Contacts of the strand formed by residues 449 - 459 (chain B) in PDB entry 3H3T
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 ILE 449 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442B ARG* 5.1 4.9 - - + -
443B ASN* 4.4 13.1 + - - +
446B GLU* 2.8 37.1 + - + +
447B THR 3.4 2.6 - - - -
448B THR* 1.3 77.2 - - - +
450B GLU* 1.3 63.5 + - - +
451B ASN* 3.6 25.6 - - - +
452B PHE* 4.2 14.8 - - + -
467B GLN* 3.0 44.4 - - + +
468B THR 3.8 3.1 - - - +
469B HIS* 3.6 17.3 - - + +
470B LYS* 3.3 16.4 + - - -
600B 16H 4.1 1.3 - - - +
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Residues in contact with GLU 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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448B THR 3.7 2.8 + - - -
449B ILE* 1.3 75.4 - - - +
451B ASN* 1.3 69.7 + - + +
468B THR* 2.7 31.1 + - - +
469B HIS 4.2 2.2 - - - -
470B LYS* 3.9 25.5 - - + +
477B GLN* 3.6 26.3 + - - +
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Residues in contact with ASN 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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449B ILE* 3.8 7.0 - - - -
450B GLU* 1.3 89.1 - - + +
452B PHE* 1.3 70.0 + - - +
453B HIS* 5.5 5.8 - - - -
466B TYR* 5.0 5.0 - - - -
467B GLN* 3.3 1.7 - - - +
468B THR* 2.8 51.9 + - - +
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Residues in contact with PHE 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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439B VAL* 3.6 44.2 - - + -
442B ARG* 4.0 25.6 - - + -
443B ASN* 4.0 20.9 - - - -
449B ILE* 4.2 16.6 - - + -
451B ASN* 1.3 82.2 + - - +
453B HIS* 1.3 80.2 + - - +
454B VAL* 4.8 2.0 - - + -
465B ILE* 4.0 13.9 - - + -
466B TYR* 3.1 7.4 - - - +
467B GLN* 3.3 27.1 - - + +
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Residues in contact with HIS 453 (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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451B ASN* 5.5 6.5 - - - -
452B PHE* 1.3 87.7 - - - +
454B VAL* 1.3 72.0 + - - +
455B VAL* 3.5 23.1 + - + -
465B ILE* 3.6 2.6 - - - +
466B TYR* 2.9 58.5 + + + -
512B ALA* 6.4 0.7 - - + -
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Residues in contact with VAL 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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439B VAL* 4.0 37.5 - - + -
452B PHE* 4.7 2.9 - - + -
453B HIS* 1.3 82.8 + - - +
455B VAL* 1.3 64.3 - - - +
456B GLU 3.7 25.4 - - - +
457B THR* 4.2 11.0 - - - +
463B ILE* 4.3 17.3 - - + -
464B ILE 3.8 5.4 - - - +
465B ILE* 4.5 3.8 - - + +
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Residues in contact with VAL 455 (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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453B HIS* 3.5 14.8 + - + -
454B VAL* 1.3 73.6 - - - +
456B GLU* 1.3 57.9 + - - +
464B ILE* 2.8 19.6 + - + +
466B TYR* 3.7 34.8 - - + +
481B LEU* 4.1 10.8 - - + -
509B HIS* 3.4 45.8 + - + +
511B SER* 4.2 11.4 - - - -
512B ALA* 4.8 5.4 - - + -
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Residues in contact with GLU 456 (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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366B ARG* 2.9 35.6 + - - -
454B VAL* 3.5 6.1 - - - +
455B VAL* 1.3 83.4 - - + +
457B THR* 1.3 75.1 + - - +
458B LEU* 3.7 11.2 + - + +
463B ILE* 3.4 6.1 - - - +
464B ILE* 3.0 34.8 + - + +
509B HIS* 2.8 29.6 + - + +
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Residues in contact with THR 457 (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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454B VAL* 4.2 11.1 - - - +
456B GLU* 1.3 83.9 + - - +
458B LEU* 1.3 60.9 + - - +
459B ALA* 3.4 26.9 - - - +
460B ASP* 5.5 0.9 - - - +
463B ILE* 4.2 12.6 - - + +
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Residues in contact with LEU 458 (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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365B HIS* 3.8 43.9 - - + +
366B ARG* 3.6 29.2 - - - +
367B PHE* 4.1 6.7 - - + -
456B GLU* 3.7 15.7 - - + +
457B THR* 1.3 74.3 - - - +
459B ALA* 1.3 63.4 + - - +
462B ALA* 2.9 18.8 + - + +
463B ILE 4.5 0.7 - - - -
464B ILE* 3.7 30.3 - - + -
483B LEU* 3.8 28.7 - - + -
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Residues in contact with ALA 459 (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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365B HIS* 4.2 14.1 - - + -
437B TRP* 5.3 0.3 - - - -
457B THR* 3.4 20.6 - - - +
458B LEU* 1.3 79.8 - - - +
460B ASP* 1.3 64.5 + - - +
461B ASN* 3.0 23.4 + - - +
462B ALA* 3.2 13.0 + - + +
463B ILE* 4.8 1.7 - - - +
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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