Contacts of the strand formed by residues 449 - 454 (chain B) in PDB entry 3HO5
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 449 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B ALA 3.8 0.3 - - - +
437B VAL* 3.4 3.3 - - - -
438B ASP* 2.7 51.0 + - - +
440B HIS* 3.2 14.6 + - - -
448B LEU* 1.3 76.9 - - - +
450B ILE* 1.3 67.7 + - - +
451B LEU* 4.7 0.9 - - + +
465B ILE* 3.7 29.6 - - + -
466B LEU 3.4 9.4 - - - +
467B GLN* 3.2 23.9 + - + +
509B TYR* 3.6 16.5 + - + +
530B TRP* 6.0 0.2 - - + -
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Residues in contact with ILE 450 (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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358B LEU* 5.1 6.1 - - + -
366B TYR* 5.3 7.2 - - + -
368B ILE* 3.9 20.6 - - + -
392B VAL* 4.9 10.8 - - + -
429B LEU* 6.5 0.2 - - + -
435B CYS* 3.6 20.0 - - + -
436B ALA 3.3 6.1 - - - +
437B VAL* 4.5 10.3 - - + -
448B LEU* 4.6 17.7 - - + +
449B THR* 1.3 78.0 - - - +
451B LEU* 1.3 61.7 + - - +
452B CYS* 3.4 22.0 - - - -
464B ARG 3.9 0.3 - - - +
465B ILE* 3.5 2.6 - - - +
466B LEU* 2.9 56.2 + - + +
468B ILE* 5.9 1.3 - - + -
480B LEU* 6.3 0.9 - - + -
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Residues in contact with LEU 451 (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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435B CYS* 3.6 0.3 - - - -
436B ALA 3.0 31.2 + - - +
449B THR* 4.2 0.4 - - + -
450B ILE* 1.3 72.5 - - - +
452B CYS* 1.3 70.3 + - - +
463B ALA* 4.2 15.3 - - + -
464B ARG 3.4 8.1 - - - +
465B ILE* 4.5 9.0 - - + +
483B PHE* 4.0 21.5 - - + -
486B PHE* 4.8 1.3 - - + -
509B TYR* 3.5 39.0 - - + +
511B PHE* 3.5 30.6 - - + -
521B LEU* 4.2 13.2 - - + -
530B TRP* 4.1 17.7 - - + -
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Residues in contact with CYS 452 (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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368B ILE* 4.4 7.2 - - - -
429B LEU* 5.0 11.0 - - + -
432B PRO* 4.5 7.6 - - + -
435B CYS* 2.0 49.1 - - - +
450B ILE* 3.4 21.3 - - - -
451B LEU* 1.3 77.4 - - - +
453B SER* 1.3 66.3 + - - +
454B ASP* 5.8 0.7 - - + -
463B ALA* 3.3 6.9 - - - +
464B ARG* 2.9 43.4 + - + +
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Residues in contact with SER 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ASP 3.6 0.2 - - - +
432B PRO* 3.2 4.7 - - - +
433B GLY* 2.9 36.7 + - - +
434B ARG 5.4 1.6 + - - -
435B CYS* 5.1 0.2 - - - -
451B LEU 4.3 0.4 + - - -
452B CYS* 1.3 73.9 - - - +
454B ASP* 1.3 59.9 + - - +
455B SER 4.2 0.4 - - - -
461B SER* 4.8 5.8 - - - -
462B SER 3.8 4.9 - - - -
463B ALA* 4.6 2.9 - - - +
486B PHE* 5.0 2.7 - - - -
491B LEU* 4.0 37.4 + - - +
493B GLY* 4.0 12.1 + - - -
511B PHE* 4.4 10.4 - - - -
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Residues in contact with ASP 454 (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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429B LEU* 3.8 2.4 - - + +
430B HIS* 2.9 20.9 + - - +
431B ASP 2.5 33.5 + - - -
432B PRO* 4.4 2.9 - - + -
452B CYS* 5.5 1.1 - - + -
453B SER* 1.3 75.2 - - - +
455B SER* 1.3 57.9 + - - +
456B ASN* 2.8 37.9 + - - +
461B SER* 3.7 3.7 - - - -
462B SER* 2.8 32.0 + - - +
464B ARG* 2.9 34.8 + - + +
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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