Contacts of the strand formed by residues 429 - 447 (chain A) in PDB entry 3M8B
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 429 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A LEU* 3.3 5.1 - - - -
426A THR* 2.6 49.1 + - - +
427A ALA* 4.1 7.6 - - + +
428A GLY* 1.3 76.5 - - - +
430A ASN* 1.3 69.5 + - - +
431A TRP* 3.4 16.2 - - + -
468A ALA* 4.2 10.5 - - + -
469A ASN 3.8 7.6 - - - +
470A PHE* 3.7 30.5 - - + -
603A C8E 6.5 0.2 - - + -
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Residues in contact with ASN 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLY 3.5 5.8 - - - +
425A LEU* 3.6 26.1 - - - +
428A GLY 4.9 3.8 + - - -
429A VAL* 1.3 71.1 - - - +
431A TRP* 1.3 59.2 + - - +
468A ALA* 3.2 4.0 - - - +
469A ASN* 2.9 57.2 + - - +
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Residues in contact with TRP 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TYR* 3.9 15.7 - + - -
422A PHE* 3.5 23.8 - - + -
423A GLU* 3.5 8.8 - - - +
424A GLY* 3.0 43.4 + - - +
426A THR* 2.8 24.9 + - - -
429A VAL* 3.4 26.2 - - + -
430A ASN* 1.3 74.1 - - - +
432A ARG* 1.3 73.2 + - - +
433A ILE* 4.4 2.2 - - + -
467A THR* 3.3 14.1 - - - +
468A ALA* 4.3 4.7 - - + -
602A C8E 3.8 32.5 - - + -
603A C8E 4.0 44.6 - - + +
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Residues in contact with ARG 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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22A VAL 4.9 3.6 + - - -
23A LEU 2.7 28.3 + - - -
24A ALA 4.5 2.6 + - - -
25A PRO* 3.8 36.5 - - - +
386A ILE* 3.4 18.2 - - - +
419A GLU* 5.3 1.2 + - - -
421A ALA* 4.1 10.4 - - + +
422A PHE 3.5 14.6 - - - +
423A GLU* 2.9 34.0 + - + +
431A TRP* 1.3 82.9 - - - +
433A ILE* 1.3 66.6 + - - +
434A SER* 3.6 16.3 + - - +
465A GLU* 3.8 5.2 - - - +
466A ALA* 3.3 3.1 - - - +
467A THR* 2.9 42.6 + - - +
603A C8E 4.9 1.4 - - - +
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Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ALA* 3.3 1.8 - - - -
422A PHE* 3.0 44.0 + - + +
431A TRP* 4.4 2.2 - - + -
432A ARG* 1.3 75.8 - - - +
434A SER* 1.3 64.1 + - - +
464A VAL* 4.2 7.9 - - + -
465A GLU 3.2 9.4 - - - +
466A ALA* 4.1 8.5 - - + -
602A C8E 5.7 1.3 - - + -
603A C8E 3.6 67.8 - - + -
605A C8E 4.0 29.6 - - + +
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Residues in contact with SER 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO* 4.2 4.0 - - - +
69A ARG* 4.3 1.3 + - - -
419A GLU* 3.1 29.4 + - - -
420A GLY 3.4 8.7 - - - -
421A ALA* 3.5 14.4 - - - +
432A ARG* 3.6 15.1 + - - +
433A ILE* 1.3 72.4 - - - +
435A GLY* 1.3 58.0 + - - +
436A TYR* 5.2 1.1 - - - -
464A VAL* 3.2 7.6 - - - +
465A GLU* 2.8 50.1 + - - +
605A C8E 4.0 5.6 - - - -
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Residues in contact with GLY 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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419A GLU* 3.3 3.4 - - - +
420A GLY 3.0 33.2 + - - -
434A SER* 1.3 73.0 - - - +
436A TYR* 1.3 61.2 + - - -
463A GLY 3.2 9.4 - - - -
464A VAL* 4.4 1.8 - - - -
605A C8E 3.5 29.9 - - - +
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Residues in contact with TYR 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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69A ARG* 3.2 80.6 + - + +
417A GLN* 5.1 8.1 - - - +
418A TRP 3.1 11.4 - - - +
419A GLU* 4.0 15.3 - - + +
434A SER 5.0 2.5 - - - -
435A GLY* 1.3 76.8 - - - +
437A ARG* 1.3 66.6 + - - +
438A ASN* 4.9 6.5 - - + -
461A ILE* 4.3 10.3 - - + -
462A LYS* 3.4 0.3 - - - -
463A GLY* 2.9 59.4 + - - -
464A VAL 4.1 8.2 + - - -
465A GLU* 4.7 2.7 - - + -
482A ASP* 5.2 3.5 + - - -
483A TYR 4.0 0.9 + - - -
484A VAL* 3.8 17.7 - - - +
605A C8E 3.1 10.0 - - - -
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Residues in contact with ARG 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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416A LYS 3.7 0.9 - - - +
417A GLN* 3.1 7.1 - - - +
418A TRP* 2.8 65.3 + - + +
436A TYR* 1.3 76.2 - - - +
438A ASN* 1.3 62.9 + - - +
439A ASP* 3.3 32.1 + - - +
460A ARG* 3.5 26.6 - - + +
461A ILE 3.3 8.5 - - - +
462A LYS* 4.5 14.5 - - + +
605A C8E 4.1 13.2 - - - +
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Residues in contact with ASN 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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69A ARG 5.5 0.2 + - - -
71A THR* 3.5 29.3 - - - +
123A ILE* 4.0 4.4 + - - +
124A GLY* 5.3 0.6 - - - -
415A SER* 2.7 21.1 + - - -
416A LYS 3.5 2.5 - - - -
417A GLN* 3.3 30.8 + - + +
436A TYR* 5.0 6.1 - - + -
437A ARG* 1.3 74.7 - - - +
439A ASP* 1.3 63.7 + - - +
440A VAL* 3.4 14.4 + - - +
459A ALA 3.6 1.4 - - - +
460A ARG* 3.5 4.3 - - - -
461A ILE* 2.8 52.6 + - + +
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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
----------------------------------------------------------
414A LYS 3.7 1.0 - - - +
415A SER* 3.4 1.9 - - - -
416A LYS* 2.9 44.4 + - + +
418A TRP* 3.6 15.4 - - + -
437A ARG* 3.3 44.5 + - - -
438A ASN* 1.3 72.5 - - - +
440A VAL* 1.3 64.2 + - - +
441A SER* 5.0 2.2 + - - -
459A ALA 3.5 4.5 - - - +
460A ARG* 3.6 13.4 - - - +
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 5.4 1.1 - - + -
75A HIS* 4.2 19.1 - - + +
123A ILE* 5.2 1.6 - - + -
413A GLU* 5.1 0.7 - - + -
414A LYS 3.3 13.2 - - - +
415A SER* 4.3 7.2 - - - -
438A ASN* 3.4 31.4 - - - +
439A ASP* 1.3 73.5 - - - +
441A SER* 1.3 68.4 + - - +
443A LEU* 3.6 29.2 - - + -
458A LYS* 3.3 5.4 - - - +
459A ALA* 2.8 48.8 + - + +
461A ILE* 4.9 7.0 - - + -
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Residues in contact with SER 441 (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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413A GLU* 3.8 2.6 - - - +
414A LYS* 2.9 43.5 + - - +
416A LYS* 6.2 0.2 - - - -
439A ASP* 5.0 2.3 + - - -
440A VAL* 1.3 77.0 - - - +
442A ASP* 1.3 72.9 + - - +
443A LEU 3.1 4.0 + - - -
457A GLY 3.7 6.3 - - - -
458A LYS* 4.3 21.1 - - - +
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Residues in contact with ASP 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ASP* 5.4 5.3 - - + +
412A PRO 3.9 12.2 - - - +
413A GLU* 3.6 8.6 - - - +
414A LYS* 3.7 22.2 - - - +
441A SER* 1.3 80.7 + - - +
443A LEU* 1.3 67.0 + - - +
444A ILE 3.3 1.2 + - - -
455A ASN* 2.9 42.4 + - - +
456A GLU* 4.1 7.4 + - - +
457A GLY 3.3 6.5 + - - -
458A LYS* 5.1 0.8 - - - +
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Residues in contact with LEU 443 (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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72A ASN* 4.2 14.6 - - - +
75A HIS* 3.9 9.0 - - + -
413A GLU* 3.6 25.4 - - + +
440A VAL* 3.6 25.8 - - + -
441A SER 3.1 0.4 - - - +
442A ASP* 1.3 75.8 - - - +
444A ILE* 1.3 60.9 - - - +
445A ASP* 3.2 14.6 + - - +
456A GLU 3.0 22.2 + - - -
457A GLY* 3.0 34.4 + - - +
458A LYS* 4.0 16.6 - - - +
459A ALA* 4.0 13.5 - - + +
495A LEU* 6.4 0.2 - - + -
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Residues in contact with ILE 444 (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 ALA 4.8 1.6 - - - +
396A PRO* 3.8 31.0 - - + -
400A GLN* 3.2 45.0 + - - +
410A LEU* 3.8 23.3 - - + -
411A ASP 4.3 1.6 - - - +
413A GLU* 2.7 37.9 + - + +
443A LEU* 1.3 70.1 - - - +
445A ASP* 1.3 62.3 + - - +
453A TYR* 3.8 21.9 - - + -
454A TYR 3.5 4.7 - - - +
455A ASN* 3.9 15.0 - - - +
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Residues in contact with ASP 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 3.2 16.4 + - - +
444A ILE* 1.3 79.6 - - - +
446A TYR* 1.3 68.6 + - - +
447A ASP 3.6 0.9 + - - -
453A TYR* 3.4 5.2 - - - -
454A TYR* 2.9 36.1 + - - +
456A GLU* 4.2 14.9 - - + +
457A GLY* 3.3 26.9 + - - -
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Residues in contact with TYR 446 (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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405A TYR* 3.8 33.0 - + + -
445A ASP* 1.3 78.1 - - - +
447A ASP* 1.3 66.9 + - - +
448A ASP* 3.7 22.3 + - + -
451A LEU* 2.8 56.8 - - - +
452A LYS 3.8 9.9 - - - -
453A TYR* 3.6 24.2 - + + +
456A GLU* 5.2 1.4 - - - +
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Residues in contact with ASP 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ASP 3.6 0.4 + - - -
446A TYR* 1.3 77.8 - - - +
448A ASP* 1.3 63.5 + - - +
449A HIS* 3.2 17.2 + - - +
450A THR* 2.7 31.5 + - - +
451A LEU* 2.9 29.3 + - - -
452A LYS 2.9 18.1 + - - +
454A TYR* 3.8 17.0 - - + -
456A GLU* 4.6 11.0 - - - +
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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