Contacts of the helix formed by residues 455 - 467 (chain B) in PDB entry 3THW
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 GLU 455 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451B ASN 3.4 9.4 + - - +
452B ILE* 3.4 13.8 + - - +
454B PHE* 1.3 77.6 - - - +
456B TYR* 1.3 57.9 + - - +
457B SER* 2.7 46.3 + - - -
458B HIS* 2.8 18.9 + - - +
459B ALA 2.8 31.7 + - - -
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Residues in contact with TYR 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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454B PHE 3.3 3.1 + - - -
455B GLU* 1.3 78.1 - - - +
457B SER* 1.3 59.9 + - - +
459B ALA* 4.0 5.2 - - - -
460B PHE* 2.7 68.0 + + + +
485B ASN* 4.6 7.3 + - - -
488B LYS* 3.5 65.5 + - + +
491B ILE* 4.1 25.8 - - + +
492B CYS* 4.2 9.0 - - - -
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Residues in contact with SER 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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455B GLU* 2.7 30.3 + - - -
456B TYR* 1.3 79.2 - - - +
458B HIS* 1.3 55.1 + - - -
460B PHE* 3.9 4.4 - - - +
461B GLN* 3.1 26.2 + - - +
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Residues in contact with HIS 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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452B ILE* 3.8 14.8 - - + +
453B TYR* 3.4 53.3 - + + +
455B GLU* 2.8 16.9 + - - +
457B SER* 1.3 71.5 - - - +
459B ALA* 1.3 62.1 + - - +
461B GLN* 3.0 13.5 + - + +
462B ALA* 2.8 39.7 + - + +
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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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453B TYR 4.1 7.4 - - - +
454B PHE 3.7 13.0 - - - +
455B GLU 2.8 22.6 + - - +
456B TYR* 3.6 5.6 - - - +
458B HIS* 1.3 74.1 - - - +
460B PHE* 1.3 59.0 + - - +
462B ALA* 3.0 5.7 + - - +
463B VAL* 2.9 26.7 + - - +
491B ILE* 4.2 5.2 - - + +
492B CYS* 3.8 13.5 - - - +
495B ALA* 3.5 28.1 - - + +
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Residues in contact with PHE 460 (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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456B TYR* 2.7 53.1 + + + +
457B SER* 3.9 4.9 - - - +
459B ALA* 1.3 71.8 - - - +
461B GLN* 1.3 66.8 + - - +
463B VAL* 4.6 2.2 - - + +
464B THR* 2.8 56.8 + - + +
485B ASN* 4.3 18.8 - - + -
491B ILE* 4.2 19.6 - - + +
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Residues in contact with GLN 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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457B SER 3.1 15.1 + - - +
458B HIS* 3.0 19.6 + - + +
460B PHE* 1.3 83.5 - - + +
462B ALA* 1.3 56.9 + - - +
464B THR* 3.2 15.4 + - - -
465B GLU* 3.1 39.8 - - - +
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Residues in contact with ALA 462 (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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458B HIS* 2.8 26.9 + - + +
459B ALA* 3.0 8.5 + - - +
461B GLN* 1.3 76.8 - - - +
463B VAL* 1.3 59.6 + - - +
465B GLU* 3.1 9.2 + - - +
466B PHE* 2.8 30.6 + - - +
495B ALA* 4.3 16.4 - - + +
498B ILE* 5.6 1.8 - - + -
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Residues in contact with VAL 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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459B ALA 2.9 16.6 + - - +
460B PHE* 4.1 4.9 - - + +
462B ALA* 1.3 75.6 - - - +
464B THR* 1.3 65.6 + - + +
466B PHE* 3.6 4.9 + - - -
467B TYR* 3.2 42.8 + - + +
484B VAL* 4.4 17.5 - - + +
491B ILE* 4.1 19.7 - - + +
494B LEU* 4.2 16.4 - - + -
495B ALA* 3.8 27.8 - - + +
498B ILE* 4.4 5.6 - - + -
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Residues in contact with THR 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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460B PHE* 2.8 57.1 + - + +
461B GLN* 3.2 18.0 + - - -
463B VAL* 1.3 80.4 - - + +
465B GLU* 1.3 56.1 + - - +
467B TYR* 3.2 18.9 - - - +
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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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461B GLN* 3.1 36.7 + - - +
462B ALA* 3.1 8.3 + - - +
464B THR* 1.3 78.2 - - - +
466B PHE* 1.3 65.1 - - - +
467B TYR 4.2 1.9 - - - +
468B ALA* 4.9 4.7 - - - +
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Residues in contact with PHE 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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462B ALA 2.8 15.1 + - - +
463B VAL 3.8 4.3 - - - +
464B THR 3.4 0.2 - - - -
465B GLU* 1.3 79.8 - - - +
467B TYR* 1.3 85.1 + + - +
468B ALA* 3.2 7.1 + - - +
498B ILE* 3.6 44.6 - - + -
502B LYS* 4.3 21.1 - - - +
507B GLU* 3.8 30.7 - - + -
508B LYS* 5.8 0.4 - - - -
510B LEU* 3.8 30.3 - - + -
511B SER* 4.7 6.7 - - - -
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Residues in contact with TYR 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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463B VAL* 3.2 39.1 + - + +
464B THR* 3.2 18.5 - - - +
465B GLU 4.2 0.3 - - - +
466B PHE* 1.3 96.8 - + - +
468B ALA* 1.3 61.1 + - - +
469B LYS 4.0 1.5 + - - +
482B GLY 5.9 3.8 - - - +
484B VAL* 4.0 17.1 - - + +
494B LEU* 4.4 12.4 - - + +
498B ILE* 4.8 2.6 - - + +
510B LEU* 3.0 31.0 + - - +
511B SER* 4.1 10.1 - - - -
513B PRO* 3.6 26.5 - - + +
516B PHE* 3.9 19.4 - - - -
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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