Contacts of the helix formed by residues 431 - 448 (chain A) in PDB entry 3MBK
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 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A GLU* 2.7 38.8 + - + +
384A MET* 3.7 43.7 - - - +
387A VAL* 4.1 4.7 - - + -
388A PHE* 4.7 0.4 - - + -
409A ASN* 3.3 23.6 - - - +
411A PRO* 4.9 2.9 - - - -
430A ILE* 1.3 75.8 - - - +
432A VAL* 1.3 65.4 + - - +
433A PHE 3.4 1.0 + - - -
434A GLY 2.9 13.5 + - - -
435A CYS* 2.9 24.4 + - - -
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A ARG* 4.7 2.0 - - - +
408A LEU 3.7 11.4 - - - +
409A ASN* 3.0 18.3 + - - +
410A MET 3.4 32.5 - - - +
411A PRO* 3.7 10.7 - - + +
412A HIS* 6.0 1.8 - - + -
431A THR* 1.3 73.4 - - - +
433A PHE* 1.3 63.0 + - + +
435A CYS* 3.2 11.4 + - + +
436A MET* 3.0 45.9 + - + +
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Residues in contact with PHE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLU* 3.6 14.4 - - - +
408A LEU 5.6 2.0 - - - -
409A ASN* 2.9 35.5 + - + +
431A THR 3.2 0.2 - - - -
432A VAL* 1.3 81.5 - - + +
434A GLY* 1.3 57.8 + - - +
436A MET* 3.2 31.0 + - + +
437A GLN* 2.9 42.2 + - + +
623A HIS* 4.9 17.7 - + + -
626A THR* 5.9 3.4 - - - -
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Residues in contact with GLY 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLY* 4.0 6.3 - - - -
382A GLU* 3.4 18.4 - - - +
430A ILE* 3.8 9.1 - - - +
431A THR* 2.9 17.3 + - - -
433A PHE* 1.3 74.5 - - - +
435A CYS* 1.3 63.3 + - - +
437A GLN* 3.4 17.1 + - - +
438A ALA* 3.1 23.0 + - - +
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Residues in contact with CYS 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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411A PRO* 6.0 6.1 - - - -
430A ILE* 3.6 24.8 - - - +
431A THR 2.9 19.1 + - - -
432A VAL* 3.2 12.5 + - + +
434A GLY* 1.3 74.8 - - - +
436A MET* 1.3 59.8 + - + +
438A ALA* 3.3 3.5 + - - +
439A ARG* 2.9 47.6 + - - +
469A ASN* 3.7 20.7 - - - +
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Residues in contact with MET 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A VAL* 3.0 25.3 + - + +
433A PHE* 3.2 58.1 + - + +
435A CYS* 1.3 75.5 - - + +
437A GLN* 1.3 65.1 + - - +
439A ARG* 3.3 14.3 + - - +
440A LEU* 2.9 35.1 + - + +
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Residues in contact with GLN 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLY* 3.5 4.9 - - - -
382A GLU* 2.9 40.8 + - - +
433A PHE* 2.9 25.3 + - + +
434A GLY* 3.4 4.1 - - - +
435A CYS 3.4 0.2 - - - -
436A MET* 1.3 76.2 - - - +
438A ALA* 1.3 63.2 + - - +
440A LEU* 3.3 4.0 + - + +
441A VAL* 3.1 28.2 + - - +
596A TYR* 3.5 18.0 - - - +
597A LEU* 3.7 15.3 - - + -
621A LEU* 4.0 17.5 - - + +
623A HIS* 3.0 38.5 + - + +
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Residues in contact with ALA 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLY 3.1 11.3 + - - +
435A CYS* 3.5 9.0 - - - +
437A GLN* 1.3 79.9 - - - +
439A ARG* 1.3 61.8 + - - +
441A VAL* 3.2 2.3 + - - +
442A GLY 3.0 17.8 + - - -
466A THR* 3.5 40.4 - - + +
469A ASN* 3.5 12.6 - - + -
470A ILE* 3.5 16.1 - - + +
597A LEU* 3.9 8.0 - - - +
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Residues in contact with ARG 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A CYS* 2.9 31.0 + - - +
436A MET* 3.7 13.6 - - - +
438A ALA* 1.3 74.8 - - - +
440A LEU* 1.3 58.5 + - + +
442A GLY 3.2 1.2 + - - -
443A GLU* 2.8 52.0 + - - +
469A ASN* 2.9 38.1 + - - +
472A LYS* 4.7 19.7 - - - +
473A GLY* 3.6 16.6 - - - +
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Residues in contact with LEU 440 (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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436A MET* 2.9 26.0 + - + +
437A GLN* 3.7 5.2 - - + +
439A ARG* 1.3 77.3 - - + +
441A VAL* 1.3 58.7 + - - +
443A GLU* 3.4 22.1 + - + +
444A ALA* 2.9 29.3 + - - +
621A LEU* 4.3 29.6 - - + -
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Residues in contact with VAL 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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437A GLN 3.1 14.2 + - - +
438A ALA 3.6 7.2 - - - +
440A LEU* 1.3 77.3 - - - +
442A GLY* 1.3 57.7 + - - +
444A ALA* 3.2 6.9 + - - +
445A LEU* 2.9 34.2 + - + +
470A ILE* 4.5 8.7 - - + -
597A LEU* 3.8 34.1 - - + +
599A PHE* 4.1 19.7 - - + -
618A ILE* 3.8 23.5 - - + +
621A LEU* 4.4 14.1 - - + -
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Residues in contact with GLY 442 (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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438A ALA 3.0 11.3 + - - -
439A ARG 3.6 2.7 - - - -
441A VAL* 1.3 78.1 - - - +
443A GLU* 1.3 60.6 + - - +
445A LEU* 3.3 7.3 + - - +
446A LEU* 3.0 19.1 + - - +
470A ILE* 3.4 34.0 - - - +
473A GLY 3.5 10.9 - - - +
474A LEU* 3.7 6.5 + - - -
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ARG* 2.8 42.0 + - - +
440A LEU* 3.7 23.1 - - + +
442A GLY* 1.3 72.9 - - - +
444A ALA* 1.3 57.8 + - - +
446A LEU* 3.3 5.7 + - + +
447A GLU* 2.9 45.7 + - - +
473A GLY* 3.5 19.6 - - - +
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Residues in contact with ALA 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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440A LEU 2.9 18.3 + - - +
441A VAL* 3.2 7.4 + - - +
443A GLU* 1.3 75.4 - - - +
445A LEU* 1.3 64.0 + - - +
447A GLU* 3.3 9.4 + - - +
448A SER* 3.0 25.8 + - - -
618A ILE* 3.6 23.2 - - + +
619A LEU 5.6 1.6 - - - +
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Residues in contact with LEU 445 (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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376A PHE* 4.9 0.7 - - + -
441A VAL* 2.9 31.6 + - + +
442A GLY* 3.3 7.8 + - - +
444A ALA* 1.3 76.1 - - - +
446A LEU* 1.3 62.1 + - - +
448A SER* 2.8 18.3 + - - -
450A THR* 3.0 46.1 + - + +
452A ILE* 4.4 19.7 - - + -
470A ILE* 4.3 17.5 - - + -
474A LEU* 4.0 9.2 - - + -
561A LEU* 4.9 3.4 - - + -
599A PHE* 4.1 25.6 - - + -
617A PRO* 4.3 5.4 - - + -
618A ILE* 3.7 18.8 - - + +
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Residues in contact with LEU 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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442A GLY 3.0 13.3 + - - +
443A GLU* 3.6 9.2 - - + +
445A LEU* 1.3 77.0 - - - +
447A GLU* 1.3 60.2 + - + +
449A ASN* 2.9 26.0 + - - +
450A THR 4.9 1.8 - - - +
473A GLY 3.9 12.6 - - - +
474A LEU* 3.7 25.0 - - + +
475A GLN* 3.6 35.2 - - + +
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Residues in contact with GLU 447 (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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443A GLU* 2.9 33.7 + - - +
444A ALA* 3.8 8.4 - - - +
445A LEU 3.3 0.2 - - - -
446A LEU* 1.3 80.9 - - + +
448A SER* 1.3 56.5 + - - +
449A ASN* 3.2 13.2 + - - +
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Residues in contact with SER 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ALA 3.0 14.6 + - - -
445A LEU* 2.8 13.2 + - - -
447A GLU* 1.3 74.9 - - - +
449A ASN* 1.3 71.2 + - - +
450A THR* 2.6 27.9 + - - -
617A PRO* 3.6 25.5 + - - +
618A ILE* 4.0 2.4 - - - +
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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
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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