Contacts of the strand formed by residues 450 - 453 (chain G) in PDB entry 1O04
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 THR 450 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427G LEU 3.3 8.5 + - - -
428G ALA* 3.2 8.3 - - - -
429G ALA 2.9 25.6 + - - +
448G ALA* 3.9 0.5 - - - +
449G GLY* 1.3 78.2 + - - +
451G VAL* 1.3 67.9 - - - +
452G TRP* 3.5 42.8 - - + +
458G VAL 5.3 0.7 - - - +
464G PRO 3.9 12.3 + - - -
465G PHE* 3.7 21.3 - - + -
490H THR* 3.2 18.8 - - + +
492H THR* 5.0 1.1 - - - +
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Residues in contact with VAL 451 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429G ALA* 3.3 8.3 - - + +
431G VAL* 4.5 6.3 - - + -
443G SER* 4.0 35.9 - - - +
446G LEU* 4.1 29.4 - - + -
448G ALA* 4.3 7.4 - - + +
450G THR* 1.3 77.2 - - - +
452G TRP* 1.3 72.4 + - - +
453G VAL* 4.6 2.0 - - + -
489H LYS* 4.0 25.8 - - + -
490H THR 2.7 11.5 + - - +
491H VAL* 3.3 7.8 - - + +
492H THR 3.0 23.7 + - - -
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Residues in contact with TRP 452 (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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303G CYS* 3.9 14.1 - - + -
428G ALA* 3.6 23.1 - - + -
429G ALA 2.9 21.4 + - - -
430G ALA* 3.1 6.2 - - + +
431G VAL 2.9 25.8 + - - +
450G THR* 3.5 21.7 - - + +
451G VAL* 1.3 75.9 - - - +
453G VAL* 1.3 62.0 + - - +
454G ASN 4.1 0.2 - - - -
455G CYS* 3.1 35.0 - - - +
456G TYR* 3.5 31.9 - + - -
457G ASP* 3.5 33.4 - - - -
458G VAL* 2.9 34.5 + - + +
459G PHE* 3.9 13.9 - + - -
465G PHE* 4.6 2.7 - + - -
492H THR* 3.3 22.5 - - - -
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Residues in contact with VAL 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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436F LEU* 3.8 28.3 - - + -
431G VAL* 3.4 14.8 - - + +
433G THR* 5.2 2.0 - - + -
439G ALA* 4.0 18.8 - - + +
443G SER* 4.6 8.1 - - - -
451G VAL* 4.5 8.3 - - + +
452G TRP* 1.3 77.4 - - - +
454G ASN* 1.3 69.8 + - - +
455G CYS* 3.2 1.7 + - - -
491H VAL* 4.2 13.9 - - + -
492H THR 2.9 9.3 + - - -
493H VAL* 4.0 27.8 - - + +
494H LYS 3.0 27.7 + - - -
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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