Contacts of the helix formed by residues 456 - 468 (chain N) in PDB entry 5D4C
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 MET 456 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126N VAL* 4.0 3.4 - - - +
129N PHE* 3.4 64.5 - - + +
130N SER 3.7 4.5 - - - +
131N LYS* 3.2 39.3 - - - +
132N TYR* 3.7 34.0 - - + -
155N ASP* 5.2 0.9 - - + +
455N ARG* 1.3 78.0 - - - +
457N GLY* 1.3 70.4 + - - +
459N GLU* 4.0 10.2 + - - +
460N ALA* 3.7 9.9 + - - -
564N GLU* 5.8 1.1 - - - +
568N ARG* 4.1 19.1 - - - +
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Residues in contact with GLY 457 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N VAL* 2.6 27.7 + - - +
127N LEU* 3.6 23.3 - - - -
129N PHE* 4.2 9.0 - - - -
456N MET* 1.3 73.8 - - - +
458N ALA* 1.3 60.2 + - - -
460N ALA* 3.0 5.7 + - - +
461N ILE* 3.0 26.2 + - - +
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Residues in contact with ALA 458 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97N THR* 5.8 0.2 + - - -
98N PRO* 3.2 30.4 + - - +
99N ALA* 3.7 0.7 - - - -
100N ALA* 3.5 25.6 - - + +
127N LEU* 3.5 14.3 + - + +
129N PHE* 5.2 1.6 - - - -
457N GLY* 1.3 68.4 - - - -
459N GLU* 1.3 59.0 + - - +
461N ILE* 4.3 4.5 - - - -
462N GLN* 2.9 32.3 + - - +
513N ILE* 3.7 10.6 - - + +
575N GLN* 4.1 5.7 + - - +
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Residues in contact with GLU 459 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97N THR* 4.2 16.2 + - - +
98N PRO* 4.5 18.7 + - + -
455N ARG* 3.7 38.1 + - - +
456N MET 4.0 9.6 + - - +
457N GLY 3.1 0.8 + - - -
458N ALA* 1.3 78.7 - - - +
460N ALA* 1.3 57.9 + - - +
462N GLN* 3.6 4.7 - - - +
463N GLN* 3.0 28.6 + - - +
571N LYS* 3.9 20.1 + - - +
139P ALA 5.5 2.4 - - - +
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Residues in contact with ALA 460 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N VAL* 4.8 0.4 - - + -
133N ILE* 3.6 29.4 - - + -
135N LEU* 4.1 9.8 - - + +
455N ARG* 3.8 22.4 - - + +
456N MET 3.7 7.6 + - - +
457N GLY 3.0 10.1 + - - +
459N GLU* 1.3 80.5 - - - +
461N ILE* 1.3 58.4 + - - +
463N GLN* 3.0 7.4 + - - +
464N LEU* 2.9 32.9 + - - +
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Residues in contact with ILE 461 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N ILE* 3.8 29.2 - - + -
116N LEU* 4.0 15.7 - - + -
118N LEU* 4.2 7.6 - - + -
123N LEU* 4.0 17.9 - - + -
126N VAL* 4.0 21.3 - - + -
127N LEU* 3.9 22.2 - - + -
133N ILE* 5.2 1.6 - - + -
457N GLY 3.0 17.2 + - - +
458N ALA* 4.3 3.6 - - - +
460N ALA* 1.3 74.8 - - + +
462N GLN* 1.3 57.7 + - - +
464N LEU* 3.3 13.5 + - + +
465N LEU* 2.9 40.8 + - + +
513N ILE* 4.1 9.9 - - + -
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Residues in contact with GLN 462 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N PRO* 5.6 1.6 - - - +
98N PRO* 3.2 29.7 - - - +
458N ALA 2.9 19.8 + - - +
459N GLU* 3.6 5.0 - - - +
461N ILE* 1.3 74.0 - - - +
463N GLN* 1.3 65.8 + - - +
465N LEU* 3.2 4.6 + - - +
466N LYS* 2.9 49.5 + - - +
510N GLU* 4.2 16.8 + - + +
513N ILE* 4.0 22.7 + - + +
515N GLU* 2.5 34.2 + - - +
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Residues in contact with GLN 463 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N LEU* 3.5 30.3 - - + -
455N ARG* 3.5 16.8 + - - +
459N GLU 3.0 13.2 + - - +
460N ALA 3.2 9.4 - - - +
462N GLN* 1.3 75.4 - - - +
464N LEU* 1.3 63.9 + - - +
466N LYS* 2.9 27.8 + - - +
467N GLU* 2.9 37.5 + - - +
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Residues in contact with LEU 464 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N LEU* 3.8 28.3 - - + +
118N LEU* 5.3 3.1 - - + -
133N ILE* 4.1 28.9 - - + -
134N VAL 4.8 1.6 - - - +
135N LEU* 4.2 26.9 - - + -
149N LYS* 5.1 1.3 - - - +
150N ARG* 4.3 32.3 + - + +
460N ALA 2.9 16.4 + - - +
461N ILE* 3.7 16.4 - - + +
463N GLN* 1.3 75.1 - - - +
465N LEU* 1.3 60.0 + - - +
467N GLU* 3.4 21.8 + - - +
468N LEU* 3.4 23.9 + - - +
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Residues in contact with LEU 465 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N ILE* 4.0 15.5 - - + -
115N LEU* 4.5 11.0 - - + -
116N LEU* 3.7 27.8 - - + -
461N ILE* 2.9 33.8 + - + +
462N GLN 3.6 5.2 - - - +
463N GLN 3.1 0.2 - - - -
464N LEU* 1.3 74.2 - - - +
466N LYS* 1.3 64.3 + - - +
468N LEU* 3.5 17.9 + - + +
508N ARG* 4.5 2.3 + - - -
509N PRO* 3.5 37.7 - - + +
510N GLU* 3.5 25.2 - - - +
512N MET* 4.4 3.1 - - + -
513N ILE* 3.8 24.7 - - + -
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Residues in contact with LYS 466 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462N GLN* 2.9 48.2 + - + +
463N GLN* 2.9 19.7 + - - +
465N LEU* 1.3 76.2 - - - +
467N GLU* 1.3 63.4 + - + +
468N LEU 3.3 6.1 + - - +
508N ARG* 4.7 4.3 + - - -
510N GLU* 3.8 29.6 - - + +
515N GLU* 4.2 5.5 + - - -
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Residues in contact with GLU 467 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N LEU* 4.2 5.4 - - - +
149N LYS* 3.1 31.1 + - - -
150N ARG* 5.7 4.8 + - - +
463N GLN* 2.9 41.1 + - - +
464N LEU* 3.7 22.2 - - - +
465N LEU 3.2 0.4 - - - -
466N LYS* 1.3 76.2 - - + +
468N LEU* 1.3 63.8 + - - +
469N ASP* 3.3 4.9 + - - +
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Residues in contact with LEU 468 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N LEU* 4.0 36.3 - - + +
116N LEU* 3.9 18.4 - - + -
150N ARG* 3.6 23.6 - - - +
464N LEU 3.4 13.2 + - - +
465N LEU* 3.7 16.2 - - + +
466N LYS 3.2 8.2 - - - +
467N GLU* 1.3 78.1 - - - +
469N ASP* 1.3 63.4 + - - +
470N LEU* 3.9 20.1 + - + +
473N LEU* 4.6 17.0 - - + -
508N ARG* 4.4 14.6 + - - -
509N PRO* 5.0 2.9 - - + -
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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