Contacts of the helix formed by residues 386 - 401 (chain A) in PDB entry 6N0M
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 THR 386 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A MET* 3.9 11.2 - - + -
374A THR* 3.2 4.5 + - - +
377A THR 3.8 17.9 - - - +
378A ILE* 4.1 22.7 - - + -
384A VAL* 3.6 11.8 + - + +
385A ASP* 1.3 73.2 + - - +
387A SER* 1.3 64.4 + - - +
388A VAL 3.1 3.1 - - - -
389A LEU* 2.9 15.2 + - - +
390A ARG* 2.8 30.7 + - - +
900A K94 2.5 41.1 + - - +
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Residues in contact with SER 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLN* 4.0 3.6 + - - -
371A TYR* 5.1 2.8 - - - -
385A ASP* 2.6 35.5 + - - -
386A THR* 1.3 71.2 - - - +
388A VAL* 1.3 53.7 + - - +
390A ARG* 3.4 27.7 - - - +
391A ARG* 2.7 54.1 + - - +
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A MET* 4.4 10.3 - - + -
268A LEU* 3.8 23.3 - - + -
269A GLN* 3.4 38.1 - - + +
385A ASP* 4.3 0.6 + - - +
386A THR 3.1 1.3 - - - -
387A SER* 1.3 79.2 + - - +
389A LEU* 1.3 56.7 + - - +
391A ARG* 3.7 24.9 - - - +
392A ALA* 3.1 25.5 + - - +
408A TYR* 3.8 2.8 + - - -
412A GLU* 4.2 8.0 - - - +
416A LEU* 3.4 27.9 - - + +
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Residues in contact with LEU 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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261A LEU* 4.2 12.1 - - + -
265A MET* 4.2 28.5 - - + -
378A ILE* 4.3 7.4 - - + -
386A THR 2.9 8.6 + - - +
388A VAL* 1.3 77.9 - - - +
390A ARG* 1.3 67.0 + - - +
392A ALA* 3.2 4.2 + - - +
393A ILE* 3.1 22.1 + - + +
416A LEU* 4.0 19.5 - - + +
417A LEU* 3.7 23.3 - - + -
444A TRP* 4.0 23.3 - - + -
900A K94 3.4 32.1 - - + -
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Residues in contact with ARG 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A TYR* 3.1 37.7 + - + +
372A SER* 4.1 7.9 + - - +
373A LEU 3.4 17.0 - - - -
374A THR* 3.2 28.7 + - - +
385A ASP* 4.6 1.6 + - - +
386A THR* 2.8 31.9 + - - +
387A SER* 3.4 33.0 - - - +
389A LEU* 1.3 73.2 - - - +
391A ARG* 1.3 65.1 + - - +
393A ILE* 3.1 5.7 + - - +
394A TRP* 3.0 24.0 + - - +
454A HIS* 4.2 6.3 - - - -
458A LEU* 3.9 14.8 - - + +
900A K94 3.1 35.4 + - - -
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Residues in contact with ARG 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A TYR* 3.7 30.7 + - - +
387A SER* 2.7 40.6 + - - +
388A VAL* 3.7 31.3 - - - +
390A ARG* 1.3 70.5 - - - +
392A ALA* 1.3 52.5 + - - +
394A TRP* 4.3 2.2 - - - -
395A ASN* 2.7 60.3 + - - +
408A TYR* 3.7 23.5 - - + +
412A GLU* 5.2 3.2 + - - -
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Residues in contact with ALA 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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388A VAL 3.1 13.6 + - - +
389A LEU 3.4 9.2 - - - +
390A ARG 3.2 0.4 - - - -
391A ARG* 1.3 74.1 - - - +
393A ILE* 1.3 63.9 + - - +
396A TYR* 3.1 26.5 + - - +
408A TYR* 3.2 23.3 + - - +
413A VAL* 4.1 8.2 - - - +
416A LEU* 3.9 14.8 - - + -
417A LEU* 3.2 24.3 - - + +
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Residues in contact with ILE 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 3.1 16.2 + - + +
390A ARG 3.1 4.9 + - - +
392A ALA* 1.3 71.8 - - - +
394A TRP* 1.3 68.8 + - - +
396A TYR* 3.7 1.4 - - - +
397A ILE* 3.1 37.0 + - + +
417A LEU* 3.9 19.7 - - + -
421A LEU* 4.5 1.8 - - + -
425A ILE* 3.6 25.8 - - + -
444A TRP* 4.1 15.5 - - + -
455A VAL* 4.1 14.8 - - + +
458A LEU* 4.3 23.6 - - + -
900A K94 3.8 32.3 - - - -
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Residues in contact with TRP 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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367A PHE* 4.9 11.4 - + + -
370A ALA* 5.0 0.2 - - + -
371A TYR* 4.4 39.4 - + + -
390A ARG 3.0 12.6 + - - +
391A ARG* 3.5 11.0 - - - +
393A ILE* 1.3 80.8 - - - +
395A ASN* 1.3 82.9 + - - +
397A ILE* 3.2 3.8 + - - +
398A HIS* 3.2 41.8 + + - +
405A TYR* 3.8 7.5 + + - -
458A LEU* 3.6 30.4 - - + +
461A GLU* 3.8 15.7 - - + -
462A ALA* 3.5 48.2 - - + +
465A GLN* 4.0 27.3 + - - -
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Residues in contact with ASN 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A TYR* 4.6 2.8 + - - -
391A ARG* 2.7 35.8 + - - +
394A TRP* 1.3 94.0 - - - +
396A TYR* 1.4 51.0 + - - +
398A HIS* 3.4 6.0 + - - +
399A CYS 2.9 27.4 + - - -
405A TYR* 3.9 19.4 - - - +
408A TYR* 3.3 51.9 - - + +
410A TYR* 3.3 19.6 + - - +
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Residues in contact with TYR 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLU* 3.9 25.5 + - + -
293A GLU* 4.1 3.0 + - - -
295A LEU* 3.5 25.6 - - - +
392A ALA 3.1 21.3 + - - +
393A ILE 3.7 2.9 - - - +
395A ASN* 1.4 73.6 - - - +
397A ILE* 1.3 60.0 + - + +
399A CYS* 2.9 10.7 + - + +
400A VAL* 2.8 45.0 + - + +
410A TYR* 4.5 0.2 - - - -
413A VAL* 3.8 22.7 - - + +
417A LEU* 3.8 15.5 - - + -
422A LYS* 3.8 33.9 + - + -
425A ILE* 3.7 33.7 - - + -
426A LYS* 3.9 13.7 + - + +
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Residues in contact with ILE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ILE* 3.1 33.9 + - + +
394A TRP 3.7 5.2 - - - +
396A TYR* 1.3 78.4 - - + +
398A HIS* 1.3 61.0 + - - +
400A VAL* 3.3 9.8 + - + +
401A PHE* 3.2 32.8 + - + -
425A ILE* 3.4 30.7 - - + -
429A ALA* 4.7 9.2 - - + -
459A LEU* 3.4 36.6 - - + +
462A ALA* 3.7 23.6 - - + +
463A ARG* 3.9 17.5 - - + +
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Residues in contact with HIS 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TRP* 3.2 23.8 + + - +
395A ASN 3.6 7.9 - - - +
397A ILE* 1.3 76.6 - - + +
399A CYS* 1.3 50.8 + - - +
401A PHE* 3.0 8.5 + - - -
402A GLY 2.7 30.5 + - - -
403A ILE* 2.8 36.5 + - + +
405A TYR* 2.7 37.4 + + + -
462A ALA* 2.7 45.1 + - + -
465A GLN* 3.6 19.9 - - + +
466A ALA* 4.0 12.2 + - + -
469A LEU* 5.2 2.0 - - + -
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Residues in contact with CYS 399 (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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287A PHE* 3.4 36.3 - - + -
290A GLU* 4.0 16.2 - - - -
291A LYS* 3.4 44.2 - - - +
395A ASN 2.9 15.5 + - - +
396A TYR* 3.1 16.2 - - - +
398A HIS* 1.3 75.9 - - - +
400A VAL* 1.3 59.9 + - - +
402A GLY* 3.1 12.5 + - - -
403A ILE 3.6 1.6 + - - -
410A TYR* 3.7 7.4 - - + -
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Residues in contact with VAL 400 (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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290A GLU 6.0 0.4 - - - +
291A LYS* 5.4 4.9 - - - +
323A TYR* 2.4 44.9 + - + +
334A PRO* 3.6 6.4 - - - +
396A TYR* 2.8 53.7 + - + +
397A ILE* 3.5 13.7 - - + +
398A HIS 3.2 0.2 - - - -
399A CYS* 1.3 73.7 - - - +
401A PHE* 1.3 62.1 + - + +
402A GLY 3.4 0.2 - - - -
426A LYS* 4.1 17.3 - - + +
429A ALA* 5.4 1.3 - - + -
430A CYS* 3.3 33.7 - - - -
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Residues in contact with PHE 401 (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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166A LEU 5.6 0.9 - - - -
167A ALA 5.0 4.3 - - - -
168A HIS 4.3 9.6 - - - -
170A PRO* 3.9 21.1 - - + -
171A TRP* 3.8 24.3 - + - +
323A TYR* 4.4 8.7 - + - -
334A PRO* 3.8 5.0 - - - +
397A ILE* 3.2 27.8 + - + +
398A HIS 3.0 9.8 + - - +
400A VAL* 1.3 78.7 - - + +
402A GLY* 1.3 49.9 + - - +
403A ILE 3.6 0.4 - - - -
429A ALA* 3.8 37.7 - - + -
430A CYS* 4.3 6.7 - - - -
463A ARG* 3.9 31.0 - - + -
466A ALA* 4.0 26.7 - - + -
467A ALA* 6.5 0.2 - - + -
470A TYR* 2.5 35.4 + - + -
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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
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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