Contacts of the helix formed by residues 379 - 396 (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 ARG 379 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C TRP* 3.8 12.7 - - - -
145C PRO* 5.6 1.2 - - - +
146C ASN* 5.2 4.0 + - - -
354C THR* 5.6 0.8 + - - -
355C ASN 3.2 26.3 + - - -
356C LEU* 3.6 27.2 + - - +
376C ASN* 3.3 28.7 - - - +
377C TYR 3.0 3.8 + - - -
378C GLY* 1.3 77.5 - - - +
380C ARG* 1.3 59.6 + - - +
381C GLU* 2.8 25.6 + - - +
382C VAL* 3.0 20.8 + - + -
383C SER* 3.0 24.9 + - - -
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Residues in contact with ARG 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C HIS 6.0 2.3 - - - +
379C ARG* 1.3 72.8 - - - +
381C GLU* 1.3 71.7 + - + +
383C SER* 4.8 3.0 + - - -
384C ASN* 2.5 51.4 + - - +
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Residues in contact with GLU 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C TRP* 3.1 62.8 + - + +
206C TYR* 5.0 0.7 + - - -
357C TYR* 5.2 0.8 - - - -
379C ARG* 2.8 18.1 + - - +
380C ARG* 1.3 87.4 - - + +
382C VAL* 1.3 54.5 + - - +
383C SER 3.2 1.6 - - - -
384C ASN* 3.7 6.1 - - - +
385C PHE* 2.7 35.6 + - - +
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Residues in contact with VAL 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C TRP* 4.9 1.8 - - + -
356C LEU 3.5 24.5 - - - +
357C TYR* 4.1 19.7 - - + +
375C TYR* 3.2 45.5 - - + +
376C ASN 3.7 13.0 - - - +
377C TYR* 4.6 1.6 - - - -
379C ARG* 3.0 25.7 + - + +
381C GLU* 1.3 75.6 - - - +
383C SER* 1.3 58.3 + - - +
385C PHE* 3.4 5.6 - - - +
386C LEU* 3.1 36.5 + - + +
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Residues in contact with SER 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C TYR 3.6 15.4 + - - -
379C ARG 3.0 16.6 + - - -
380C ARG* 4.7 2.0 + - - -
382C VAL* 1.3 75.7 - - - +
384C ASN* 1.3 64.1 + - - +
385C PHE 3.1 1.1 - - - -
386C LEU 3.1 0.7 + - - -
387C VAL* 2.5 53.1 + - - +
438C PHE* 4.1 16.5 - - - -
441C ASN* 6.0 1.0 - - - +
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Residues in contact with ASN 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C HIS 3.1 43.5 + - - +
119C LEU* 5.3 1.1 - - - +
121C PRO* 3.4 19.3 - - + +
380C ARG* 2.5 46.1 + - - +
381C GLU* 3.4 8.3 + - + +
383C SER* 1.3 80.7 + - - +
385C PHE* 1.3 58.4 + - - +
387C VAL* 4.8 2.7 - - - -
388C GLY* 2.9 28.8 + - - +
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Residues in contact with PHE 385 (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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205C PRO* 4.1 26.9 - - + -
206C TYR* 3.6 31.4 + + - +
305C LEU* 4.1 27.1 - - + -
306C TYR* 3.4 23.1 + + - -
348C LEU* 4.2 14.1 - - + -
357C TYR* 4.0 18.6 - + + -
375C TYR* 3.6 30.7 - + - -
381C GLU 2.7 20.6 + - - +
382C VAL* 3.4 8.1 - - - +
384C ASN* 1.3 77.8 - - - +
386C LEU* 1.3 73.8 + - + +
389C ASN* 3.3 21.7 + - + +
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Residues in contact with LEU 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LEU* 5.3 4.5 - - + -
336C TRP* 2.7 31.1 - - + +
337C VAL 5.4 0.7 - - - +
338C PRO* 4.2 14.4 - - + -
375C TYR* 3.5 42.8 - - + +
377C TYR* 3.3 24.5 - - + -
382C VAL* 3.1 16.5 + - + +
383C SER 3.1 1.4 + - - -
385C PHE* 1.3 86.5 - - + +
387C VAL* 1.3 63.0 + - - +
388C GLY 3.0 1.3 - - - -
389C ASN* 2.8 13.7 + - + +
438C PHE* 3.3 33.2 - - + -
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Residues in contact with VAL 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 5.1 5.6 - - + +
336C TRP* 4.3 7.2 - - - -
383C SER* 2.5 37.7 + - - +
384C ASN* 4.7 2.5 - - - +
386C LEU* 1.3 72.2 - - - +
388C GLY* 1.3 59.3 + - - +
390C ALA* 3.3 8.0 + - - +
391C LEU* 3.0 38.1 + - + +
438C PHE* 4.1 5.6 - - + -
441C ASN* 5.8 2.0 - - + -
442C THR* 3.7 27.6 - - - +
445C ILE* 3.8 35.9 - - + -
446C LEU* 4.3 7.4 - - + -
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Residues in contact with GLY 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU 3.5 18.6 + - - -
121C PRO* 4.3 4.0 - - - -
122C TYR* 3.1 26.9 - - - -
306C TYR* 3.2 8.5 - - - -
384C ASN 2.9 22.1 + - - -
387C VAL* 1.3 77.3 - - - +
389C ASN* 1.3 63.7 + - - +
391C LEU* 3.5 1.9 + - - -
392C TYR 3.1 6.6 + - - -
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Residues in contact with ASN 389 (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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290C ASN* 6.0 0.2 - - - -
305C LEU* 3.2 40.1 + - + +
306C TYR* 3.1 36.4 + - + +
336C TRP* 2.7 25.2 + - + +
385C PHE* 3.3 12.6 + - + +
386C LEU* 2.8 18.4 + - + +
388C GLY* 1.3 77.5 - - - +
390C ALA* 1.3 58.6 + - - +
392C TYR* 3.2 10.2 - - - +
393C TRP* 3.1 36.4 + - - +
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Residues in contact with ALA 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C TRP* 3.5 24.6 - - + +
386C LEU 3.2 1.8 + - - -
387C VAL 3.5 9.9 - - - +
388C GLY 3.1 0.6 - - - -
389C ASN* 1.3 75.3 - - - +
391C LEU* 1.3 65.2 + - - +
392C TYR 3.0 2.3 + - - -
393C TRP* 3.3 5.7 + - - +
394C ILE* 3.3 26.8 + - - +
402C LEU* 3.5 27.7 - - + +
446C LEU* 4.1 16.4 - - + -
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Residues in contact with LEU 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 4.4 10.1 - - + +
120C ARG* 3.4 45.3 - - + +
122C TYR* 3.7 11.8 + - + +
387C VAL* 3.0 35.4 + - + +
388C GLY* 3.5 5.1 + - - +
390C ALA* 1.3 78.0 - - - +
392C TYR* 1.3 56.9 + - - +
394C ILE* 3.9 5.4 - - - -
395C GLU* 2.8 46.9 + - - +
445C ILE* 4.4 4.7 - - + -
446C LEU* 3.6 24.0 - - + -
449C GLN* 4.2 12.3 - - + -
450C VAL* 4.7 10.1 - - + -
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Residues in contact with TYR 392 (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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122C TYR* 3.7 26.4 - + + -
208C PHE* 3.5 32.2 + + - +
223C LEU* 5.1 1.6 - - + -
224C PRO* 4.9 5.5 - - + +
306C TYR* 2.7 53.9 + + + -
308C PRO* 4.7 0.3 - - - +
315C ARG* 5.9 0.2 + - - -
388C GLY 3.1 14.1 + - - +
389C ASN* 3.2 10.8 - - - +
390C ALA 3.0 0.2 - - - -
391C LEU* 1.3 76.1 - - - +
393C TRP* 1.3 111.6 + + - +
394C ILE 3.0 0.3 + - - -
396C ARG* 2.8 44.7 + - + +
397C PHE* 3.5 20.7 - + - -
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Residues in contact with TRP 393 (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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289C ILE* 3.8 14.4 - - + -
290C ASN* 4.1 12.4 - - + -
305C LEU 3.1 29.3 + - - -
307C ALA 4.3 0.9 - - - -
308C PRO* 3.7 25.4 - - + -
318C PHE* 3.7 20.2 - + - -
334C LEU* 3.5 32.5 - - + +
336C TRP* 4.2 11.0 - + - -
389C ASN* 3.1 35.9 + - - +
390C ALA* 3.3 5.8 + - - +
392C TYR* 1.3 94.3 - + - +
394C ILE* 1.3 57.3 + - - +
397C PHE* 3.2 42.8 - + + +
398C GLY 3.1 19.2 + - - -
399C ILE* 3.2 20.5 + - + +
402C LEU* 4.7 0.9 - - + -
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Residues in contact with ILE 394 (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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227C VAL 4.5 2.9 - - - +
229C GLN* 5.2 6.1 - - + +
390C ALA 3.3 13.0 + - - +
391C LEU* 4.1 4.3 - - - +
392C TYR 3.0 1.0 + - - -
393C TRP* 1.3 76.0 - - - +
395C GLU* 1.3 63.2 + - + +
398C GLY* 2.8 26.5 - - - -
399C ILE* 3.6 34.3 - - + +
401C ALA* 5.3 3.6 - - - +
402C LEU* 3.9 24.9 - - + +
446C LEU* 4.8 4.7 - - + -
450C VAL* 4.1 31.2 - - + -
453C ALA* 3.9 29.4 - - + +
454C VAL 5.9 0.4 - - - +
455C THR* 6.2 0.4 - - + -
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Residues in contact with GLU 395 (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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120C ARG* 2.9 38.7 + - - -
122C TYR* 3.9 7.2 + - - +
226C LYS* 2.9 36.9 + - + +
227C VAL* 2.5 41.3 + - - +
391C LEU* 2.8 28.4 + - - +
394C ILE* 1.3 75.9 - - + +
396C ARG* 1.3 55.7 + - + +
449C GLN 4.4 1.9 - - - +
450C VAL* 3.6 28.7 - - + +
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Residues in contact with ARG 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C TYR* 3.7 23.5 + - + +
123C GLU* 2.5 40.4 + - - +
223C LEU* 3.4 26.1 + - + +
224C PRO* 3.2 48.8 + - + +
225C GLU* 4.8 2.2 + - - +
226C LYS* 3.5 39.4 + - - +
227C VAL* 4.4 0.4 - - - -
319C ARG* 2.9 26.9 + - - -
392C TYR* 2.8 31.6 + - + +
395C GLU* 1.3 73.6 - - - +
397C PHE* 1.3 58.8 + - + +
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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