Contacts of the helix formed by residues 264 - 279 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262C TRP 3.9 0.8 + - - -
263C LEU* 1.3 75.7 - - - +
265C TYR* 1.3 66.7 + - - +
266C ARG* 3.6 7.3 + - - +
267C GLU* 2.5 48.1 + - - +
268C LEU* 3.0 14.4 + - - +
312C PHE* 3.4 22.0 - - - +
317C ASP* 5.4 2.5 - - - -
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Residues in contact with TYR 265 (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 LEU* 3.6 25.8 - - + -
264C SER* 1.3 75.3 - - - +
266C ARG* 1.3 58.4 + - - +
268C LEU* 4.4 3.8 - - + -
269C ALA* 3.3 21.1 + - - +
289C ILE* 4.4 5.2 + - - +
308C PRO* 4.2 5.4 - - + +
309C THR* 2.8 47.3 + - - +
312C PHE* 3.1 38.4 + + + +
313C GLY* 3.6 12.6 - - - -
314C THR 3.9 4.5 - - - -
317C ASP* 3.4 37.0 - - + +
318C PHE* 3.5 40.0 - + + -
321C PHE* 3.5 20.8 - + + +
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Residues in contact with ARG 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C SER* 3.1 7.6 + - - +
265C TYR* 1.3 77.6 - - - +
267C GLU* 1.3 60.9 + - + +
268C LEU 3.4 0.4 - - - -
269C ALA* 4.1 3.0 - - - +
270C ASP* 3.6 23.9 + - - +
316C ASP* 4.2 17.6 + - - +
317C ASP* 3.8 35.7 + - + +
320C TYR* 3.8 55.2 - - + +
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Residues in contact with GLU 267 (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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256C HIS* 2.8 38.4 + - - -
262C TRP 3.9 1.2 - - - +
263C LEU* 3.1 8.2 - - + -
264C SER* 2.5 48.8 + - - +
266C ARG* 1.3 79.0 - - - +
268C LEU* 1.3 62.0 + - - +
269C ALA 3.4 0.4 - - - -
270C ASP* 3.6 5.8 + - - +
271C GLN* 3.2 40.5 + - - +
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C LEU* 3.6 50.9 - - + +
253C TRP* 4.2 12.1 - - + -
254C ARG 5.6 0.2 - - - +
263C LEU* 4.1 33.7 - - + +
264C SER 3.0 22.0 + - - +
265C TYR* 4.4 5.6 - - + -
267C GLU* 1.3 76.6 - - - +
269C ALA* 1.3 58.4 + - - +
270C ASP 3.0 5.2 - - - -
271C GLN* 4.7 0.2 - - - -
272C LEU* 2.6 51.5 + - + +
273C VAL 3.1 3.5 + - - -
312C PHE* 5.1 2.2 - - + -
321C PHE* 3.4 19.7 - - + -
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Residues in contact with ALA 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C TYR 3.3 16.0 + - - +
266C ARG 4.4 2.2 - - - +
267C GLU 3.4 0.4 - - - -
268C LEU* 1.3 78.9 - - - +
270C ASP* 1.3 62.8 + - - +
273C VAL* 3.5 17.6 - - - +
274C PRO* 3.3 16.6 - - - +
320C TYR* 4.1 19.5 - - + -
321C PHE* 3.7 8.3 - - + -
324C ALA* 3.6 26.6 - - + +
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Residues in contact with ASP 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ARG 3.6 17.0 - - - +
267C GLU* 3.6 9.0 + - - +
268C LEU 3.0 0.6 - - - -
269C ALA* 1.3 87.9 - - - +
271C GLN* 1.3 63.8 + - + +
274C PRO* 3.3 20.0 - - - +
320C TYR* 4.9 8.0 + - - -
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Residues in contact with GLN 271 (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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253C TRP* 3.5 9.8 - - + -
254C ARG* 2.6 45.3 + - - +
256C HIS* 4.7 4.8 + - - -
263C LEU* 3.3 28.5 - - + +
267C GLU* 3.2 25.0 + - - +
270C ASP* 1.3 86.2 - - + +
272C LEU* 1.3 65.3 + - - +
273C VAL 3.6 0.2 - - - -
274C PRO* 3.9 2.0 - - - +
275C TYR* 3.2 25.3 + - - +
727D ALA* 3.6 33.1 - - + +
728D GLU* 4.8 2.8 + - - +
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C TYR* 3.9 27.8 - - + -
248C VAL* 4.2 15.7 - - + -
250C LEU* 3.6 22.2 - - + -
253C TRP* 3.6 32.0 - - + -
268C LEU* 2.6 26.8 + - + +
271C GLN* 1.3 73.3 - - - +
273C VAL* 1.3 59.8 + - - +
275C TYR* 3.4 2.4 + - - +
276C ALA* 2.8 30.5 + - - +
284C LEU* 4.4 11.7 - - + -
321C PHE* 3.3 30.7 - - + -
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Residues in contact with VAL 273 (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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268C LEU 3.1 1.9 + - - +
269C ALA* 3.5 24.9 - - - +
272C LEU* 1.3 78.0 - - - +
274C PRO* 1.4 62.7 - - + +
276C ALA* 3.0 8.8 + - - +
277C LYS* 2.8 32.7 + - - +
284C LEU* 4.8 4.9 - - + -
321C PHE* 4.2 16.2 - - + +
324C ALA* 3.5 9.9 - - + +
325C ALA* 3.9 25.4 - - + +
328C ALA* 3.3 32.8 - - + -
330C LEU* 3.8 8.3 - - + +
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Residues in contact with PRO 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ALA 3.3 12.6 - - - +
270C ASP* 3.3 29.6 - - - +
271C GLN 3.9 1.3 - - - +
272C LEU 3.8 0.4 - - - -
273C VAL* 1.4 101.5 - - + +
275C TYR* 1.3 57.1 + - - +
277C LYS* 3.8 4.9 - - + +
278C TRP* 3.0 23.9 + - - +
328C ALA* 5.7 0.9 - - + -
612D HIS* 3.4 29.1 + - + +
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Residues in contact with TYR 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C TYR* 3.6 27.8 - + - -
253C TRP* 3.5 22.9 - + + -
254C ARG* 5.1 4.5 - - - +
271C GLN 3.2 19.5 + - - +
272C LEU 3.4 2.2 + - - +
273C VAL 3.2 0.4 - - - -
274C PRO* 1.3 75.3 - - - +
276C ALA* 1.3 71.8 + - - +
278C TRP* 3.4 8.5 + + - +
279C MET* 3.1 52.3 + - + +
281C PHE* 5.9 1.1 - + - -
571C GLU* 2.9 32.6 + - - +
586C TRP* 3.9 17.9 - + - -
600C GLN* 3.3 24.4 + - - -
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Residues in contact with ALA 276 (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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246C TYR* 4.5 9.6 - - + -
272C LEU 2.8 14.3 + - - +
273C VAL* 3.2 9.4 - - - +
275C TYR* 1.3 84.9 - - - +
277C LYS* 1.3 64.2 + - - +
279C MET* 3.1 15.4 + - - +
281C PHE* 3.5 21.6 + - + +
283C HIS 5.9 0.2 - - - +
284C LEU* 4.2 20.4 - - + -
330C LEU* 3.8 18.6 - - + -
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Residues in contact with LYS 277 (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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273C VAL 2.8 18.1 + - - +
274C PRO* 3.8 6.3 - - + +
276C ALA* 1.3 73.7 - - - +
278C TRP* 1.3 64.1 + - - +
280C GLY* 3.0 15.9 + - - -
281C PHE 4.4 2.7 + - - +
328C ALA* 3.4 40.2 - - + +
329C GLY 5.4 0.7 - - - +
330C LEU* 4.1 13.2 - - + +
608C LEU* 6.0 0.2 - - - +
611C ARG* 5.2 0.7 + - - -
612D HIS* 3.0 51.3 + - - +
614D LYS* 6.0 2.2 - - - +
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Residues in contact with TRP 278 (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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274C PRO 3.0 19.8 + - - +
275C TYR* 3.7 9.6 - + - +
276C ALA 3.4 0.2 - - - -
277C LYS* 1.3 77.0 - - - +
279C MET* 1.3 69.4 - - + +
280C GLY 3.2 1.3 + - - -
604C ARG* 2.8 70.7 + - - +
608C LEU* 5.2 2.1 - - - +
605D ASP* 5.1 1.6 - - - -
608D LEU* 3.4 34.5 - - + -
609D THR* 3.9 26.0 - - + -
612D HIS* 3.9 32.2 - + + +
613D HIS* 5.5 2.2 - + - -
678D ILE 5.9 1.8 - - - -
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Residues in contact with MET 279 (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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275C TYR* 3.1 53.9 + - + +
276C ALA 3.1 7.0 + - - +
278C TRP* 1.3 88.3 - - + +
280C GLY* 1.3 58.5 + - - +
281C PHE* 3.5 15.5 - - + -
571C GLU* 4.3 11.4 - - + -
600C GLN* 3.1 42.4 - - + +
603C VAL* 4.3 7.9 - - + -
604C ARG* 3.3 34.2 - - - +
607C ASN* 2.8 23.2 + - - -
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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