Contacts of the helix formed by residues 457 - 472 (chain H) in PDB entry 6MZL
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 PRO 457 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444H ASN* 3.9 27.1 - - + +
445H GLN* 5.3 1.1 - - - +
448H TYR* 5.1 0.4 - - + -
456H GLY* 1.3 68.1 - - - -
458H LEU* 1.3 52.7 + - - +
459H LEU 3.1 2.0 - - - -
460H CYS* 2.8 10.2 + - + +
461H SER* 2.4 36.9 + - - -
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Residues in contact with LEU 458 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428H LEU* 3.6 24.2 - - + +
454H SER 5.2 2.2 - - - +
455H LEU* 3.1 8.4 + - - +
456H GLY 4.8 1.3 - - - +
457H PRO* 1.3 75.0 - - - +
459H LEU* 1.3 60.7 + - - +
461H SER* 3.7 10.8 - - - -
462H GLN* 2.8 31.2 + - - +
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Residues in contact with LEU 459 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428H LEU* 3.5 10.3 - - + +
432H ALA* 4.6 10.5 - - - +
435H LEU* 5.7 9.0 - - + -
447H ALA* 6.0 6.1 - - + -
451H GLU* 6.4 1.6 - - + -
455H LEU* 2.4 44.6 + - + +
456H GLY* 4.0 4.9 - - - +
458H LEU* 1.3 70.4 - - - +
460H CYS* 1.3 57.0 + - - +
462H GLN* 3.7 2.4 - - - +
463H VAL* 2.8 28.5 + - - +
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Residues in contact with CYS 460 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442H PRO 6.0 0.7 - - - +
444H ASN* 3.7 33.2 - - + +
447H ALA* 5.6 4.9 - - + -
457H PRO* 2.8 13.2 + - + +
459H LEU* 1.3 75.1 - - - +
461H SER* 1.3 60.9 + - - +
463H VAL* 3.4 8.7 - - - +
464H VAL* 2.8 27.7 + - - +
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Residues in contact with SER 461 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457H PRO* 2.4 30.2 + - - -
458H LEU* 3.8 10.3 - - - -
459H LEU 3.3 0.2 - - - -
460H CYS* 1.3 66.6 - - - +
462H GLN* 1.3 60.4 + - - +
464H VAL* 3.1 8.8 + - - +
465H LYS* 2.9 25.5 + - - +
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Residues in contact with GLN 462 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428H LEU* 4.8 11.0 - - + +
429H LYS* 5.5 9.4 - - + -
432H ALA* 4.1 19.5 - - + +
458H LEU 2.8 20.5 + - - +
459H LEU 3.9 2.5 - - - +
461H SER* 1.3 75.9 - - - +
463H VAL* 1.3 57.0 + - - +
465H LYS* 3.3 9.9 + - + +
466H ALA* 2.8 29.1 + - - +
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Residues in contact with VAL 463 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432H ALA* 4.7 5.8 - - - +
435H LEU 6.0 0.2 - - - -
436H ALA* 4.2 25.8 - - + +
441H PRO* 5.6 11.4 - - + -
459H LEU 2.8 19.9 + - - +
460H CYS* 3.4 11.4 - - - +
461H SER 3.1 0.2 - - - -
462H GLN* 1.3 75.4 - - - +
464H VAL* 1.3 59.3 + - - +
466H ALA* 3.3 6.9 + - - +
467H ARG* 2.9 29.6 + - - +
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Residues in contact with VAL 464 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441H PRO* 6.3 1.1 - - - +
460H CYS 2.8 13.7 + - - +
461H SER* 3.1 11.2 + - - +
463H VAL* 1.3 75.0 - - - +
465H LYS* 1.3 57.6 + - - +
467H ARG* 3.4 6.9 + - - +
468H ALA* 2.9 29.3 + - - +
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Residues in contact with LYS 465 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461H SER 2.9 13.2 + - - +
462H GLN* 3.4 14.1 - - + +
464H VAL* 1.3 77.7 - - - +
466H ALA* 1.3 56.5 + - - +
468H ALA* 3.3 8.2 + - - +
469H GLN* 2.9 27.0 + - - +
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Residues in contact with ALA 466 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432H ALA* 5.6 2.9 - - + -
433H PRO* 5.1 14.1 - - + -
436H ALA* 4.9 11.0 - - + -
462H GLN 2.8 16.6 + - - +
463H VAL* 3.3 8.0 + - - +
465H LYS* 1.3 74.4 - - - +
467H ARG* 1.3 61.2 + - - +
469H GLN* 3.2 8.1 + - - +
470H ALA* 2.9 28.9 + - - +
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Residues in contact with ARG 467 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436H ALA* 5.8 1.2 - - + +
441H PRO* 6.3 4.5 - - + -
463H VAL 2.9 17.8 + - - +
464H VAL* 3.7 7.4 - - - +
466H ALA* 1.3 76.7 - - - +
468H ALA* 1.3 58.7 + - - +
470H ALA* 3.3 7.2 + - - +
471H ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 468 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464H VAL 2.9 18.3 + - - +
465H LYS* 3.4 9.2 - - - +
466H ALA 3.2 0.2 - - - -
467H ARG* 1.3 76.9 - - - +
469H GLN* 1.3 57.1 + - - +
471H ALA* 3.3 6.2 + - - +
472H LEU* 2.9 28.9 + - - +
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Residues in contact with GLN 469 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465H LYS 2.9 16.3 + - - +
466H ALA* 3.2 9.4 + - - +
468H ALA* 1.3 76.7 - - - +
470H ALA* 1.3 62.4 + - - +
472H LEU* 3.5 17.7 + - - +
473H GLN* 4.4 1.7 + - - +
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Residues in contact with ALA 470 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466H ALA 2.9 16.7 + - - +
467H ARG* 3.6 8.5 - - - +
468H ALA 3.2 0.2 - - - -
469H GLN* 1.3 79.7 - - - +
471H ALA* 1.3 59.8 + - - +
472H LEU 3.2 1.3 + - - -
473H GLN* 3.6 14.9 + - - +
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Residues in contact with ALA 471 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467H ARG 2.9 17.4 + - - +
468H ALA* 3.6 6.1 - - - +
470H ALA* 1.3 74.2 - - - +
472H LEU* 1.3 63.6 + - - +
473H GLN 3.2 11.3 - - - +
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Residues in contact with LEU 472 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468H ALA 2.9 15.5 + - - +
469H GLN* 3.5 14.1 - - - +
470H ALA 3.2 1.4 - - - -
471H ALA* 1.3 75.8 - - - +
473H GLN* 1.3 62.6 + - - +
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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