Contacts of the helix formed by residues 431 - 448 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B GLU* 2.7 38.5 + - + +
384B MET* 3.7 43.1 - - - +
387B VAL* 4.2 5.2 - - + -
388B PHE* 4.7 0.2 - - + -
409B ASN* 3.3 23.6 - - - +
411B PRO* 4.9 2.7 - - - -
430B ILE* 1.3 76.1 - - - +
432B VAL* 1.3 63.7 + - - +
433B PHE 3.4 0.5 + - - -
434B GLY 2.9 13.9 + - - -
435B CYS* 2.9 25.1 + - - -
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ARG* 4.9 2.2 - - - +
408B LEU 3.6 11.0 - - - +
409B ASN* 2.9 20.4 + - - +
410B MET 3.5 32.8 - - - +
411B PRO* 3.7 10.9 - - + -
412B HIS* 6.2 0.7 - - - +
431B THR* 1.3 71.4 - - - +
433B PHE* 1.3 62.3 + - + +
435B CYS* 3.2 11.3 + - - +
436B MET* 3.0 43.3 + - + +
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Residues in contact with PHE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLU* 3.8 13.5 - - - +
408B LEU 5.5 2.5 - - - -
409B ASN* 2.9 36.6 + - + +
432B VAL* 1.3 79.3 - - + +
434B GLY* 1.3 58.8 + - - +
436B MET* 3.2 32.1 + - + +
437B GLN* 2.8 42.9 + - + +
623B HIS* 5.4 13.0 - + + -
626B THR* 6.1 1.8 - - - -
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Residues in contact with GLY 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLY* 4.0 5.4 - - - -
382B GLU* 3.5 19.6 - - - +
430B ILE* 3.9 8.9 - - - +
431B THR* 2.9 17.5 + - - -
433B PHE* 1.3 74.3 - - - +
435B CYS* 1.3 63.5 + - - +
437B GLN* 3.4 17.8 + - - +
438B ALA* 3.1 23.4 + - - +
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Residues in contact with CYS 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B PRO* 6.0 6.1 - - - -
430B ILE* 3.7 18.3 - - - +
431B THR 2.9 20.2 + - - -
432B VAL* 3.2 12.1 + - + +
434B GLY* 1.3 75.2 - - - +
436B MET* 1.3 59.1 + - + +
438B ALA* 3.3 2.9 + - - +
439B ARG* 2.9 45.2 + - - +
465B GLN* 5.9 0.4 - - - -
469B ASN* 3.7 32.0 - - - +
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Residues in contact with MET 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL* 3.0 20.8 + - + +
433B PHE* 3.2 56.7 + - + +
435B CYS* 1.3 75.1 - - + +
437B GLN* 1.3 65.6 + - - +
439B ARG* 3.3 13.4 + - - +
440B LEU* 2.9 34.7 + - + +
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Residues in contact with GLN 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLY* 3.4 4.7 - - - -
382B GLU* 2.8 41.3 + - - +
433B PHE* 2.8 29.5 + - + +
434B GLY* 3.4 5.5 + - - +
436B MET* 1.3 72.2 - - - +
438B ALA* 1.3 63.3 + - - +
440B LEU* 3.3 4.7 + - - +
441B VAL* 3.1 27.5 + - - +
596B TYR* 3.5 18.4 - - - +
597B LEU* 3.7 15.0 - - + -
621B LEU* 4.0 20.4 - - + +
623B HIS* 3.0 36.2 + - + +
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B GLY 3.1 11.2 + - - +
435B CYS* 3.5 8.7 - - - +
437B GLN* 1.3 79.5 - - - +
439B ARG* 1.3 62.2 + - - +
441B VAL* 3.2 1.9 + - - +
442B GLY 3.0 18.2 + - - -
466B THR* 3.5 40.6 - - + +
469B ASN* 3.5 11.9 - - + -
470B ILE* 3.4 16.6 - - + +
597B LEU* 3.9 8.0 - - - +
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Residues in contact with ARG 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B CYS* 2.9 33.5 + - - +
436B MET* 3.3 12.1 + - - +
438B ALA* 1.3 74.6 - - - +
440B LEU* 1.3 57.7 + - + +
442B GLY 3.2 1.2 + - - -
443B GLU* 2.8 44.6 + - - +
469B ASN* 2.7 44.5 + - - +
472B LYS* 4.2 29.1 - - + +
473B GLY* 3.5 8.4 - - - +
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B MET* 2.9 25.5 + - + +
437B GLN* 3.7 4.9 - - + +
439B ARG* 1.3 78.0 - - + +
441B VAL* 1.3 58.2 + - - +
443B GLU* 3.4 23.2 + - + +
444B ALA* 2.9 29.5 + - - +
621B LEU* 4.4 28.5 - - + -
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Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B GLN 3.1 14.3 + - - +
438B ALA 3.2 6.9 + - - +
440B LEU* 1.3 74.1 - - - +
442B GLY* 1.3 65.4 + - - +
444B ALA* 3.2 6.9 + - - +
445B LEU* 3.0 28.7 + - + +
470B ILE* 4.5 9.0 - - + -
597B LEU* 3.8 34.5 - - + +
599B PHE* 4.1 20.2 - - + -
618B ILE* 3.8 22.6 - - + +
619B LEU 6.1 0.4 - - - +
621B LEU* 4.6 13.2 - - + -
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Residues in contact with GLY 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ALA 3.0 11.5 + - - -
439B ARG 3.2 3.3 + - - -
441B VAL* 1.3 77.2 - - - +
443B GLU* 1.3 55.9 + - - +
445B LEU* 3.2 5.3 + - - +
446B LEU 2.9 23.6 + - - -
470B ILE* 3.4 33.8 - - - +
473B GLY 3.4 10.4 - - - +
474B LEU* 3.6 8.7 + - - +
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Residues in contact with GLU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ARG* 2.8 33.4 + - - +
440B LEU* 3.6 24.2 - - + +
442B GLY* 1.3 72.9 - - - +
444B ALA* 1.3 58.7 + - - +
446B LEU* 3.3 5.8 + - + +
447B GLU* 2.8 48.3 + - - +
473B GLY* 3.5 20.3 + - - +
475B GLN* 6.4 0.2 - - - +
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Residues in contact with ALA 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B LEU 2.9 17.4 + - - +
441B VAL* 3.2 7.6 + - - +
443B GLU* 1.3 72.9 - - - +
445B LEU* 1.3 65.4 + - - +
447B GLU* 3.4 10.8 + - - +
448B SER* 3.0 26.7 + - - -
618B ILE* 3.6 23.7 - - + +
619B LEU 5.5 2.2 - - - +
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Residues in contact with LEU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B PHE* 4.9 0.2 - - + -
441B VAL* 3.0 31.3 + - + +
442B GLY* 3.6 2.2 - - - +
444B ALA* 1.3 76.5 - - - +
446B LEU* 1.3 59.9 + - - +
448B SER* 3.0 7.3 + - - -
450B THR* 2.9 58.2 + - + +
452B ILE* 4.4 15.5 - - + -
470B ILE* 4.3 17.5 - - + -
474B LEU* 3.5 18.4 - - + -
561B LEU* 4.9 3.8 - - + -
599B PHE* 4.2 25.8 - - + -
617B PRO* 4.4 3.8 - - + -
618B ILE* 3.8 19.1 - - + -
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B GLY 2.9 14.2 + - - +
443B GLU* 3.5 9.0 - - + +
445B LEU* 1.3 76.6 - - - +
447B GLU* 1.3 63.7 + - + +
449B ASN* 2.9 21.7 + - - +
450B THR 5.2 0.4 - - - -
473B GLY 3.8 12.6 - - - +
474B LEU* 3.9 20.2 - - + +
475B GLN* 3.6 38.4 - - + +
476B GLN* 6.0 2.0 - - - +
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Residues in contact with GLU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B GLU* 2.8 38.7 + - - +
444B ALA* 3.9 9.2 - - - +
446B LEU* 1.3 77.3 - - + +
448B SER* 1.3 59.0 + - - +
449B ASN* 3.2 2.0 + - - +
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Residues in contact with SER 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ALA 3.0 18.6 + - - -
445B LEU* 3.0 6.8 + - - -
447B GLU* 1.3 74.9 - - - +
449B ASN* 1.3 67.9 + - - +
450B THR* 2.8 25.3 + - - -
617B PRO* 3.8 18.6 - - - -
618B ILE* 3.9 4.3 - - - +
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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