Contacts of the helix formed by residues 445 - 462 (chain H) in PDB entry 4D1Q
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 GLU 445 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444H GLN* 1.3 81.1 - - + +
446H LYS* 1.3 64.6 + - + +
447H VAL* 3.5 0.4 - - - -
448H ALA* 3.8 15.2 + - - +
449H GLN* 3.7 15.3 - - - +
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Residues in contact with LYS 446 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427H ILE* 5.2 3.6 - - + +
430H TYR* 3.5 48.6 + - + -
442H MET* 3.8 42.8 - - + -
444H GLN* 2.5 12.9 + - + +
445H GLU* 1.3 75.8 - - + +
447H VAL* 1.3 62.7 + - - +
448H ALA 3.0 0.9 + - - -
449H GLN* 3.3 32.9 + - + +
450H ILE* 2.9 30.6 + - + +
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Residues in contact with VAL 447 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434H PHE* 4.6 12.6 - - + -
442H MET* 3.5 11.8 + - - +
443H GLN* 4.0 9.0 - - - +
444H GLN 2.8 27.1 + - - +
445H GLU 4.9 0.2 - - - -
446H LYS* 1.3 72.4 - - - +
448H ALA* 1.3 68.8 + - + +
450H ILE* 3.5 10.0 - - - +
451H LYS* 3.1 19.9 + - + +
524H PHE* 4.3 11.8 - - + -
528H ARG* 2.9 50.3 - - - +
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Residues in contact with ALA 448 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445H GLU* 3.9 11.7 - - - +
446H LYS 3.0 0.6 + - - -
447H VAL* 1.3 83.5 - - + +
449H GLN* 1.3 58.3 + - + +
451H LYS* 2.9 23.5 + - - +
452H GLU* 3.0 10.5 + - - +
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Residues in contact with GLN 449 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427H ILE* 4.4 17.7 - - + +
445H GLU* 3.7 11.7 - - - +
446H LYS* 3.5 39.5 + - + +
448H ALA* 1.3 76.5 - - - +
450H ILE* 1.3 64.8 + - - +
452H GLU* 3.5 20.3 - - - +
453H PHE* 3.1 22.0 + - - +
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Residues in contact with ILE 450 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427H ILE* 4.1 20.6 - - + -
430H TYR* 3.5 31.4 - - + +
431H THR* 3.8 13.7 - - + -
434H PHE* 3.3 43.7 - - + -
442H MET* 4.3 10.3 - - + -
446H LYS* 2.9 34.1 + - + +
447H VAL* 3.5 8.1 - - - +
448H ALA 3.1 0.2 - - - -
449H GLN* 1.3 75.5 - - - +
451H LYS* 1.3 54.3 + - - +
453H PHE* 3.1 7.3 + - - +
454H CYS* 2.8 35.2 + - - -
524H PHE* 4.2 0.7 - - + -
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Residues in contact with LYS 451 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447H VAL* 3.1 6.6 + - + +
448H ALA* 2.9 10.8 + - - +
450H ILE* 1.3 77.8 - - - +
452H GLU* 1.3 65.9 + - - +
454H CYS* 3.8 0.2 - - - +
455H LEU* 3.1 47.7 + - + +
521H SER* 4.5 16.1 + - - -
524H PHE* 3.2 42.1 - - + -
525H GLU* 2.7 45.8 + - - +
528H ARG* 5.9 1.3 - - - +
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Residues in contact with GLU 452 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448H ALA 3.0 7.3 + - - +
449H GLN* 3.5 24.7 - - - +
451H LYS* 1.3 77.6 - - - +
453H PHE* 1.3 61.8 + - - +
455H LEU* 3.6 8.5 + - - +
456H SER* 3.1 22.1 + - - -
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Residues in contact with PHE 453 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427H ILE* 3.6 34.8 - - + -
428H TRP* 3.8 45.1 - + - -
431H THR* 3.7 34.3 - - + -
449H GLN 3.1 9.6 + - - +
450H ILE 3.1 7.8 + - - +
452H GLU* 1.3 78.6 - - - +
454H CYS* 1.3 64.8 + - - +
456H SER* 3.1 9.4 + - - -
457H LYS* 2.9 57.0 + - + +
557H LEU* 5.3 2.0 - - + -
561H LEU* 4.5 6.7 - - + -
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Residues in contact with CYS 454 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431H THR* 3.9 15.0 - - - -
434H PHE* 5.0 0.2 - - - -
435H PHE* 3.9 20.6 - - - -
450H ILE* 2.8 33.5 + - - +
451H LYS 3.8 4.7 - - - +
453H PHE* 1.3 75.7 - - - +
455H LEU* 1.3 52.3 + - - +
457H LYS* 3.4 3.5 + - - +
458H MET* 2.7 53.8 + - + +
524H PHE* 3.7 24.5 - - + -
554H LEU* 4.9 0.9 - - + -
557H LEU* 4.1 11.7 - - + +
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Residues in contact with LEU 455 (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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451H LYS* 3.1 50.0 + - + +
452H GLU* 3.7 6.5 - - - +
454H CYS* 1.3 74.7 - - - +
456H SER* 1.3 67.7 + - - +
458H MET* 2.9 33.9 + - + +
459H GLU* 3.0 21.5 + - + +
520H PRO* 3.8 20.9 - - + -
521H SER* 4.1 20.2 - - - +
524H PHE* 4.6 4.0 - - + -
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Residues in contact with SER 456 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452H GLU* 3.1 12.7 + - - -
453H PHE* 3.1 14.7 + - - -
455H LEU* 1.3 79.8 - - - +
457H LYS* 1.3 72.5 + - - +
459H GLU* 3.4 18.9 + - - +
460H ASP* 3.5 14.8 + - - +
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Residues in contact with LYS 457 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H ASP* 4.3 17.8 - - - +
261H ILE* 6.2 1.6 - - - -
428H TRP* 4.1 26.0 - - + -
453H PHE* 2.9 45.1 + - + +
454H CYS* 3.5 8.5 - - - +
456H SER* 1.3 89.1 + - - +
458H MET* 1.3 62.7 + - - +
459H GLU 3.0 5.9 + - - -
460H ASP* 3.1 27.8 + - - +
461H LEU* 3.5 9.6 + - - +
557H LEU* 4.1 24.2 - - + -
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Residues in contact with MET 458 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454H CYS* 2.7 40.7 + - + +
455H LEU* 2.9 25.6 + - + +
457H LYS* 1.3 71.2 - - - +
459H GLU* 1.3 62.5 + - - +
460H ASP 3.4 0.2 - - - -
461H LEU* 3.6 10.9 + - + +
462H GLU* 3.4 26.0 + - - +
520H PRO* 4.3 27.1 - - + +
523H GLU* 5.3 0.7 - - - +
524H PHE* 4.9 2.0 - - + -
553H LYS* 3.7 29.2 - - + +
554H LEU* 3.6 45.3 - - + -
557H LEU* 4.4 11.9 - - + -
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Residues in contact with GLU 459 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455H LEU* 3.0 21.6 + - + +
456H SER* 3.4 12.8 - - - +
457H LYS 3.0 0.4 - - - -
458H MET* 1.3 79.5 - - - +
460H ASP* 1.3 64.0 + - - +
462H GLU* 3.1 36.7 + - - +
463H LEU* 3.4 15.3 + - - +
520H PRO* 3.7 23.4 - - - +
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Residues in contact with ASP 460 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H ASP* 4.9 12.2 - - - +
456H SER* 3.5 19.8 + - - +
457H LYS* 3.1 25.1 + - - +
459H GLU* 1.3 76.8 - - - +
461H LEU* 1.3 59.9 + - - +
462H GLU 3.1 1.6 - - - -
463H LEU* 2.9 43.8 + - + +
464H ILE* 3.8 5.9 + - - +
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Residues in contact with LEU 461 (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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172H LYS* 3.9 33.0 - - + +
173H ASP* 4.2 13.2 - - + +
457H LYS 3.5 8.7 + - - +
458H MET* 3.6 12.1 + - + +
459H GLU 3.3 0.6 - - - -
460H ASP* 1.3 74.1 - - - +
462H GLU* 1.3 57.8 + - + +
463H LEU 3.1 4.9 - - - -
464H ILE* 3.0 37.0 - - + +
553H LYS* 4.8 6.7 - - + +
556H LYS* 3.7 53.1 + - + +
557H LEU* 4.3 15.3 - - + +
560H SER* 5.6 2.2 - - - +
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Residues in contact with GLU 462 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458H MET* 3.4 15.6 - - - +
459H GLU* 3.1 33.2 + - - +
460H ASP 3.1 0.4 - - - -
461H LEU* 1.3 75.1 - - + +
463H LEU* 1.3 56.9 + - - +
464H ILE 3.1 6.8 + - - -
465H ASN* 2.9 24.4 + - - +
520H PRO* 3.9 16.1 - - - +
553H LYS* 3.7 40.1 + - + +
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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) + - + + + + + -
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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