LYS* 1.3 71.6 - - - +
279B MET* 1.3 68.0 + - + +
280B GLY* 2.9 10.9 + - - -
604B ARG* 2.9 74.7 + - - +
608B LEU* 5.0 2.1 - - - +
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Residues in contact with MET 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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275B TYR* 2.9 46.5 + - + +
276B ALA 3.7 0.4 - - - +
277B LYS 3.3 0.2 - - - -
278B TRP* 1.3 81.1 - - + +
280B GLY* 1.3 53.9 + - - +
281B PHE* 3.4 22.2 - - + -
571B GLU* 4.0 15.3 - - + -
600B GLN* 3.4 47.1 - - + +
603B VAL* 3.9 23.1 - - + -
604B ARG* 3.3 31.2 + - - +
607B ASN* 2.7 25.1 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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