Contacts of the helix formed by residues 438 - 445 (chain B) in PDB entry 3J0A
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 LEU 438 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417B THR 6.5 0.4 - - - -
418B LEU* 4.8 19.5 - - + -
419B PRO* 4.7 1.3 - - - +
436B GLU* 3.4 22.1 - - + +
437B ASN* 1.3 91.9 - - - +
439B ASP* 1.3 66.9 + - - +
440B ILE 3.2 2.6 + - - -
441B LEU* 3.3 12.9 + - + +
442B TYR* 3.4 33.4 + - + +
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Residues in contact with ASP 439 (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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416B VAL* 3.2 27.8 + - + +
417B THR 3.7 21.0 - - - +
418B LEU* 5.7 0.2 - - - +
419B PRO* 3.4 17.4 - - + +
435B LEU* 3.4 27.9 - - - +
436B GLU* 3.0 34.8 + - - +
438B LEU* 1.3 76.9 - - - +
440B ILE* 1.3 66.5 + - + +
443B PHE* 3.1 26.9 - - - +
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Residues in contact with ILE 440 (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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430B LEU* 5.1 4.3 - - + -
435B LEU* 3.6 30.1 - - + -
436B GLU 3.2 13.5 - - - +
438B LEU 3.2 1.0 - - - +
439B ASP* 1.3 108.4 - - - +
441B LEU* 1.3 68.3 + - - +
443B PHE* 3.1 29.4 - - + -
444B LEU* 3.2 20.0 - - + +
453B LEU* 6.3 1.1 - - + -
455B LEU* 4.9 12.6 - - + -
460B PHE* 4.5 12.1 - - + -
468B THR* 3.4 35.4 - - + +
469B PRO* 5.3 0.7 - - + -
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Residues in contact with LEU 441 (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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437B ASN 3.5 13.9 + - - +
438B LEU* 3.3 6.4 + - + +
440B ILE* 1.3 78.7 - - - +
442B TYR* 1.3 87.6 + - + +
444B LEU* 3.1 14.7 + - - +
445B LEU* 3.2 34.4 + - + +
467B GLN* 3.3 56.3 - - + +
468B THR* 3.5 10.9 + - - +
470B SER* 4.4 10.9 - - - +
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Residues in contact with TYR 442 (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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418B LEU* 5.3 16.2 - - + -
419B PRO* 4.3 20.0 - - + +
421B ILE* 5.5 1.0 - - - +
438B LEU* 3.4 26.9 + - + +
441B LEU* 1.3 104.7 - - + +
443B PHE* 1.3 61.5 + - - +
445B LEU* 3.3 35.3 + - + +
446B ARG* 4.3 4.7 + - - +
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Residues in contact with PHE 443 (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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419B PRO* 3.5 22.1 - - + +
421B ILE* 3.3 33.6 - - + +
428B ILE* 3.4 48.2 - - + -
430B LEU* 4.9 8.1 - - + -
439B ASP 3.1 13.7 + - - +
440B ILE* 3.1 38.3 + - + -
441B LEU 3.2 0.8 - - - -
442B TYR* 1.3 78.1 - - - +
444B LEU* 1.3 86.5 + - + +
446B ARG 4.1 2.4 + - - -
447B VAL* 3.2 17.7 - - + +
453B LEU* 4.1 15.0 - - + -
455B LEU* 6.6 0.4 - - + -
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Residues in contact with LEU 444 (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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440B ILE* 3.2 22.9 + - + +
441B LEU 3.1 4.3 + - - +
443B PHE* 1.3 100.0 - - + +
445B LEU* 1.3 56.2 + - - +
446B ARG 3.0 11.2 + - - -
447B VAL* 3.4 20.5 + - + +
450B LEU* 4.9 6.5 - - + -
453B LEU* 4.5 15.3 - - + -
468B THR 3.2 24.2 - - - +
469B PRO* 3.8 15.5 - - + -
470B SER 3.6 11.9 - - - +
471B GLU 2.7 25.8 - - - +
472B ASN* 4.7 17.5 - - + +
475B LEU* 5.8 0.2 - - + -
478B LEU* 6.5 0.4 - - + -
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Residues in contact with LEU 445 (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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441B LEU* 3.2 32.3 + - + +
442B TYR* 3.3 43.4 + - + +
444B LEU* 1.3 76.7 - - - +
446B ARG* 1.3 70.0 + - + +
447B VAL 3.8 0.2 - - - -
448B PRO* 5.3 2.7 - - - +
470B SER* 4.4 3.6 - - - +
471B GLU* 3.1 40.1 - - - +
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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