Contacts of the helix formed by residues 460 - 469 (chain M) in PDB entry 5XTD
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 HIS 460 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445M LEU* 3.6 23.3 - - + +
451M ILE* 4.8 11.2 - - + +
454M ASP* 2.7 45.2 + - + +
455M ILE* 3.7 21.3 - - + -
458M GLY 3.5 0.9 - - - +
459M SER* 1.3 72.4 - - - +
461M PRO* 1.3 72.5 - - + +
462M PHE* 3.1 33.4 - + + +
463M SER* 2.1 37.5 + - - +
464M GLN 2.8 5.4 + - - -
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Residues in contact with PRO 461 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459M SER 3.4 6.9 - - - +
460M HIS* 1.3 99.9 - - + +
462M PHE* 1.3 55.9 + - - +
464M GLN* 3.0 14.3 + - + +
465M VAL* 2.9 31.3 + - - +
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Residues in contact with PHE 462 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400M VAL 5.5 2.0 - - - -
401M LEU* 3.4 31.4 - - + -
428M LYS* 5.5 11.2 - - + -
429M VAL* 5.1 1.8 - - - -
430M ALA* 3.5 34.8 - - + -
443M ASP* 3.6 20.4 - - + -
445M LEU* 4.2 16.4 - - + -
455M ILE* 4.1 15.0 - - + -
460M HIS* 3.1 20.2 - + + +
461M PRO* 1.3 80.5 - - - +
463M SER* 1.3 57.2 + - - +
465M VAL* 3.0 18.5 + - + +
466M LEU* 2.9 48.3 + - + +
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Residues in contact with SER 463 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455M ILE* 3.5 40.8 - - - -
458M GLY* 2.9 26.3 + - - -
460M HIS* 2.1 30.7 + - - -
462M PHE* 1.3 76.5 - - - +
464M GLN* 1.3 59.5 + - - +
466M LEU* 3.0 15.4 + - - +
467M LYS* 2.9 26.3 + - - +
503M THR* 5.7 0.7 - - - +
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Residues in contact with GLN 464 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458M GLY 4.2 11.9 - - - +
459M SER 5.7 0.4 - - - +
460M HIS 2.8 6.5 + - - +
461M PRO* 3.0 22.4 + - + +
463M SER* 1.3 76.2 + - - +
465M VAL* 1.3 57.0 + - + +
467M LYS* 3.1 42.1 + - - +
468M GLU* 2.9 28.9 + - - +
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Residues in contact with VAL 465 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399M VAL* 5.1 7.2 - - + +
428M LYS* 3.3 45.3 - - + +
461M PRO 2.9 18.7 + - - +
462M PHE* 3.1 20.9 - - + +
464M GLN* 1.3 75.2 - - + +
466M LEU* 1.3 64.8 + - + +
468M GLU* 3.1 20.3 + - + +
469M ALA* 3.1 17.2 + - + +
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Residues in contact with LEU 466 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399M VAL* 5.1 18.2 - - + +
401M LEU* 4.1 22.2 - - + -
455M ILE* 3.9 26.5 - - + -
462M PHE* 2.9 54.8 + - + +
463M SER* 3.0 12.5 + - - +
465M VAL* 1.3 81.2 - - + +
467M LYS* 1.3 58.2 + - - +
469M ALA 3.2 16.6 - - - +
472M PRO* 5.5 0.4 - - + +
496M ILE* 4.6 0.4 - - + -
500M ILE* 3.5 48.2 - - + +
503M THR* 4.5 0.9 + - - -
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Residues in contact with LYS 467 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463M SER 2.9 11.0 + - - +
464M GLN* 3.1 41.4 + - - +
465M VAL 3.2 0.2 - - - -
466M LEU* 1.3 76.0 - - - +
468M GLU* 1.3 66.0 + - - +
469M ALA 3.3 4.0 + - - +
503M THR* 3.5 48.5 + - + +
504M SER 5.1 4.2 - - - +
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Residues in contact with GLU 468 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464M GLN* 2.9 16.7 + - - +
465M VAL* 3.1 19.5 + - + +
467M LYS* 1.3 81.9 - - - +
469M ALA* 1.3 60.0 + - + +
470M LYS 4.2 0.5 + - - -
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Residues in contact with ALA 469 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398M ASP* 4.7 9.9 - - - +
399M VAL* 3.7 33.4 - - + +
465M VAL* 3.1 14.5 + - + +
466M LEU 3.2 15.4 - - - +
467M LYS 4.1 3.5 - - - +
468M GLU* 1.3 82.6 - - + +
470M LYS* 1.3 62.9 + - - +
472M PRO* 4.9 3.6 - - - +
500M ILE* 5.4 1.0 - - - +
503M THR* 5.6 0.3 + - - -
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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