Contacts of the helix formed by residues 379 - 397 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D TRP* 3.0 35.1 - - - -
145D PRO* 4.9 3.6 - - - +
146D ASN* 5.4 3.2 - - - +
355D ASN 4.2 10.5 + - - -
356D LEU* 3.5 28.8 + - - +
376D ASN* 2.8 30.4 + - - +
377D TYR 3.0 1.8 - - - -
378D GLY* 1.3 76.1 - - - +
380D ARG* 1.3 56.2 + - - +
381D GLU* 3.3 16.4 + - - +
382D VAL* 3.0 21.4 + - + +
383D SER* 2.7 36.0 + - - -
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Residues in contact with ARG 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D HIS* 3.0 56.2 + - + +
119D LEU* 5.2 8.5 - - - +
378D GLY 3.7 3.8 + - - -
379D ARG* 1.3 71.5 - - - +
381D GLU* 1.3 64.8 + - - +
383D SER* 3.6 10.4 + - - -
384D ASN* 2.7 56.6 + - - +
445D ILE* 5.8 5.9 - - - +
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Residues in contact with GLU 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D HIS* 6.0 1.8 - - + -
143D TRP* 3.5 54.1 + - + +
172D SER 5.4 2.1 - - - +
206D TYR* 4.9 1.4 + - - -
357D TYR* 5.2 0.5 - - - -
379D ARG* 3.3 25.4 + - - +
380D ARG* 1.3 82.6 + - + +
382D VAL* 1.3 60.4 + - - +
384D ASN* 3.6 12.5 - - - +
385D PHE* 2.9 29.1 + - - +
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Residues in contact with VAL 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D TRP* 4.6 4.5 - - + -
356D LEU 3.6 13.0 - - - +
357D TYR* 3.7 20.6 - - + +
375D TYR* 3.7 32.3 - - + -
376D ASN* 3.2 24.2 - - + +
377D TYR* 4.5 1.8 - - - +
379D ARG* 3.0 34.3 + - + +
381D GLU* 1.3 75.8 - - - +
383D SER* 1.3 58.3 + - - +
385D PHE* 3.1 8.3 - - - +
386D LEU* 3.0 31.7 + - + +
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Residues in contact with SER 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D TYR 3.8 15.0 + - - -
379D ARG 2.7 16.2 + - - -
380D ARG* 3.6 13.9 + - - -
382D VAL* 1.3 75.1 - - - +
384D ASN* 1.3 66.8 + - - +
386D LEU* 3.2 0.7 + - - +
387D VAL* 2.8 35.8 + - - +
438D PHE* 3.7 25.0 - - - -
441D ASN* 5.7 3.6 - - - +
445D ILE* 6.0 0.7 - - - +
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Residues in contact with ASN 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D HIS* 2.6 55.1 + - - +
119D LEU 4.5 0.2 - - - +
121D PRO* 3.5 20.5 - - + +
380D ARG* 2.7 61.9 + - - +
381D GLU* 3.6 10.9 - - - +
383D SER* 1.3 71.9 - - - +
385D PHE* 1.3 54.7 + - - +
387D VAL* 4.6 3.6 - - - -
388D GLY* 2.6 35.0 + - - -
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Residues in contact with PHE 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D PRO* 3.6 26.9 - - + -
206D TYR* 3.5 36.5 + + - +
305D LEU* 4.3 17.5 - - + -
306D TYR* 2.6 48.7 + + - -
348D LEU* 4.0 26.0 - - + -
357D TYR* 4.0 19.5 - + + +
375D TYR* 4.0 8.5 - + - -
381D GLU 2.9 16.0 + - - +
382D VAL* 3.1 12.1 - - - +
384D ASN* 1.3 77.4 - - - +
386D LEU* 1.3 79.1 + - + +
389D ASN* 2.9 12.0 + - + +
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Residues in contact with LEU 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D LEU* 5.3 6.5 - - + -
336D TRP* 2.9 26.9 - - + +
338D PRO* 4.2 15.0 - - + +
375D TYR* 3.6 43.3 - - + +
377D TYR* 3.6 34.1 - - + -
382D VAL* 3.0 20.9 + - + +
385D PHE* 1.3 84.4 - - + +
387D VAL* 1.3 65.3 + - - +
389D ASN* 3.0 14.3 + - + +
390D ALA 3.1 0.2 + - - -
438D PHE* 3.4 24.0 - - + -
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Residues in contact with VAL 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D HIS 5.9 0.4 - - - +
119D LEU* 4.9 6.3 - - + +
336D TRP* 4.7 3.4 - - - -
383D SER* 2.8 30.6 + - - +
384D ASN* 4.1 3.8 - - - +
386D LEU* 1.3 72.2 - - - +
388D GLY* 1.3 62.1 + - - +
390D ALA* 2.9 17.4 + - + +
391D LEU* 3.0 34.4 + - + +
438D PHE* 3.9 8.5 - - + -
441D ASN* 5.8 1.3 - - + -
442D THR* 3.7 29.4 - - + +
445D ILE* 3.8 38.6 - - + -
446D LEU* 5.2 0.4 - - + -
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Residues in contact with GLY 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D LEU 3.5 18.8 + - - -
121D PRO* 4.1 1.1 - - - -
122D TYR* 3.1 16.4 - - - -
306D TYR* 3.2 9.4 - - - -
384D ASN 2.6 23.9 + - - -
387D VAL* 1.3 69.4 - - - +
389D ASN* 1.3 66.0 + - - +
391D LEU* 3.1 1.9 + - - -
392D TYR* 2.7 21.7 + - - +
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Residues in contact with ASN 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ASN* 5.4 0.3 + - - -
305D LEU* 3.1 47.2 + - + +
306D TYR* 2.8 31.3 + - + -
336D TRP* 2.8 26.9 + - - +
385D PHE* 2.9 9.9 + - + +
386D LEU* 3.2 15.3 - - + +
388D GLY* 1.3 75.9 - - - +
390D ALA* 1.3 63.6 + - - +
392D TYR* 3.0 17.4 - - - +
393D TRP* 3.2 27.0 + - - +
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Residues in contact with ALA 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D TRP* 3.7 24.4 - - + +
386D LEU 3.1 4.4 + - - -
387D VAL* 2.9 15.5 + - - +
389D ASN* 1.3 78.8 - - - +
391D LEU* 1.3 59.9 + - - +
392D TYR 3.2 0.5 + - - -
393D TRP* 3.3 3.7 + - - +
394D ILE* 3.2 27.5 + - - +
402D LEU* 3.6 25.5 - - + +
442D THR* 4.8 0.4 - - + -
446D LEU* 4.2 16.4 - - + -
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Residues in contact with LEU 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D LEU* 4.3 7.9 - - + +
120D ARG* 4.2 24.0 - - + +
122D TYR* 3.6 13.0 - - + +
387D VAL* 3.0 50.1 + - + +
388D GLY 3.1 4.0 + - - +
390D ALA* 1.3 72.6 - - - +
392D TYR* 1.3 57.5 + - - +
394D ILE* 4.5 3.1 - - - -
395D GLU* 2.6 43.3 + - - +
445D ILE* 4.3 6.7 - - + -
446D LEU* 3.7 23.8 - - + -
449D GLN* 3.9 26.9 - - + -
450D VAL* 4.0 15.9 - - + -
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Residues in contact with TYR 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D TYR* 3.5 28.0 + + + -
208D PHE* 3.7 19.5 + + - +
223D LEU* 3.8 20.9 - - + -
224D PRO* 4.9 3.5 - - + +
306D TYR* 2.4 61.0 + + + -
315D ARG* 5.0 0.2 + - - -
388D GLY 2.7 12.5 + - - +
389D ASN* 3.0 20.0 - - - +
391D LEU* 1.3 74.1 - - - +
393D TRP* 1.3 78.1 + + - +
396D ARG* 2.6 44.7 + - + +
397D PHE* 3.4 33.5 - + - -
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Residues in contact with TRP 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D ILE* 3.3 24.2 - - + -
290D ASN* 4.4 8.8 - - - +
305D LEU 3.4 19.6 + - - -
306D TYR 4.6 0.7 - - - -
307D ALA 4.5 1.1 - - - -
308D PRO* 4.0 19.5 - - + -
318D PHE* 3.7 19.1 - + - -
334D LEU* 3.6 22.6 - - + +
336D TRP* 4.2 13.1 - + - -
389D ASN* 3.2 41.3 + - - +
390D ALA* 3.7 6.3 - - - +
392D TYR* 1.3 91.3 - + - +
394D ILE* 1.3 62.8 + - - +
397D PHE* 3.2 49.9 + + + +
398D GLY 3.1 18.2 + - - -
399D ILE* 3.3 25.3 + - + +
402D LEU* 4.4 2.9 - - + -
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Residues in contact with ILE 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D VAL 4.5 4.3 - - - +
229D GLN* 5.2 7.9 - - + +
390D ALA 3.2 17.6 + - - +
391D LEU 3.9 2.5 - - - +
393D TRP* 1.3 75.2 - - - +
395D GLU* 1.3 59.9 + - - +
398D GLY* 3.2 23.2 - - - -
399D ILE* 3.5 33.2 - - + +
401D ALA* 5.8 0.4 - - - -
402D LEU* 4.1 19.5 - - + +
446D LEU* 4.2 11.9 - - + -
450D VAL* 3.4 48.0 - - + -
453D ALA* 4.0 19.1 - - + +
455D THR* 6.2 0.9 - - + -
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Residues in contact with GLU 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ARG* 2.7 39.9 + - - -
122D TYR* 3.2 18.5 + - - +
226D LYS* 3.2 32.1 + - + +
227D VAL* 2.6 38.5 + - - +
391D LEU* 2.6 28.9 + - - +
394D ILE* 1.3 77.1 - - - +
396D ARG* 1.3 56.9 + - + +
398D GLY 4.3 0.2 - - - -
449D GLN 5.1 2.8 - - - +
450D VAL* 4.3 18.3 - - + +
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Residues in contact with ARG 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D TYR* 4.0 14.5 + - + +
123D GLU* 2.7 39.4 + - - +
223D LEU* 3.7 25.7 + - + +
224D PRO* 3.1 45.1 + - + +
225D GLU* 3.8 6.8 + - - +
226D LYS* 3.8 35.0 - - - +
227D VAL* 4.3 1.1 - - - -
319D ARG* 2.7 27.1 + - - -
392D TYR* 2.6 39.3 + - + +
395D GLU* 1.3 75.2 - - - +
397D PHE* 1.3 63.1 + - + +
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Residues in contact with PHE 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D PRO* 3.9 22.7 - - + -
227D VAL* 4.1 6.0 - - - +
308D PRO* 3.8 16.4 - - + -
315D ARG* 3.7 30.3 - - + -
318D PHE* 3.8 21.8 - + + -
319D ARG* 4.1 26.9 - - + +
322D ILE* 3.1 27.4 - - + +
323D ASP* 4.6 0.7 - - - +
326D HIS* 4.6 0.3 - - - -
392D TYR* 3.4 33.2 - + - -
393D TRP* 3.2 43.6 + + + +
396D ARG* 1.3 83.4 - - + +
398D GLY* 1.3 59.5 + - - +
399D ILE* 3.3 7.4 - - + -
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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