Contacts of the helix formed by residues 379 - 397 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A TRP* 3.5 15.7 - - + -
145A PRO* 4.5 6.5 - - - +
146A ASN* 4.7 8.1 - - - +
354A THR* 5.4 1.4 + - - -
355A ASN 3.3 16.4 + - - -
356A LEU* 3.2 47.7 + - - +
376A ASN* 2.9 36.5 + - - +
377A TYR 3.8 0.7 - - - +
378A GLY* 1.3 72.0 - - - +
380A ARG* 1.3 70.5 + - - +
381A GLU* 4.0 11.2 + - - +
382A VAL* 2.8 25.9 + - + +
383A SER 3.0 8.0 + - - -
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Residues in contact with ARG 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A HIS* 2.9 66.4 + - + +
119A LEU* 6.1 0.8 - - - +
378A GLY 2.9 8.8 + - - -
379A ARG* 1.3 69.4 - - - +
381A GLU* 1.3 70.6 + - - +
383A SER* 2.7 32.3 + - - -
384A ASN* 2.8 27.4 + - - +
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Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A HIS* 5.9 4.1 - - + -
143A TRP* 3.1 64.9 + - + +
172A SER 5.4 1.9 - - - +
206A TYR* 4.8 1.4 + - - -
357A TYR* 4.9 1.2 - - - -
379A ARG* 4.0 8.1 + - - +
380A ARG* 1.3 91.7 + - - +
382A VAL* 1.3 57.0 + - - +
384A ASN* 3.1 14.3 + - - +
385A PHE* 2.8 30.5 + - - +
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Residues in contact with VAL 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TRP* 4.6 2.5 - - + -
356A LEU 3.8 2.5 - - - +
357A TYR* 3.7 46.4 - - + +
375A TYR* 4.2 17.0 - - + -
376A ASN 3.2 24.9 - - - +
377A TYR* 4.3 2.9 - - - +
379A ARG* 2.8 36.6 + - + +
381A GLU* 1.3 77.8 - - - +
383A SER* 1.3 59.6 + - - +
385A PHE* 3.2 7.5 - - - +
386A LEU* 3.2 25.9 + - + +
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Residues in contact with SER 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 3.6 21.7 + - - +
378A GLY 5.5 0.2 - - - -
379A ARG 3.0 4.4 + - - -
380A ARG* 2.7 16.6 + - - -
382A VAL* 1.3 74.4 - - - +
384A ASN* 1.3 58.6 + - - -
386A LEU* 3.3 1.0 + - - +
387A VAL* 2.8 48.4 + - - +
438A PHE* 3.8 20.0 - - - -
441A ASN* 5.9 1.9 - - - +
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Residues in contact with ASN 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A HIS* 2.9 49.7 + - - +
119A LEU* 6.1 1.6 - - - +
121A PRO* 3.3 17.2 - - + +
380A ARG* 2.8 46.0 + - - +
381A GLU* 3.1 14.6 + - - +
383A SER* 1.3 79.1 + - - +
385A PHE* 1.3 58.2 + - - +
387A VAL* 4.8 3.9 - - - +
388A GLY* 2.8 30.7 + - - +
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Residues in contact with PHE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PRO* 3.8 30.7 - - + -
206A TYR* 3.1 42.6 + + - +
305A LEU* 4.4 17.9 - - + -
306A TYR* 2.8 43.1 + + - -
348A LEU* 4.2 16.2 - - + -
357A TYR* 4.0 20.4 - + + -
375A TYR* 4.0 20.4 - + - -
381A GLU 2.8 13.4 + - - +
382A VAL* 3.2 11.9 - - - +
384A ASN* 1.3 77.6 - - - +
386A LEU* 1.3 71.3 + - + +
389A ASN* 3.0 13.0 + - + +
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 5.5 5.6 - - + -
336A TRP* 3.1 26.0 - - + -
338A PRO* 4.0 10.8 - - + +
375A TYR* 3.7 40.2 - - + +
377A TYR* 3.6 29.4 - - + -
382A VAL* 3.2 16.9 + - + +
383A SER 3.9 0.2 - - - +
385A PHE* 1.3 86.7 - - + +
387A VAL* 1.3 68.0 + - - +
388A GLY 3.1 0.9 - - - -
389A ASN* 2.9 15.0 + - + +
390A ALA 3.1 0.3 + - - -
438A PHE* 3.2 33.0 - - + -
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 4.9 10.1 - - + +
383A SER* 2.8 33.7 + - - +
384A ASN* 4.6 3.4 - - - +
386A LEU* 1.3 70.9 - - - +
388A GLY* 1.3 63.2 + - - +
390A ALA* 3.2 16.6 + - - +
391A LEU* 3.3 16.1 + - + +
438A PHE* 3.6 9.8 - - + -
441A ASN* 5.7 1.8 - - + -
442A THR* 3.6 33.9 - - + +
445A ILE* 3.7 42.6 - - + -
446A LEU* 5.6 1.1 - - + +
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Residues in contact with GLY 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU 3.0 25.1 + - - -
121A PRO* 4.0 3.8 - - - -
122A TYR* 3.0 11.7 - - - -
306A TYR* 3.4 7.4 - - - -
384A ASN* 2.8 21.4 + - - +
387A VAL* 1.3 77.7 - - - +
389A ASN* 1.3 56.4 + - - +
391A LEU* 3.1 2.0 + - - +
392A TYR 2.9 24.4 + - - -
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Residues in contact with ASN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ASN* 5.4 0.2 + - - -
305A LEU* 3.1 39.9 + - + +
306A TYR* 2.9 28.8 + - + +
336A TRP* 2.9 22.6 + - + +
385A PHE* 3.0 16.3 + - + +
386A LEU* 2.9 10.7 + - + +
388A GLY* 1.3 75.6 - - - +
390A ALA* 1.3 59.9 + - - +
392A TYR* 3.5 14.3 - - - -
393A TRP* 3.1 33.8 + - - +
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Residues in contact with ALA 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TRP* 3.6 28.2 - - + +
386A LEU 3.1 4.4 + - - -
387A VAL 3.2 9.6 + - - +
389A ASN* 1.3 75.4 - - - +
391A LEU* 1.3 63.5 + - - +
393A TRP* 4.3 2.6 - - - +
394A ILE* 3.0 33.1 + - - +
402A LEU* 3.4 24.8 - - + +
442A THR* 4.6 2.5 - - + -
446A LEU* 3.7 13.9 - - + -
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.8 30.5 - - + +
120A ARG* 3.2 37.2 - - - +
122A TYR* 3.9 6.1 - - + +
387A VAL* 3.3 12.7 + - + +
388A GLY 3.1 9.1 + - - +
390A ALA* 1.3 78.8 - - - +
392A TYR* 1.3 59.1 + - - +
394A ILE* 3.6 2.1 + - - +
395A GLU* 3.0 38.2 + - - +
445A ILE* 4.7 5.6 - - + -
446A LEU* 4.2 29.4 - - + -
449A GLN* 4.1 24.5 - - + -
450A VAL* 4.6 6.1 - - + -
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Residues in contact with TYR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TYR* 3.6 28.7 - + + -
208A PHE* 3.6 34.8 + + - +
223A LEU* 4.5 1.6 - - + -
224A PRO* 4.2 8.4 - - + +
306A TYR* 2.4 59.3 + + + -
315A ARG* 5.2 0.2 + - - -
388A GLY 2.9 12.9 + - - +
389A ASN* 3.4 16.8 - - - +
391A LEU* 1.3 75.2 - - - +
393A TRP* 1.3 80.9 + + - +
396A ARG* 2.7 65.0 + - + +
397A PHE* 3.6 17.6 - + - -
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Residues in contact with TRP 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ILE* 3.6 22.9 - - + -
290A ASN* 4.1 15.2 - - - +
305A LEU 3.2 20.9 + - - -
306A TYR 4.2 1.1 - - - -
307A ALA 4.6 1.8 - - - -
308A PRO* 3.7 37.2 - - + -
318A PHE* 4.0 3.1 - + - -
334A LEU* 4.1 7.7 - - + +
336A TRP* 4.1 18.2 - + - -
389A ASN* 3.1 42.0 + - - +
390A ALA 4.4 0.9 - - - +
392A TYR* 1.3 88.6 - + - +
394A ILE* 1.3 60.5 + - - +
397A PHE* 3.1 51.8 + + - +
398A GLY 3.3 2.9 + - - -
399A ILE* 3.3 30.5 + - + +
402A LEU* 4.2 14.6 - - + -
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Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A VAL 4.3 4.5 - - - +
229A GLN* 5.4 7.3 + - + +
233A ARG* 5.3 0.3 + - - -
390A ALA 3.0 22.4 + - - +
391A LEU* 3.6 4.6 + - - +
392A TYR 3.3 0.6 - - - -
393A TRP* 1.3 76.7 - - - +
395A GLU* 1.3 60.5 + - + +
398A GLY* 3.1 22.9 + - - -
399A ILE* 3.4 25.8 - - + +
401A ALA 5.4 0.9 - - - +
402A LEU* 3.8 21.1 - - + +
446A LEU* 3.1 33.7 - - + -
450A VAL* 4.0 20.4 - - + -
453A ALA* 4.0 21.3 - - + -
454A VAL 6.0 0.7 - - - +
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Residues in contact with GLU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ARG* 2.7 42.8 + - - -
122A TYR* 3.5 9.4 + - - +
123A GLU* 4.5 0.5 - - - +
226A LYS* 3.4 34.4 + - + +
227A VAL 2.6 39.0 + - - +
391A LEU 3.0 17.0 + - - +
394A ILE* 1.3 75.6 - - + +
396A ARG* 1.3 61.7 + - + +
397A PHE 3.4 0.7 - - - -
449A GLN 4.3 2.4 - - - +
450A VAL* 3.4 30.4 - - + +
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Residues in contact with ARG 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TYR* 4.2 10.2 + - + -
123A GLU* 3.5 22.6 + - - +
223A LEU* 3.5 36.7 + - + +
224A PRO* 2.9 58.0 + - + +
225A GLU* 2.5 29.0 + - - +
226A LYS* 3.7 28.6 + - - +
227A VAL* 4.2 2.5 - - - -
319A ARG* 3.3 10.0 + - - -
392A TYR* 2.7 48.2 + - + +
395A GLU* 1.3 75.8 - - + +
397A PHE* 1.3 59.5 + - + +
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Residues in contact with PHE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PRO* 3.6 21.5 - - + -
227A VAL* 3.6 8.6 - - - +
308A PRO* 3.7 16.6 - - + -
315A ARG* 3.3 29.6 - - - -
318A PHE* 3.3 35.2 - + + -
319A ARG* 4.0 23.7 + - + +
322A ILE* 3.2 27.6 - - + +
323A ASP* 4.9 0.7 - - - +
326A HIS* 4.7 0.2 - - - -
392A TYR* 3.6 26.9 - + - -
393A TRP* 3.1 34.2 + + + +
396A ARG* 1.3 84.5 - - + +
398A GLY* 1.3 60.9 + - - +
399A ILE* 3.3 10.5 - - + -
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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