Contacts of the helix formed by residues 460 - 469 (chain B) in PDB entry 3H44
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 ARG 460 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325B TYR* 4.9 6.9 - - - -
328B SER* 3.6 22.1 - - - +
411B PHE* 5.1 0.4 - - - -
458B GLU* 3.5 31.4 + - - +
459B PHE* 1.3 81.9 - - - +
461B PRO* 1.3 55.5 - - - +
462B ASP* 2.2 63.6 + - - -
463B LEU* 2.9 40.7 + - + +
464B ILE* 3.1 18.4 + - - +
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Residues in contact with PRO 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B PRO* 3.4 29.9 - - + +
459B PHE* 2.9 36.1 - - + +
460B ARG* 1.3 84.0 - - - +
462B ASP* 1.3 61.0 + - - +
463B LEU 3.4 0.2 - - - -
464B ILE* 3.8 3.6 - - + -
465B GLU* 3.0 28.1 + - - +
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Residues in contact with ASP 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B ARG* 2.2 49.4 + - - +
461B PRO* 1.3 79.9 - - - +
463B LEU* 1.3 62.6 + - - +
465B GLU* 3.4 5.5 + - - +
466B MET* 2.8 33.0 + - - +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B TYR* 3.5 54.5 - - + +
328B SER* 3.2 25.1 - - - +
330B PRO* 3.8 15.7 - - + -
460B ARG* 2.9 41.8 + - + +
462B ASP* 1.3 75.0 - - - +
464B ILE* 1.3 69.8 + - - +
465B GLU 3.0 0.7 - - - -
466B MET* 2.9 22.1 + - + +
467B VAL* 3.0 18.1 + - + +
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Residues in contact with ILE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B SER* 5.4 4.5 - - - +
330B PRO* 4.0 23.3 - - + +
333B TYR* 3.4 47.8 - - + -
334B LEU* 4.0 11.1 - - + +
406B PRO* 3.8 24.5 - - + -
411B PHE* 5.4 1.3 - - + -
459B PHE* 4.0 19.7 - - + -
460B ARG* 3.1 24.4 + - + +
461B PRO 3.7 7.4 - - - +
463B LEU* 1.3 81.9 - - + +
465B GLU* 1.3 63.3 + - - +
467B VAL* 3.8 2.1 - - - +
468B LEU* 3.1 27.3 + - + +
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Residues in contact with GLU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B ARG* 5.6 11.3 - - + +
405B GLY* 6.2 0.7 - - - -
406B PRO* 5.0 8.5 - - + -
461B PRO 3.0 18.3 + - - +
462B ASP* 3.4 6.1 + - - +
463B LEU 3.0 0.2 - - - -
464B ILE* 1.3 78.7 - - + +
466B MET* 1.3 63.8 + - - +
468B LEU* 4.1 15.7 - - + -
469B ASP* 3.0 37.5 + - + +
472B ARG* 5.9 0.2 + - - -
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Residues in contact with MET 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B PRO* 4.2 17.9 - - + -
322B LEU* 5.2 4.0 - - - -
325B TYR* 5.6 8.3 - - - +
462B ASP 2.8 21.8 + - - +
463B LEU* 2.9 16.1 + - + +
465B GLU* 1.3 76.2 - - - +
467B VAL* 1.3 74.0 + - - +
469B ASP* 3.3 16.0 - - - +
470B LYS* 3.5 37.8 + - + +
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Residues in contact with VAL 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B ILE* 4.8 13.9 - - + -
322B LEU* 3.6 44.2 - - + -
330B PRO* 4.1 13.0 - - + -
331B GLY* 5.3 1.3 - - - -
334B LEU* 3.5 19.7 - - + -
373B PHE* 4.9 11.4 - - + -
463B LEU* 3.0 14.3 + - + +
464B ILE 3.8 2.5 - - - +
466B MET* 1.3 81.7 - - - +
468B LEU* 1.3 58.7 + - - +
469B ASP 3.1 1.6 - - - -
470B LYS* 2.7 32.3 + - - +
471B LEU* 3.6 7.9 + - + +
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Residues in contact with LEU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B LEU* 3.9 28.7 - - + +
338B ILE* 5.7 0.2 - - + -
398B ILE* 3.9 23.1 - - + +
401B LEU* 4.1 21.1 - - + +
402B ARG* 3.2 53.1 + - + +
405B GLY* 5.6 0.2 - - - -
406B PRO* 5.4 4.3 - - + -
464B ILE* 3.1 22.4 + - + +
465B GLU* 3.8 16.8 - - + +
467B VAL* 1.3 78.4 - - - +
469B ASP* 1.3 57.9 + - - +
471B LEU* 3.1 29.8 + - + +
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Residues in contact with ASP 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ARG* 4.4 2.7 - - - +
465B GLU* 3.0 30.2 + - + +
466B MET* 3.3 9.8 - - - +
467B VAL 3.1 0.2 - - - -
468B LEU* 1.3 77.9 - - - +
470B LYS* 1.3 56.2 + - - +
471B LEU 3.3 0.7 - - - -
472B ARG* 2.4 61.3 + - - +
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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