Contacts of the helix formed by residues 358 - 376 (chain B) in PDB entry 1ECX
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 THR 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 5.2 0.2 - - - +
264B HIS* 4.7 3.4 - - + -
268B LEU* 3.9 8.1 - - - -
356B TYR 3.6 11.2 - - - +
357B ASN* 1.3 80.8 - - - +
359B GLU* 1.3 59.4 + - - +
360B GLU* 3.3 14.5 + - - +
361B GLU* 2.8 39.4 + - - +
362B VAL* 3.0 27.7 + - - +
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Residues in contact with GLU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B HIS* 5.1 2.0 + - - +
267B LYS* 5.0 9.7 + - - +
268B LEU* 3.7 22.2 - - + +
271B LYS* 2.8 41.0 + - + +
358B THR* 1.3 71.2 - - - +
360B GLU* 1.3 60.3 + - - +
362B VAL* 3.6 3.0 - - - +
363B ASP* 2.8 34.7 + - - +
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Residues in contact with GLU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.7 22.4 - - + +
358B THR* 3.1 11.7 + - - +
359B GLU* 1.3 79.4 - - - +
361B GLU* 1.3 59.1 + - - +
363B ASP* 3.4 9.4 + - - +
364B TYR* 3.1 21.8 + - - +
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Residues in contact with GLU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.8 21.3 - - + -
2B ARG 4.0 13.7 - - - +
3B VAL* 4.3 18.7 - - + +
4B TYR 5.0 1.0 + - - -
5B PHE* 4.2 12.8 - - + -
356B TYR 4.8 2.3 - - - +
357B ASN* 2.8 33.5 + - - +
358B THR* 2.8 34.5 + - - +
360B GLU* 1.3 77.5 - - - +
362B VAL* 1.3 59.1 + - - +
364B TYR* 3.2 4.7 + - - +
365B PHE* 3.0 29.3 + - - +
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Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 4.4 11.7 - - + -
268B LEU* 3.9 32.3 - - + -
271B LYS* 4.1 20.9 - - + -
272B LEU* 3.3 32.8 - - + -
353B LEU* 5.3 0.7 - - + -
358B THR 3.0 17.8 + - - +
359B GLU* 3.2 9.4 + - - +
361B GLU* 1.3 76.1 - - - +
363B ASP* 1.3 64.3 + - - +
365B PHE* 3.5 6.3 + - - +
366B LEU* 3.0 35.6 + - + +
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Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LYS* 2.7 38.8 + - - -
359B GLU* 2.8 24.4 + - - +
360B GLU* 3.5 8.9 - - - +
362B VAL* 1.3 78.1 - - - +
364B TYR* 1.3 56.7 + - - +
366B LEU* 3.6 6.1 + - - +
367B LYS* 3.0 30.4 + - - +
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Residues in contact with TYR 364 (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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1B MET* 3.6 48.3 + - + -
3B VAL* 3.8 12.3 - - + -
314B TYR* 3.0 23.5 + - - +
316B ILE* 3.6 30.3 - - + -
360B GLU 3.1 13.5 + - - +
361B GLU 3.4 7.9 - - - +
363B ASP* 1.3 74.5 - - - +
365B PHE* 1.3 61.5 + - - +
367B LYS* 3.1 8.7 + - + +
368B LYS* 2.8 68.6 + - + +
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Residues in contact with PHE 365 (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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3B VAL* 5.2 1.8 - - + -
5B PHE* 3.7 24.7 - + + -
272B LEU* 3.9 14.8 - - + -
276B LEU* 4.0 21.3 - - + -
311B LEU* 4.1 10.3 - - + -
316B ILE* 3.4 44.8 - - + +
318B VAL* 4.0 15.9 - - + -
349B ILE* 4.9 3.1 - - + -
351B ILE* 3.3 29.8 - - + -
361B GLU 3.0 15.9 + - - +
362B VAL* 3.7 4.5 - - - +
364B TYR* 1.3 77.8 - - - +
366B LEU* 1.3 68.8 + - + +
368B LYS* 3.9 0.3 - - - +
369B ILE* 2.9 47.1 + - + +
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LYS* 3.8 29.6 - - + +
272B LEU* 4.3 8.1 - - + +
275B GLY* 3.8 32.5 - - - +
276B LEU* 3.9 21.5 - - + +
279B LEU* 4.0 8.5 - - + +
362B VAL* 3.0 32.6 + - + +
363B ASP* 3.8 6.5 - - - +
365B PHE* 1.3 78.9 - - + +
367B LYS* 1.3 64.6 + - - +
369B ILE* 3.3 5.7 - - - +
370B GLU* 3.3 24.1 + - - +
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Residues in contact with LYS 367 (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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363B ASP 3.0 17.9 + - - +
364B TYR* 3.1 8.9 + - + +
366B LEU* 1.3 78.5 - - - +
368B LYS* 1.3 83.3 + - + +
370B GLU* 3.5 9.0 + - - +
371B GLU* 3.4 27.6 + - + +
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Residues in contact with LYS 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B TYR* 3.7 32.6 - - + -
316B ILE* 4.1 14.8 - - + -
364B TYR* 2.8 66.5 + - + +
367B LYS* 1.3 84.5 - - - +
369B ILE* 1.3 65.3 + - - +
370B GLU 3.1 1.6 - - - -
371B GLU* 3.0 37.7 + - - +
372B ILE* 3.0 19.0 + - + +
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Residues in contact with ILE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 4.1 13.0 - - + -
279B LEU* 3.9 13.5 - - + -
299B PHE* 4.0 27.1 - - + -
307B LEU* 4.1 28.0 - - + -
311B LEU* 4.2 14.9 - - + +
349B ILE* 5.1 1.8 - - + -
365B PHE* 2.9 42.2 + - + +
366B LEU* 3.3 14.8 - - - +
368B LYS* 1.3 76.9 - - - +
370B GLU* 1.3 60.4 + - - +
372B ILE* 3.4 6.5 + - + +
373B LEU* 2.9 35.7 + - + +
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Residues in contact with GLU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 3.6 33.7 - - + +
366B LEU 3.3 14.9 + - - +
367B LYS* 3.6 10.1 - - - +
368B LYS 3.1 0.8 - - - -
369B ILE* 1.3 80.5 - - - +
371B GLU* 1.3 64.9 + - - +
373B LEU* 3.4 6.5 + - + +
374B SER* 3.0 23.4 + - - -
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Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B TYR* 3.5 26.6 + - - +
367B LYS* 3.4 20.7 + - + +
368B LYS* 3.0 32.9 + - - +
370B GLU* 1.3 75.9 - - + +
372B ILE* 1.3 67.5 + - - +
374B SER* 2.7 27.6 + - - -
375B PHE* 2.9 25.9 + - + -
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Residues in contact with ILE 372 (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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307B LEU* 4.4 11.9 - - + -
310B LEU* 3.5 30.3 - - + -
311B LEU* 3.6 46.9 - - + +
314B TYR* 3.6 33.9 - - + +
368B LYS 3.0 12.7 + - - +
369B ILE* 3.7 7.4 - - - +
371B GLU* 1.3 75.8 - - - +
373B LEU* 1.3 62.7 + - - +
375B PHE* 3.5 9.8 + - - +
376B LEU* 3.1 38.6 + - + +
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Residues in contact with LEU 373 (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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279B LEU* 4.1 24.7 - - + +
299B PHE* 3.5 42.0 - - + -
302B ILE* 3.4 31.4 - - + -
307B LEU* 5.1 7.4 - - + -
369B ILE* 2.9 33.3 + - + +
370B GLU* 3.7 6.1 - - + +
372B ILE* 1.3 75.0 - - + +
374B SER* 1.3 59.6 + - - +
376B LEU* 2.9 28.0 + - + +
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Residues in contact with SER 374 (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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370B GLU* 3.0 13.5 + - - -
371B GLU* 2.7 24.2 + - - +
373B LEU* 1.3 76.8 - - - +
375B PHE* 1.3 63.4 + - - +
376B LEU 2.7 16.7 - - - +
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Residues in contact with PHE 375 (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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314B TYR* 4.0 19.7 - - - -
371B GLU* 2.9 35.9 + - + +
372B ILE* 3.8 8.1 - - - +
374B SER* 1.3 85.9 + - - +
376B LEU* 1.3 62.4 + - + +
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Residues in contact with LEU 376 (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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302B ILE* 3.6 39.3 - - + -
306B THR* 5.3 5.6 - - + -
307B LEU* 5.9 1.3 - - + -
310B LEU* 4.8 15.7 - - + -
372B ILE* 3.1 34.5 + - + +
373B LEU* 2.9 14.4 + - - +
374B SER 2.7 16.6 - - - +
375B PHE* 1.3 82.9 - - + +
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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
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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