Contacts of the helix formed by residues 451 - 464 (chain N) in PDB entry 3HOU
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 LYS 451 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449N ASN* 2.5 23.6 + - - +
450N ALA* 1.3 74.7 - - - +
452N THR* 1.3 56.5 + - - -
453N ILE 3.3 0.9 - - - -
454N THR* 3.7 9.4 - - + -
455N SER* 2.9 41.5 + - - +
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Residues in contact with THR 452 (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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420N LEU* 4.2 19.3 - - + +
423N LYS* 4.3 33.2 - - + -
424N LEU* 5.3 9.8 - - - +
427N ASP* 6.1 1.4 - - - -
449N ASN* 3.0 25.9 + - - +
451N LYS* 1.3 77.5 - - - +
453N ILE* 1.3 62.8 + - + +
455N SER* 3.3 5.3 + - - -
456N GLY* 3.0 27.0 + - - -
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Residues in contact with ILE 453 (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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128N LEU* 4.6 3.6 - - + -
167N ILE* 3.4 36.8 - - + +
168N GLY* 4.2 9.9 - - - -
169N ARG 3.8 0.4 - - - +
417N PHE* 3.3 44.2 - - + -
420N LEU* 4.5 20.6 - - + -
421N PHE* 4.2 12.6 - - + +
424N LEU* 3.6 18.4 - - + -
449N ASN 5.7 0.2 - - - +
450N ALA 4.3 1.6 + - - -
451N LYS 3.3 0.2 - - - -
452N THR* 1.3 80.3 - - - +
454N THR* 1.3 63.9 + - - +
456N GLY 4.1 0.4 - - - -
457N LEU* 3.3 30.6 + - + +
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Residues in contact with THR 454 (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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166N PHE* 4.1 1.9 - - - -
168N GLY* 2.8 12.5 - - - -
169N ARG* 2.6 59.3 + - + +
171N PRO* 5.1 0.3 - - - +
450N ALA 2.9 7.1 + - - -
451N LYS* 3.2 14.5 + - + -
453N ILE* 1.3 82.0 - - - +
455N SER* 1.3 63.1 + - - +
457N LEU* 4.0 3.5 + - - +
458N LYS* 3.6 30.8 + - - +
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Residues in contact with SER 455 (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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451N LYS* 2.9 31.1 + - - +
452N THR* 3.3 7.3 + - - -
454N THR* 1.3 78.4 - - - +
456N GLY* 1.3 74.1 + - - +
458N LYS* 2.8 11.1 + - - +
459N TYR* 2.8 24.7 + - - +
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Residues in contact with GLY 456 (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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416N LEU* 4.8 2.6 - - - +
420N LEU* 3.7 22.2 - - - -
452N THR 3.0 14.7 + - - -
455N SER* 1.3 83.3 + - - +
457N LEU* 1.3 63.1 + - - +
458N LYS 3.2 0.2 + - - -
459N TYR* 3.3 7.8 + - - +
460N ALA* 3.3 20.4 + - - +
468N GLU* 6.6 0.2 - - - -
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Residues in contact with LEU 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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54N PHE* 6.5 0.4 - - + -
128N LEU* 5.5 0.4 - - + -
169N ARG 3.5 11.7 - - - +
170N LEU* 3.5 22.0 - - + -
171N PRO* 3.4 37.2 - - + -
413N LEU* 4.8 15.5 - - + +
416N LEU* 4.6 12.1 - - + -
417N PHE* 4.6 24.7 - - + +
420N LEU* 3.8 14.5 - - + +
453N ILE* 3.3 25.0 + - + +
454N THR 4.0 1.6 - - - +
455N SER 3.2 0.6 - - - -
456N GLY* 1.3 74.3 - - - +
458N LYS* 1.3 64.0 - - - +
460N ALA* 3.6 2.1 + - - +
461N LEU* 3.2 28.8 + - + +
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Residues in contact with LYS 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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122N LEU 5.3 0.2 - - - -
123N THR* 2.6 46.0 + - + +
125N SER* 5.6 2.2 - - - -
169N ARG* 6.3 1.8 - - - +
171N PRO* 5.2 4.5 - - + -
205N ILE* 4.1 20.8 - - + +
206N ASN* 3.5 19.3 + - - +
454N THR* 3.7 23.3 - - + +
455N SER* 2.8 17.2 + - - +
457N LEU* 1.3 71.2 - - - +
459N TYR* 1.3 69.2 + - - +
460N ALA 2.8 1.2 + - - -
461N LEU 3.0 2.9 + - - -
462N ALA* 2.7 26.5 + - + +
958N GLN* 5.2 7.3 + - - -
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Residues in contact with TYR 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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264 T 5.0 11.7 - - - -
455N SER 2.8 14.1 + - - +
456N GLY* 3.5 12.6 - - - +
458N LYS* 1.3 72.9 - - - +
460N ALA* 1.3 70.3 + - + +
462N ALA* 3.2 5.5 - - + +
463N THR* 2.9 54.9 + - + +
465N ASN* 3.4 26.5 + - + +
468N GLU* 3.1 35.3 + - - -
469N GLN* 3.1 42.6 - - + +
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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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416N LEU* 3.3 35.2 - - + -
456N GLY 3.3 6.4 + - - +
457N LEU 3.7 5.6 - - - +
458N LYS 2.8 3.4 + - - -
459N TYR* 1.3 79.0 - - + +
461N LEU* 1.3 54.9 + - - +
462N ALA 2.6 16.5 + - - -
463N THR* 4.2 2.2 - - - -
464N GLY* 2.8 25.2 + - - +
465N ASN 4.2 9.4 - - - +
466N TRP* 3.4 20.2 - - + +
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Residues in contact with LEU 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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171N PRO* 4.1 13.2 - - + -
203N PHE* 3.5 40.6 - - + -
205N ILE* 3.6 26.5 - - + -
210N LYS* 2.9 25.8 - - + +
212N LEU* 4.6 8.3 - - + -
413N LEU* 4.3 13.5 - - + -
416N LEU* 4.6 2.9 - - + -
457N LEU* 3.2 17.0 - - - +
458N LYS 3.0 3.4 + - - +
460N ALA* 1.3 70.8 - - + +
462N ALA* 1.3 56.1 + - - +
466N TRP* 3.2 29.6 - - + -
480N SER* 2.7 24.2 + - - +
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Residues in contact with ALA 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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254 G 4.9 8.7 - - - +
264 T 4.6 18.4 - - - +
205N ILE* 4.4 13.5 - - + -
206N ASN* 5.7 4.0 - - + +
210N LYS* 2.8 29.2 + - - +
458N LYS* 2.7 21.7 + - + +
459N TYR* 3.2 8.7 - - + +
460N ALA 2.6 4.9 + - - -
461N LEU* 1.3 71.8 - - - +
463N THR* 1.3 67.2 + - + +
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Residues in contact with THR 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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254 G 6.2 1.1 - - - -
264 T 4.3 25.6 - - - +
66 A 6.1 1.2 - - - +
210N LYS* 5.2 0.3 - - - -
459N TYR* 2.9 41.9 + - + +
460N ALA 3.0 0.2 + - - -
462N ALA* 1.3 84.6 - - + +
464N GLY* 1.3 64.9 + - - -
465N ASN* 3.2 31.3 + - - +
478N GLY 5.3 0.5 + - - -
480N SER 3.7 9.7 - - - +
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Residues in contact with GLY 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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460N ALA 2.8 14.8 + - - -
463N THR* 1.3 77.8 + - - +
465N ASN* 1.3 64.4 + - - +
466N TRP* 3.3 1.7 + - - -
477N ALA* 2.9 18.8 - - - -
478N GLY 3.0 8.5 + - - -
479N VAL* 2.9 40.0 - - - +
480N SER* 4.0 2.5 - - - -
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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