Contacts of the helix formed by residues 5001 - 5010 (chain z) in PDB entry 3A0B
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 MET5001 (chain z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5002z THR* 1.3 69.4 + - - +
5003z ILE* 3.4 11.0 - - - +
5004z LEU* 3.0 58.1 - - + +
5005z PHE* 3.2 5.9 + - - +
5057z LEU* 3.1 40.8 - - + -
5060z PHE* 3.4 44.4 - - + +
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Residues in contact with THR5002 (chain z).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5014k ALA* 5.1 9.4 - - + -
5001z MET* 1.3 78.0 + - - +
5003z ILE* 1.3 68.1 + - - +
5005z PHE* 3.1 21.7 + - + +
5006z GLN* 3.6 15.9 + - - +
5060z PHE 4.5 9.1 + - - -
5061z VAL 3.8 18.2 + - - +
5062z VAL* 3.9 17.3 + - - -
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Residues in contact with ILE5003 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5001z MET* 4.1 8.5 - - - +
5002z THR* 1.3 82.5 - - - +
5004z LEU* 1.3 65.7 + - + +
5005z PHE 2.9 11.2 + - - -
5006z GLN* 3.5 29.1 + - - +
5007z LEU* 4.1 13.6 + - + +
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Residues in contact with LEU5004 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5001z MET* 3.0 68.9 - - + +
5003z ILE* 1.3 82.4 - - + +
5005z PHE* 1.3 63.3 + - - +
5007z LEU* 4.1 10.1 + - - +
5008z ALA* 3.8 13.9 + - - +
5057z LEU* 4.3 1.7 - - + +
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Residues in contact with PHE5005 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5014k ALA* 4.2 30.1 - - + -
5015k TYR* 4.4 22.2 - + - -
5018k PHE* 5.9 1.1 - + - -
5001z MET 3.2 7.5 + - - +
5002z THR* 3.1 17.3 - - + +
5003z ILE 2.9 2.8 + - - -
5004z LEU* 1.3 75.7 - - - +
5006z GLN* 1.3 67.7 + - + +
5007z LEU 2.5 6.2 + - - -
5008z ALA* 2.5 33.3 + - - +
5009z LEU* 3.7 8.8 + - + -
5054z VAL* 3.3 33.4 - - + -
5057z LEU* 3.1 50.5 - - + -
5058z ASN* 4.1 14.6 - - - -
5060z PHE 5.3 6.3 - - - +
5061z VAL* 5.9 4.9 - - + -
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Residues in contact with GLN5006 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5014k ALA* 4.7 15.3 - - + +
5017k ILE* 4.4 21.1 - - + +
5018k PHE* 4.4 5.3 - - + -
5002z THR* 3.6 13.6 + - + +
5003z ILE* 3.5 36.4 + - - +
5005z PHE* 1.3 83.3 - - + +
5007z LEU* 1.3 58.4 + - + +
5009z LEU* 2.7 31.0 - - + +
5010z ALA* 2.8 12.6 - - - +
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Residues in contact with LEU5007 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5003z ILE* 4.1 12.5 + - + +
5004z LEU* 4.4 10.1 - - - +
5005z PHE 2.5 6.3 + - - -
5006z GLN* 1.3 78.1 - - + +
5008z ALA* 1.3 57.0 + - - +
5009z LEU 3.3 1.8 - - - -
5010z ALA* 3.8 18.2 - - + +
5011z ALA* 3.0 23.7 + - - +
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Residues in contact with ALA5008 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5004z LEU 3.8 7.4 + - - +
5005z PHE 2.5 11.8 + - - +
5007z LEU* 1.3 73.5 - - - +
5009z LEU* 1.3 54.8 + - - +
5011z ALA* 3.3 14.7 - - - +
5012z LEU 3.8 0.9 + - - -
5050z LEU* 3.3 16.3 - - - +
5053z VAL* 3.9 16.4 - - + -
5054z VAL* 3.2 13.9 - - + +
5057z LEU* 3.0 36.8 - - + -
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Residues in contact with LEU5009 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5015k TYR* 5.5 3.6 - - + -
5018k PHE* 3.1 47.1 - - + -
6052k BCR 5.2 18.4 - - + -
5005z PHE* 3.7 6.5 + - + +
5006z GLN* 2.7 32.3 - - - +
5008z ALA* 1.3 77.6 - - - +
5010z ALA* 1.3 68.3 + - - +
5011z ALA 2.5 16.0 + - - -
5012z LEU* 2.5 18.4 + - + +
5013z VAL* 2.7 20.5 + - + +
5054z VAL* 3.1 34.1 - - + -
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Residues in contact with ALA5010 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5018k PHE* 4.5 8.3 - - + -
5006z GLN 2.8 21.5 + - - +
5007z LEU* 3.9 20.6 - - + +
5008z ALA 3.7 0.2 - - - -
5009z LEU* 1.3 85.2 - - + +
5011z ALA* 1.3 54.3 + - - +
5013z VAL* 3.1 26.8 - - + +
5014z ILE* 3.6 14.2 - - - +
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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