Contacts of the helix formed by residues 373 - 389 (chain A) in PDB entry 6S1M
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 LYS 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A LEU* 4.7 7.9 - - - +
371A TYR* 3.4 7.1 + - - +
372A GLU* 1.3 88.3 - - + +
374A GLU* 1.3 65.4 + - - +
375A GLU* 3.3 28.2 + - - +
376A ASP* 3.5 28.8 + - - +
377A LEU* 3.6 8.0 + - - +
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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
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333A PRO* 3.3 34.4 - - - +
334A VAL* 3.9 8.1 + - + +
357A LEU* 3.7 28.5 - - + +
373A LYS* 1.3 72.3 - - - +
375A GLU* 1.3 62.0 + - - +
377A LEU* 3.1 6.3 + - + +
378A LEU* 3.0 38.3 + - + +
409A ARG* 3.7 24.0 + - - +
413A LEU* 3.8 20.9 - - + +
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Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LYS* 3.3 28.5 - - + +
374A GLU* 1.3 85.6 + - - +
376A ASP* 1.3 62.8 + - - +
378A LEU* 3.5 3.8 + - - +
379A GLN* 3.0 37.4 + - + +
413A LEU* 4.6 25.8 - - + +
414A LYS 5.7 0.2 - - - +
415A VAL* 3.8 30.9 - - + +
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Residues in contact with ASP 376 (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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371A TYR* 3.7 27.5 - - + +
372A GLU 4.8 2.1 + - - -
373A LYS* 3.7 28.5 + - - +
375A GLU* 1.3 81.7 - - - +
377A LEU* 1.3 57.5 + - - +
379A GLN* 3.8 7.3 - - - +
380A ALA* 2.9 32.2 + - - +
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Residues in contact with LEU 377 (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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334A VAL* 3.8 24.7 - - + +
335A ILE 4.1 14.4 - - - +
336A GLN 4.7 0.4 - - - +
337A ILE* 4.4 17.2 - - + +
355A LEU* 3.7 29.9 - - + +
356A THR 3.4 22.7 - - - +
357A LEU* 3.9 15.0 - - + -
371A TYR* 3.7 17.9 - - + -
373A LYS 3.6 6.5 + - - +
374A GLU* 3.1 13.3 + - - +
376A ASP* 1.3 78.3 - - - +
378A LEU* 1.3 63.2 + - + +
380A ALA* 3.4 2.8 + - - +
381A TRP* 3.1 24.1 + - - +
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Residues in contact with LEU 378 (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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334A VAL* 5.5 8.7 - - + -
337A ILE* 5.0 6.1 - - + -
374A GLU* 3.0 25.0 + - + +
375A GLU* 4.1 5.4 - - - +
377A LEU* 1.3 75.3 - - + +
379A GLN* 1.3 65.0 + - + +
381A TRP* 3.4 3.8 + - - +
382A SER* 3.0 17.8 + - - -
406A LEU* 3.8 35.0 - - + +
409A ARG* 4.8 10.8 - - + +
410A ALA* 4.4 24.0 - - + +
413A LEU* 5.0 9.6 - - + -
415A VAL* 5.2 8.7 - - + -
418A PHE* 3.5 39.8 - - + -
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Residues in contact with GLN 379 (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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375A GLU* 3.0 22.6 + - - +
376A ASP* 3.8 7.5 - - - +
378A LEU* 1.3 76.8 - - - +
380A ALA* 1.3 57.8 + - - +
382A SER* 2.7 23.2 + - - +
383A THR* 2.9 21.7 + - - +
415A VAL* 4.0 26.0 - - + +
416A GLN* 6.1 0.6 - - - +
417A THR* 5.1 15.0 + - - -
418A PHE* 5.3 2.5 - - + +
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Residues in contact with ALA 380 (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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78A ARG* 5.1 5.9 + - - +
355A LEU* 4.5 10.2 - - + +
369A GLN* 5.3 0.4 - - - +
371A TYR* 3.3 31.2 - - + +
376A ASP 2.9 19.3 + - - +
377A LEU 3.7 4.5 - - - +
379A GLN* 1.3 76.4 - - - +
381A TRP* 1.3 59.2 + - - +
383A THR* 3.5 5.9 + - - -
384A PHE* 3.0 28.8 + - - +
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Residues in contact with TRP 381 (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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313A LEU* 4.7 3.8 - - + +
315A PHE* 4.2 40.8 - + + -
337A ILE* 4.0 34.7 - - + +
339A SER* 3.6 19.3 + - - -
353A LEU* 5.9 0.2 - - + -
355A LEU* 4.1 17.9 - - + +
377A LEU 3.1 17.7 + - - +
378A LEU* 3.9 4.0 - - - +
380A ALA* 1.3 77.5 - - - +
382A SER* 1.3 58.0 + - - +
384A PHE* 3.4 16.9 + + - +
385A ILE* 3.0 51.1 + - + +
393A ILE* 6.3 2.5 - - + -
403A LEU* 4.8 8.7 - - + -
406A LEU* 4.3 18.6 - - + -
418A PHE* 4.3 21.8 - + - -
421A LEU* 5.0 12.8 - - + -
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Residues in contact with SER 382 (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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378A LEU 3.0 12.4 + - - -
379A GLN* 2.7 26.2 + - - +
381A TRP* 1.3 78.9 - - - +
383A THR* 1.3 58.8 + - - +
385A ILE* 3.3 12.0 - - - +
386A ARG* 3.0 31.4 + - - +
417A THR* 4.7 6.6 + - - +
418A PHE* 4.1 23.0 - - - -
421A LEU* 4.2 14.8 - - - +
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Residues in contact with THR 383 (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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78A ARG* 5.5 4.9 - - - +
379A GLN* 2.9 19.3 + - - +
380A ALA* 3.9 5.8 - - - -
382A SER* 1.3 76.5 + - - +
384A PHE* 1.3 64.3 + - - +
386A ARG* 3.3 28.8 + - - +
387A ILE* 3.0 43.2 + - + +
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Residues in contact with PHE 384 (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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78A ARG* 3.5 49.0 - - + +
313A LEU* 4.0 20.9 - - + -
339A SER* 4.3 13.0 - - - -
351A LEU* 3.6 28.5 - - + -
353A LEU* 4.1 21.5 - - + -
355A LEU* 5.7 1.1 - - + -
380A ALA 3.0 18.0 + - - +
381A TRP* 3.8 21.5 - + + +
383A THR* 1.3 75.9 - - - +
385A ILE* 1.3 66.2 + - + +
387A ILE* 4.7 3.1 - - - -
388A MET* 3.0 54.4 + - + +
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Residues in contact with ILE 385 (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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313A LEU* 3.6 31.0 - - + -
381A TRP* 3.0 33.6 + - + +
382A SER* 3.3 14.1 - - - +
384A PHE* 1.3 89.0 - - + +
386A ARG* 1.3 63.6 + - + +
388A MET* 5.3 1.1 - - - -
389A ASP* 3.6 13.7 + - - -
390A PRO* 3.7 25.1 - - + +
393A ILE* 5.2 9.4 - - + -
421A LEU* 3.6 35.0 - - + +
454A ARG* 4.0 10.2 + - - +
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Residues in contact with ARG 386 (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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283A GLN* 3.5 32.2 - - - +
382A SER* 3.0 21.9 + - - +
383A THR* 3.7 35.2 + - - +
384A PHE 3.3 0.2 - - - -
385A ILE* 1.3 78.3 - - - +
387A ILE* 1.3 71.4 + - + +
389A ASP* 3.6 19.2 + - - +
417A THR* 5.8 5.5 - - - +
421A LEU 6.1 0.2 - - - -
454A ARG* 4.8 7.2 - - - +
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Residues in contact with ILE 387 (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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78A ARG* 4.0 28.5 - - - +
79A TRP 4.6 2.6 - - - +
80A LEU* 4.4 31.9 - - + +
81A ARG* 5.4 1.2 + - - +
383A THR* 3.0 38.1 + - + +
384A PHE* 3.3 2.4 + - - +
386A ARG* 1.3 86.2 - - + +
388A MET* 1.3 66.2 + - - +
389A ASP* 3.4 3.6 + - - +
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Residues in contact with MET 388 (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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78A ARG 4.5 1.8 - - - +
79A TRP 4.1 13.9 - - - +
81A ARG* 4.6 3.6 + - - +
311A ARG* 3.3 44.9 + - + +
312A VAL 4.4 14.8 - - - +
313A LEU* 3.9 17.0 - - + -
341A GLY* 4.5 9.6 - - - -
342A LEU 5.1 0.4 - - - +
350A PHE* 4.7 11.2 - - + -
351A LEU* 4.6 9.6 - - + -
384A PHE* 3.0 49.1 + - + +
385A ILE* 5.2 0.9 - - - -
387A ILE* 1.3 77.9 - - - +
389A ASP* 1.3 67.1 + - - +
390A PRO* 4.0 26.7 - - + -
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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
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81A ARG* 3.2 29.9 + - + +
136A SER* 4.2 14.2 + - - -
283A GLN* 5.1 14.3 - - - +
284A CYS* 5.6 1.7 - - - -
311A ARG* 4.7 0.2 - - - -
385A ILE 3.6 5.4 + - - -
386A ARG 3.6 15.2 - - - +
387A ILE 3.3 4.8 - - - +
388A MET* 1.3 79.8 - - - +
390A PRO* 1.3 70.3 - - - +
423A ARG* 3.6 23.3 + - - +
454A ARG* 3.0 28.6 + - - +
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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
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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