Contacts of the helix formed by residues 371 - 394 (chain A) in PDB entry 1MS4
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 LEU 371 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER* 4.8 2.7 - - - +
319A LEU* 4.3 9.2 - - + -
333A VAL* 3.9 34.3 - - + +
345A VAL* 5.2 4.7 - - + -
352A LEU* 2.9 46.8 + - + +
353A TYR 4.1 7.6 - - - +
354A CYS* 3.8 25.6 - - + -
369A ALA* 4.1 14.8 - - + -
370A ARG* 1.3 72.8 - - - +
372A VAL* 1.3 63.9 + - - +
374A GLU* 3.3 27.1 - - + +
375A LEU* 3.3 20.8 + - - +
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Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLY* 3.5 30.5 - - - +
5A SER* 3.1 1.2 + - - -
6A SER* 6.1 0.2 - - - +
351A LYS* 6.0 5.8 - - + -
370A ARG* 2.8 27.1 + - + +
371A LEU* 1.3 73.7 - - - +
373A GLY* 1.3 65.4 + - - +
375A LEU* 3.9 4.0 - - - +
376A ARG* 3.3 36.4 + - - +
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Residues in contact with GLY 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 4.2 7.4 - - - -
3A PRO* 3.4 19.9 + - - -
5A SER* 3.0 12.0 + - - -
372A VAL* 1.3 80.7 - - - +
374A GLU* 1.3 62.5 + - - +
376A ARG* 3.2 15.9 + - - +
377A ILE* 3.0 32.2 + - - +
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Residues in contact with GLU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 5.6 0.7 - - - +
2A ALA* 3.1 21.8 - - + +
5A SER* 2.7 25.5 + - - -
319A LEU* 4.0 17.5 - - + -
330A VAL* 3.8 26.0 - - + +
331A GLY 5.8 2.0 - - - +
332A GLN 4.2 4.2 - - - +
333A VAL* 4.2 21.4 - - + +
352A LEU* 4.5 1.1 - - + -
371A LEU* 3.3 36.6 - - + +
372A VAL 3.4 0.2 - - - -
373A GLY* 1.3 70.1 - - - +
375A LEU* 1.3 55.8 + - - +
377A ILE* 3.2 5.6 + - + +
378A ILE* 2.7 40.1 + - - +
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ILE* 4.5 16.2 - - + -
347A TYR* 4.3 15.0 - - + -
350A ASP* 3.5 30.5 - - - +
351A LYS* 4.2 10.3 - - + -
352A LEU* 4.1 18.3 - - + +
371A LEU 3.3 15.6 + - - +
372A VAL* 3.9 4.3 - - - +
373A GLY 3.3 0.4 - - - -
374A GLU* 1.3 77.5 - - - +
376A ARG* 1.3 52.1 + - - +
378A ILE* 2.7 13.3 + - + +
379A LYS* 2.6 64.9 + - + +
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Residues in contact with ARG 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PRO* 2.6 49.5 + - - +
4A GLY* 5.1 1.6 - - - -
372A VAL* 3.3 26.3 + - + +
373A GLY* 3.2 16.5 + - - +
375A LEU* 1.3 78.8 - - - +
377A ILE* 1.3 67.5 + - + +
379A LYS* 3.2 8.7 + - - +
380A SER* 2.9 22.0 + - - -
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Residues in contact with ILE 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 5.8 4.3 - - + -
3A PRO* 6.4 1.8 - - + -
328A TYR* 3.7 36.8 - - + +
330A VAL* 4.1 22.7 - - + +
373A GLY* 3.0 23.4 + - - +
374A GLU* 3.6 8.7 - - + +
376A ARG* 1.3 77.4 - - + +
378A ILE* 1.3 70.0 + - - +
380A SER* 3.0 16.9 + - - +
381A VAL* 3.0 14.9 + - + +
437A ARG* 6.0 1.6 - - - +
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Residues in contact with ILE 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ILE* 4.1 15.3 - - + -
301A LEU* 3.9 22.9 - - + -
319A LEU* 4.2 6.1 - - + -
321A LEU* 4.0 21.0 - - + +
328A TYR* 6.0 0.2 - - - -
330A VAL* 3.7 28.7 - - + -
352A LEU* 4.2 21.8 - - + -
374A GLU 2.7 23.5 + - - +
375A LEU* 2.7 14.7 + - + +
377A ILE* 1.3 72.6 - - - +
379A LYS* 1.3 61.6 + - - +
381A VAL* 3.4 3.4 + - - +
382A LEU* 3.0 42.7 + - + +
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Residues in contact with LYS 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ILE* 4.2 11.4 - - + -
295A GLU* 2.9 37.0 + - + +
350A ASP* 2.7 40.9 + - - -
375A LEU* 2.6 45.1 + - + +
376A ARG* 3.7 7.4 - - - +
378A ILE* 1.3 70.5 - - - +
380A SER* 1.3 66.4 + - - +
382A LEU* 3.5 7.6 + - - +
383A GLN* 3.2 23.6 + - - +
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Residues in contact with SER 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ARG* 2.9 14.5 + - - -
377A ILE* 3.0 10.7 + - - -
379A LYS* 1.3 76.3 - - - +
381A VAL* 1.3 64.0 + - - +
383A GLN* 2.9 18.2 + - - +
384A SER* 3.0 12.3 + - - -
437A ARG* 2.6 35.3 + - - -
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 4.0 12.6 - - + -
328A TYR* 3.5 47.3 - - + +
377A ILE* 3.0 13.2 + - + +
378A ILE 3.8 6.5 - - - +
380A SER* 1.3 75.5 - - - +
382A LEU* 1.3 57.7 + - - +
384A SER* 2.9 4.4 + - - -
385A TRP* 2.9 67.8 + - + +
436A TYR 4.6 1.6 - - - +
437A ARG* 3.9 22.7 - - + +
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ILE* 3.8 38.1 - - + +
295A GLU* 5.5 5.4 - - + -
297A MET* 3.2 43.4 - - + +
299A VAL* 3.7 21.1 - - + -
321A LEU* 4.1 6.7 - - + -
378A ILE* 3.0 38.6 + - + +
379A LYS* 3.8 6.3 - - - +
380A SER 3.2 0.2 - - - -
381A VAL* 1.3 76.6 - - - +
383A GLN* 1.3 59.7 + - + +
385A TRP* 3.7 17.9 - - + +
386A LYS* 2.9 24.3 + - - +
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Residues in contact with GLN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU* 6.2 4.7 - - + -
379A LYS 3.2 11.2 + - - +
380A SER* 2.9 11.6 + - - +
382A LEU* 1.3 80.5 - - + +
384A SER* 1.3 60.4 + - - +
386A LYS* 3.8 18.7 - - + +
387A ASN* 2.6 74.5 + - - +
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Residues in contact with SER 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A SER 3.0 3.4 + - - -
381A VAL 2.9 7.4 + - - -
383A GLN* 1.3 77.3 - - - +
385A TRP* 1.3 63.7 + - - +
387A ASN* 3.2 4.7 + - - +
388A TRP* 2.9 39.1 + - - -
435A ALA 4.3 9.9 - - - -
437A ARG* 2.7 44.9 + - - -
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Residues in contact with TRP 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A MET* 4.1 9.4 - - + -
299A VAL* 4.8 0.9 - - + -
321A LEU* 3.9 23.8 - - + -
322A THR 4.4 0.4 - - - -
323A ASP* 3.7 34.8 - - + -
326A ARG* 3.6 44.6 - - + +
328A TYR* 4.2 4.5 - - + -
381A VAL* 2.9 35.5 + - + +
382A LEU* 3.7 30.7 - - + +
384A SER* 1.3 76.1 - - - +
386A LYS* 1.3 63.7 + - - +
388A TRP 3.5 0.2 + - - -
389A ASP* 3.0 31.4 + - - +
436A TYR* 2.8 54.3 + + - +
438A CYS* 4.1 9.6 - - - -
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Residues in contact with LYS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLU 5.3 10.8 + - - +
297A MET* 3.7 16.8 - - + +
382A LEU 2.9 18.4 + - - +
383A GLN* 3.9 21.5 - - + +
385A TRP* 1.3 77.9 - - - +
387A ASN* 1.3 69.1 + - - +
389A ASP* 3.5 4.6 + - - +
390A SER* 3.0 26.3 + - - -
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Residues in contact with ASN 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLN* 2.6 54.6 + - - +
384A SER* 3.2 5.9 + - - +
386A LYS* 1.3 82.5 - - - +
388A TRP* 1.3 63.7 + - + +
390A SER* 3.1 8.2 + - - -
391A HIS* 2.9 30.0 + - - +
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Residues in contact with TRP 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A SER* 2.9 36.2 + - - +
387A ASN* 1.3 75.6 - - + +
389A ASP* 1.3 64.0 + - - +
391A HIS* 3.5 28.1 - + + +
392A LEU* 3.0 29.9 + - + +
422A PHE* 5.3 2.9 - + + -
426A SER* 5.9 2.7 - - - -
435A ALA* 3.2 46.0 + - + +
436A TYR* 3.8 22.9 - + + +
629A THR* 3.5 46.2 - - + -
632A HIS* 4.5 20.2 - - + -
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Residues in contact with ASP 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLN* 4.8 1.7 + - - -
326A ARG* 2.6 49.6 + - - -
385A TRP 3.0 16.9 + - - +
386A LYS* 3.9 4.7 - - - +
388A TRP* 1.3 75.4 - - - +
390A SER* 1.3 58.6 + - - +
392A LEU* 3.1 3.1 + - - +
393A SER* 2.9 34.6 + - - +
416A THR* 3.7 22.8 - - + +
436A TYR* 3.0 10.9 + - - -
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LYS* 3.0 21.6 + - - -
387A ASN* 3.4 8.5 - - - -
389A ASP* 1.3 72.9 - - - +
391A HIS* 1.3 66.5 - - - +
393A SER* 3.8 4.7 - - - -
394A SER* 3.0 30.8 + - - -
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Residues in contact with HIS 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ASN 2.9 16.1 + - - +
388A TRP* 3.5 29.5 - + + +
390A SER* 1.3 76.9 - - - +
392A LEU* 1.3 77.8 + - + +
394A SER* 3.2 17.4 + - - -
395A ILE* 3.4 16.8 - - + +
422A PHE* 5.2 1.1 - + - -
626A LEU 4.3 9.4 - - - -
627A ILE* 3.2 27.1 + - - -
628A GLY 3.5 8.6 + - - -
629A THR* 5.2 1.6 - - + -
632A HIS* 3.0 47.6 + + + -
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A TRP* 3.0 15.4 + - + +
389A ASP 3.7 2.7 - - - +
391A HIS* 1.3 93.1 - - + +
393A SER* 1.3 61.4 + - - +
394A SER 3.2 0.2 + - - -
395A ILE* 3.3 21.4 + - + +
414A VAL* 3.9 27.5 + - + +
416A THR* 4.0 10.1 - - + -
419A LEU* 3.5 32.3 - - + -
422A PHE* 4.5 18.4 - - + -
436A TYR* 3.5 11.9 - - - +
606A LEU* 5.0 5.8 - - + -
608A TYR* 5.6 0.7 - - - +
627A ILE* 3.9 37.5 - - + +
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Residues in contact with SER 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ASP* 2.9 17.6 + - - +
390A SER* 4.0 5.4 - - - -
392A LEU* 1.3 76.2 - - - +
394A SER* 1.3 57.3 + - - +
395A ILE 3.4 2.9 + - - +
413A ALA* 4.3 18.1 - - - +
414A VAL 4.2 13.3 + - - -
416A THR* 3.9 17.3 + - - +
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Residues in contact with SER 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER* 3.0 23.4 + - - -
391A HIS* 3.2 11.8 + - - -
392A LEU 3.2 0.2 - - - -
393A SER* 1.3 75.0 - - - +
395A ILE* 1.3 65.8 + - - +
396A CYS* 3.3 4.3 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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