Contacts of the helix formed by residues 418 - 439 (chain A) in PDB entry 5M64
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 VAL 418 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A ARG* 1.3 70.3 - - - +
419A ILE* 1.3 61.0 + - - +
420A PHE 3.1 2.7 - - - -
421A SER* 3.0 13.5 + - - +
422A ARG* 2.9 27.6 + - + +
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A LEU* 3.6 22.2 - - + +
402A ASP* 3.7 28.9 - - + +
403A LEU* 3.7 24.5 - - + -
417A ARG* 3.6 20.6 - - + +
418A VAL* 1.3 77.7 - - - +
420A PHE* 1.3 59.8 + - - +
422A ARG* 3.3 40.9 + - - +
423A LEU* 3.0 26.7 + - - +
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Residues in contact with PHE 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU* 5.6 2.7 - - + -
417A ARG* 3.6 27.5 + - + +
418A VAL 3.1 0.6 - - - -
419A ILE* 1.3 79.8 - - + +
421A SER* 1.3 61.1 + - - +
422A ARG 3.1 0.2 - - - -
423A LEU* 3.2 37.5 - - + +
424A MET* 3.1 42.1 + - + +
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Residues in contact with SER 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ARG 3.9 3.2 + - - -
418A VAL* 3.0 22.4 + - - -
420A PHE* 1.3 79.9 - - - +
422A ARG* 1.3 57.4 + - - +
424A MET* 4.2 18.2 - - - +
425A ASN* 3.0 27.7 + - - +
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Residues in contact with ARG 422 (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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395A LEU* 4.0 25.8 - - + +
399A LEU* 3.3 29.5 - - + +
418A VAL* 2.9 16.7 + - + +
419A ILE* 3.4 26.0 - - + +
420A PHE 3.1 0.4 - - - -
421A SER* 1.3 78.9 - - - +
423A LEU* 1.3 56.8 + - - +
425A ASN* 3.8 9.7 - - + +
426A ALA* 2.9 25.2 + - - +
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ILE* 5.9 1.3 - - + -
399A LEU* 3.6 19.5 - - + -
403A LEU* 3.7 30.3 - - + -
419A ILE 3.0 9.2 + - - +
420A PHE* 3.2 52.3 - - + +
422A ARG* 1.3 76.1 - - - +
424A MET* 1.3 64.5 + - + +
426A ALA* 3.2 8.9 + - + +
427A PHE* 2.8 58.7 + - + -
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Residues in contact with MET 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LYS* 4.6 10.8 - - - +
314A TYR* 3.7 36.1 - - + -
420A PHE* 3.1 29.8 + - + +
421A SER* 4.2 19.3 - - - +
423A LEU* 1.3 80.6 - - + +
425A ASN* 1.3 58.6 + - + +
427A PHE* 3.2 15.8 + - + +
428A VAL* 3.0 27.5 + - + +
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Residues in contact with ASN 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A SER* 3.0 21.9 + - - +
422A ARG* 4.1 10.5 - - - +
424A MET* 1.3 74.6 - - - +
426A ALA* 1.3 53.5 + - - +
428A VAL* 3.1 18.1 - - - +
429A THR* 2.5 48.7 + - - +
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Residues in contact with ALA 426 (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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392A THR* 6.0 0.9 - - + -
395A LEU* 4.9 11.7 - - + -
396A ILE* 3.7 32.3 - - + -
399A LEU* 5.0 2.2 - - + -
422A ARG 2.9 21.6 + - - +
423A LEU* 3.2 10.5 + - - +
425A ASN* 1.3 76.4 - - - +
427A PHE* 1.3 57.3 + - - +
429A THR* 3.2 7.2 + - - -
430A ILE* 2.8 34.7 + - - +
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Residues in contact with PHE 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PRO* 5.5 1.1 - - + -
83A VAL* 3.8 36.8 - - + -
316A LEU* 5.6 14.6 - - + -
396A ILE* 3.5 26.0 - - + -
423A LEU* 2.8 41.4 + - + -
424A MET* 3.2 16.1 + - + +
426A ALA* 1.3 77.1 - - - +
428A VAL* 1.3 56.4 + - - +
430A ILE* 4.0 3.1 - - - +
431A GLN* 3.0 29.6 + - - +
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Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A THR* 5.8 5.5 - - - +
250A LYS* 5.0 30.1 - - + +
314A TYR* 5.5 2.9 - - + -
424A MET* 3.0 10.8 + - + +
425A ASN* 3.0 35.9 - - - +
427A PHE* 1.3 76.9 - - - +
429A THR* 1.3 65.0 + - + +
431A GLN* 3.8 6.1 - - + +
432A ASN* 2.9 28.1 + - + +
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Residues in contact with THR 429 (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 LYS* 5.6 2.0 - - - -
392A THR* 4.4 9.8 - - - +
425A ASN* 2.5 42.7 + - - +
426A ALA* 3.2 13.9 + - - -
428A VAL* 1.3 80.0 - - + +
430A ILE* 1.3 58.7 + - - +
432A ASN* 3.2 10.1 + - + +
433A ASP* 2.9 40.7 + - - +
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Residues in contact with ILE 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 5.4 9.6 - - + -
82A PRO* 4.9 15.7 - - + -
83A VAL* 5.1 11.2 - - + +
85A CYS* 6.3 1.8 - - + -
389A VAL* 4.6 9.7 - - + +
392A THR* 3.5 42.2 - - + +
393A SER* 3.5 14.4 - - - +
396A ILE* 3.7 23.1 - - + -
426A ALA 2.8 24.6 + - - +
427A PHE 4.0 2.9 - - - +
429A THR* 1.3 71.9 + - - +
431A GLN* 1.3 64.5 + - - +
433A ASP* 3.2 5.8 + - + +
434A VAL* 3.0 28.6 + - + +
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Residues in contact with GLN 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A CYS* 2.9 40.9 - - - +
86A TYR* 3.7 26.7 + - + +
88A PRO* 5.8 0.9 - - - +
249A THR* 3.8 17.9 - - + +
250A LYS 5.3 3.1 - - - +
317A SER* 5.7 2.0 + - - -
427A PHE 3.0 20.3 + - - +
428A VAL* 3.8 7.0 - - + +
430A ILE* 1.3 79.1 - - - +
432A ASN* 1.3 57.9 + - - +
433A ASP 3.0 1.0 + - - -
434A VAL* 3.2 5.0 + - - +
435A ASN* 2.9 60.6 + - - +
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Residues in contact with ASN 432 (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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249A THR* 5.5 2.0 + - + +
428A VAL* 2.9 21.8 + - + +
429A THR* 3.2 14.0 + - + +
431A GLN* 1.3 73.8 - - - +
433A ASP* 1.3 60.1 + - - +
435A ASN* 3.1 19.7 + - - +
436A ALA* 3.2 13.5 - - - +
442A LYS* 4.6 1.2 + - - +
443A ALA* 3.5 25.3 - - - +
444A GLN* 5.3 6.3 - - - +
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Residues in contact with ASP 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LEU* 5.0 4.2 - - - +
388A LYS* 2.5 48.6 + - + +
389A VAL* 3.9 22.4 - - + +
392A THR* 3.1 16.0 + - - +
429A THR* 2.9 23.0 + - - +
430A ILE* 3.6 6.3 - - + +
431A GLN 3.0 0.4 - - - -
432A ASN* 1.3 82.2 - - - +
434A VAL* 1.3 60.2 + - - +
435A ASN 3.4 0.2 - - - -
436A ALA* 3.5 5.5 + - - +
437A PHE* 3.1 24.3 + - - +
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Residues in contact with VAL 434 (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 LEU* 5.1 6.7 - - + -
85A CYS* 3.4 37.5 - - + -
357A MET* 5.9 1.3 - - + -
360A LEU* 3.6 39.5 - - + -
389A VAL* 4.3 8.3 - - + +
430A ILE* 3.0 22.1 + - + +
431A GLN* 3.2 9.9 - - - +
433A ASP* 1.3 73.7 - - - +
435A ASN* 1.3 63.8 + - - +
437A PHE* 3.1 9.9 + - + +
438A ILE* 3.1 25.6 + - + +
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Residues in contact with ASN 435 (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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85A CYS* 5.6 1.1 - - - -
88A PRO* 4.6 9.0 - - + -
249A THR* 2.6 40.2 - - + +
431A GLN* 2.9 41.0 + - - +
432A ASN* 3.1 15.9 + - - +
434A VAL* 1.3 76.3 - - - +
436A ALA* 1.3 73.3 + - - +
438A ILE* 3.3 14.6 - - + +
439A ASP* 2.7 32.4 + - - +
442A LYS* 3.0 28.3 + - + +
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Residues in contact with ALA 436 (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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385A LEU* 4.2 18.9 - - + +
432A ASN 3.2 20.4 - - - +
433A ASP* 3.5 8.0 + - - +
434A VAL 3.2 0.4 - - - -
435A ASN* 1.3 85.2 + - - +
437A PHE* 1.3 60.2 + - - +
439A ASP 2.8 21.4 + - - +
440A SER* 4.9 1.4 - - - -
442A LYS* 3.8 2.2 - - - +
443A ALA* 4.3 13.0 - - + -
455A GLY* 5.3 2.9 - - - -
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Residues in contact with PHE 437 (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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360A LEU* 4.9 20.6 - - + -
361A VAL 5.6 5.6 - - - -
363A PRO* 5.8 1.8 - - + -
382A GLN* 4.0 29.4 - - + -
385A LEU* 3.5 31.8 - - + +
386A LEU* 3.9 35.7 - - + -
389A VAL* 4.9 4.7 - - + -
433A ASP 3.1 14.1 + - - +
434A VAL* 3.1 13.0 + - + +
436A ALA* 1.3 77.0 - - - +
438A ILE* 1.3 65.7 + - + +
455A GLY* 4.0 5.4 - - - -
456A VAL* 3.2 45.6 + - + +
1191B ALA* 4.8 18.2 - - + -
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Residues in contact with ILE 438 (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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87A ASN* 4.5 6.5 - - - +
88A PRO* 3.6 30.7 - - + +
89A LEU* 4.3 20.8 - - + +
434A VAL* 3.1 10.7 + - + +
435A ASN* 3.3 24.0 - - - +
437A PHE* 1.3 87.8 - - + +
439A ASP* 1.3 57.3 + - + +
456A VAL* 3.6 31.9 - - + +
457A LYS* 3.9 9.6 - - - +
1191B ALA 5.0 0.7 - - - +
1192B MET* 3.9 32.5 - - + +
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Residues in contact with ASP 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PRO* 4.8 10.3 - - + +
248A PHE* 5.2 2.6 - - - -
435A ASN 2.7 21.0 + - - +
436A ALA* 2.8 24.8 - - - +
437A PHE 3.5 1.0 - - - -
438A ILE* 1.3 82.5 - - + +
440A SER* 1.3 70.3 + - - +
441A THR* 3.1 28.5 + - - +
442A LYS* 3.2 31.1 + - - +
443A ALA* 5.2 0.2 - - - +
457A LYS* 3.5 17.8 + - - +
458A GLN* 4.9 1.1 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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