Contacts of the helix formed by residues 379 - 387 (chain B) in PDB entry 3PDC
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 PHE 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ZYI 4.2 16.2 - - + -
372B SER 4.7 2.7 - - - -
373B ILE* 3.5 44.5 - - + +
376B ASN* 3.3 32.3 + - + +
378B VAL* 1.3 78.2 - - + +
380B ASP* 1.3 62.6 + - - +
381B TYR* 3.0 24.2 - + - -
382B GLN* 3.0 45.8 + - - +
383B LEU 3.7 0.7 + - - -
497B VAL* 4.1 20.2 - - + -
498B LEU* 5.2 0.7 - - + -
502B MET* 3.9 31.0 - - + -
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Residues in contact with ASP 380 (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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373B ILE 4.5 1.1 + - - -
376B ASN 4.4 1.2 + - - -
377B PRO* 3.7 16.3 + - + +
378B VAL 2.9 3.4 + - - +
379B PHE* 1.3 76.6 - - - +
381B TYR* 1.3 61.6 + - - +
382B GLN 3.1 0.2 - - - -
383B LEU* 3.2 30.4 + - + +
384B TYR* 3.3 9.7 + - - +
419B HIS 4.4 6.1 - - - +
420B LYS* 3.9 11.6 - - + +
421B VAL* 3.2 26.3 + - + +
422B CYS* 3.2 30.0 + - - +
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Residues in contact with TYR 381 (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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2B ZYI 2.9 50.6 + + + -
378B VAL* 2.9 27.4 + - + +
379B PHE* 3.0 24.3 - + - -
380B ASP* 1.3 79.1 + - - +
382B GLN* 1.3 86.0 + - + +
384B TYR* 3.0 23.0 - - - +
385B PHE* 3.0 36.8 + + + -
418B MET* 3.9 19.3 - - + -
421B VAL* 3.7 27.4 - - + +
427B LEU* 4.4 4.5 - - + -
465B TYR* 4.2 0.7 - + - -
497B VAL* 3.3 23.6 - - + +
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Residues in contact with GLN 382 (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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2B ZYI 3.3 25.2 - - - +
373B ILE* 3.3 37.4 - - + +
379B PHE* 3.0 32.2 + - - +
381B TYR* 1.3 107.6 + - + +
383B LEU* 1.3 61.8 + - - +
384B TYR 3.0 1.6 - - - -
385B PHE* 2.8 24.1 + - - +
386B GLN* 3.0 21.4 + - - +
465B TYR* 3.8 19.8 - - + -
468B MET* 5.0 4.9 - - + +
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Residues in contact with LEU 383 (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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373B ILE* 3.7 28.7 - - + +
374B LYS* 3.6 44.2 - - + +
379B PHE 4.2 1.3 - - - +
380B ASP* 3.2 27.9 + - + +
382B GLN* 1.3 77.0 - - + +
384B TYR* 1.3 60.8 + - - +
385B PHE 3.4 0.2 + - - -
386B GLN* 3.4 28.7 + - + +
387B GLU* 4.2 3.5 + - - +
422B CYS* 4.6 4.7 - - - -
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Residues in contact with TYR 384 (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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380B ASP 3.3 5.0 + - - +
381B TYR* 3.0 12.6 - - - +
382B GLN 3.0 0.2 - - - -
383B LEU* 1.3 81.3 - - - +
385B PHE* 1.3 75.7 + + - +
387B GLU* 4.2 9.9 + - - +
390B VAL* 3.5 28.9 + - + +
391B ALA* 3.7 31.9 - - + +
394B GLU* 2.8 34.4 + - - +
395B LEU* 6.0 0.2 - - + -
421B VAL* 3.7 28.3 - - + -
422B CYS* 3.6 26.9 - - - -
425B GLY* 5.0 2.4 - - - -
426B GLY* 3.6 18.7 - - - -
427B LEU* 4.3 2.2 - - + -
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Residues in contact with PHE 385 (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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2B ZYI 4.0 22.0 - - + -
265B PHE* 3.8 24.9 - + - -
381B TYR* 3.0 36.8 + + + -
382B GLN* 2.8 12.4 + - - +
384B TYR* 1.3 95.3 - + - +
386B GLN* 1.3 64.4 + - - +
387B GLU 3.2 7.3 + - - +
391B ALA* 3.7 24.4 - - + +
395B LEU* 4.5 6.1 - - + -
427B LEU* 4.9 7.2 - - + -
462B LEU* 3.7 19.5 - - + +
465B TYR* 3.8 36.8 - + + -
466B ARG* 3.2 20.1 + - - -
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Residues in contact with GLN 386 (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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373B ILE* 6.1 1.8 - - - +
382B GLN* 3.0 25.4 + - - +
383B LEU* 3.4 25.8 + - + +
385B PHE* 1.3 76.0 - - - +
387B GLU* 1.3 63.5 + - - +
388B PRO* 3.1 12.3 - - - +
465B TYR* 2.9 36.2 + - - +
466B ARG* 3.2 28.0 + - - +
468B MET* 5.1 10.9 + - - +
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Residues in contact with GLU 387 (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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383B LEU 4.2 4.0 + - - +
384B TYR 4.4 5.6 - - - +
385B PHE 3.2 6.0 + - - +
386B GLN* 1.3 76.0 - - - +
388B PRO* 1.3 79.2 - - - +
389B GLY 3.5 0.7 + - - -
390B VAL* 3.3 39.9 + - + +
391B ALA 4.4 1.4 + - - -
466B ARG* 3.1 9.6 + - - -
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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