Contacts of the helix formed by residues 445 - 461 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444G GLN* 1.3 72.2 - - + +
446G LYS* 1.3 69.7 + - + +
447G VAL* 3.2 3.4 - - - -
448G ALA* 2.9 23.1 + - - +
449G GLN* 3.6 14.1 + - + +
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Residues in contact with LYS 446 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430G TYR* 3.9 45.1 + - + -
442G MET* 3.4 42.0 - - + +
444G GLN* 2.4 32.6 + - + +
445G GLU* 1.3 72.7 - - + +
447G VAL* 1.3 52.3 + - - +
448G ALA 2.7 0.5 + - - -
449G GLN* 2.7 54.9 + - - +
450G ILE* 2.7 24.3 + - + -
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Residues in contact with VAL 447 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434G PHE* 4.9 15.3 - - + -
439G ALA 6.1 0.9 - - - +
442G MET 3.6 10.5 + - - +
443G GLN* 3.4 25.4 - - + +
444G GLN 2.8 9.1 + - - +
445G GLU* 4.1 3.6 - - - +
446G LYS* 1.3 76.0 - - - +
448G ALA* 1.3 61.1 + - + +
450G ILE* 3.7 10.8 - - + +
451G LYS* 3.2 24.8 + - - +
524G PHE* 4.0 5.2 - - + -
528G ARG* 4.1 44.8 + - + +
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Residues in contact with ALA 448 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445G GLU* 2.9 12.4 + - - +
446G LYS 2.7 4.6 + - - -
447G VAL* 1.3 79.1 - - + +
449G GLN* 1.3 59.9 + - + +
450G ILE 3.2 0.9 - - - -
451G LYS* 3.9 5.3 - - - +
452G GLU* 3.0 27.3 + - - +
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Residues in contact with GLN 449 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427G ILE* 4.2 18.7 - - + +
430G TYR* 5.8 1.3 - - - -
445G GLU* 3.9 12.0 - - + +
446G LYS* 2.7 41.4 + - - +
448G ALA* 1.3 70.9 - - + +
450G ILE* 1.3 67.8 - - - +
452G GLU* 3.3 17.6 + - - +
453G PHE* 2.9 24.4 + - - +
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Residues in contact with ILE 450 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427G ILE* 4.2 9.2 - - + +
430G TYR* 3.8 15.7 - - + +
431G THR* 4.1 18.2 - - - +
434G PHE* 3.5 53.2 - - + -
442G MET* 4.4 5.4 - - + -
446G LYS* 2.7 35.9 + - + +
447G VAL* 3.7 10.8 - - - +
449G GLN* 1.3 77.1 - - - +
451G LYS* 1.3 64.0 + - - +
453G PHE* 3.1 9.5 + - - +
454G CYS* 2.9 38.5 + - - -
524G PHE* 4.2 0.7 - - + -
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Residues in contact with LYS 451 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447G VAL 3.2 16.2 + - - +
448G ALA* 3.9 6.3 - - - +
449G GLN 3.3 0.4 - - - -
450G ILE* 1.3 77.2 - - - +
452G GLU* 1.3 67.0 + - - +
453G PHE 2.9 1.6 + - - -
454G CYS* 2.9 12.1 + - - -
455G LEU* 2.9 48.6 - - + +
521G SER* 4.1 16.9 + - - +
524G PHE* 3.5 33.4 - - + -
525G GLU* 3.0 33.4 + - - +
528G ARG* 5.7 1.8 - - - +
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Residues in contact with GLU 452 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448G ALA 3.0 17.3 + - - +
449G GLN* 3.3 19.2 - - - +
451G LYS* 1.3 76.6 - - - +
453G PHE* 1.3 61.9 + - - +
455G LEU* 3.7 8.5 + - - +
456G SER* 3.2 21.5 + - - -
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Residues in contact with PHE 453 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427G ILE* 3.6 30.1 - - + -
428G TRP* 3.9 39.3 - + - -
431G THR* 2.9 44.4 - - + -
449G GLN 2.9 13.2 + - - +
450G ILE 3.1 8.3 - - - +
451G LYS 2.9 0.2 + - - -
452G GLU* 1.3 74.8 - - - +
454G CYS* 1.3 62.5 + - - +
456G SER* 3.0 10.8 + - - -
457G LYS* 2.9 51.6 + - + +
557G LEU* 5.7 2.2 - - + -
561G LEU* 4.5 8.1 - - + -
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Residues in contact with CYS 454 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431G THR* 4.2 10.3 - - - -
435G PHE* 3.9 26.0 - - + -
450G ILE* 2.9 38.4 + - - -
451G LYS 2.9 5.5 + - - +
453G PHE* 1.3 75.5 - - - +
455G LEU* 1.3 59.9 + - + +
457G LYS* 3.2 6.8 + - - +
458G MET* 2.8 51.4 + - + +
524G PHE* 4.2 12.1 - - + -
554G LEU* 5.1 0.2 - - + -
557G LEU* 4.5 7.6 - - + -
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Residues in contact with LEU 455 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451G LYS* 2.9 66.9 + - + +
452G GLU* 3.8 7.0 - - - +
454G CYS* 1.3 81.7 - - + +
456G SER* 1.3 61.0 + - - +
458G MET* 3.6 10.9 + - + +
459G GLU* 2.8 38.1 + - - +
520G PRO* 4.7 6.3 - - + -
521G SER* 4.4 21.8 - - - +
524G PHE* 4.4 10.1 - - + -
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Residues in contact with SER 456 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452G GLU* 3.2 10.5 + - - -
453G PHE* 3.0 13.9 + - - -
455G LEU* 1.3 81.5 - - - +
457G LYS* 1.3 58.7 + - - +
459G GLU* 3.8 11.3 - - - +
460G ASP* 3.3 21.4 - - - +
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Residues in contact with LYS 457 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G ASP* 3.7 27.3 - - + +
244G LYS* 6.2 0.7 - - - +
261G ILE* 5.4 7.0 - - - +
428G TRP* 3.8 28.8 - - + -
453G PHE* 2.9 37.9 + - + +
454G CYS* 3.7 8.5 - - - +
456G SER* 1.3 74.2 - - - +
458G MET* 1.3 65.5 + - - +
459G GLU 3.2 1.6 - - - -
460G ASP* 3.1 32.3 + - - +
461G LEU* 3.6 6.9 + - - +
557G LEU* 4.2 25.1 - - + -
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Residues in contact with MET 458 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454G CYS* 2.8 41.1 + - + +
455G LEU* 3.6 13.2 + - + +
457G LYS* 1.3 70.9 - - - +
459G GLU* 1.3 62.1 + - - +
461G LEU* 3.4 22.1 + - + +
462G GLU* 3.8 13.0 + - - +
520G PRO* 4.5 36.8 - - + +
523G GLU* 5.2 1.8 - - - -
524G PHE* 5.1 1.8 - - + -
553G LYS* 3.7 42.4 - - + +
554G LEU* 3.3 36.6 - - + -
557G LEU* 4.7 11.7 - - + -
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Residues in contact with GLU 459 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455G LEU* 2.8 31.5 - - - +
456G SER* 3.8 9.4 - - - +
457G LYS 3.2 0.2 - - - -
458G MET* 1.3 74.0 - - - +
460G ASP* 1.3 63.7 + - - +
461G LEU 3.1 0.2 - - - -
462G GLU* 3.0 41.0 + - - +
463G LEU* 3.9 4.2 + - - +
520G PRO* 4.3 18.9 - - - +
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Residues in contact with ASP 460 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G ASP* 4.3 15.5 - - - +
456G SER 3.3 19.9 - - - +
457G LYS* 3.3 30.0 + - - +
459G GLU* 1.3 79.0 - - - +
461G LEU* 1.3 59.6 + - - +
462G GLU 3.2 1.3 + - - -
463G LEU* 3.5 27.0 + - + +
464G ILE* 5.4 0.2 - - - -
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Residues in contact with LEU 461 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G GLU 5.2 1.1 - - - +
172G LYS* 4.1 34.8 - - + +
173G ASP* 4.6 10.3 - - + +
457G LYS 3.6 4.6 + - - +
458G MET* 3.4 17.2 + - + +
459G GLU 3.1 1.0 - - - -
460G ASP* 1.3 78.5 - - - +
462G GLU* 1.3 56.1 + - - +
463G LEU 3.3 3.1 - - - -
464G ILE* 3.0 33.0 - - + +
553G LYS* 4.5 13.0 - - + +
556G LYS* 3.8 56.9 + - + +
557G LEU* 4.7 7.9 - - + +
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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