Contacts of the helix formed by residues 5012 - 5017 (chain k) 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 PRO5012 (chain k).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5072c LEU* 3.5 14.1 - - + -
5108c THR* 4.4 15.3 - - - +
5109c PHE* 5.9 2.2 - - + -
5112c PHE* 4.0 19.3 - - + -
5010k LYS 3.6 4.0 - - - +
5011k LEU* 1.4 91.4 - - + -
5013k GLU* 1.3 52.3 + - - +
5014k ALA* 3.0 2.4 + - - +
5015k TYR* 2.6 53.1 + - + +
5061z VAL* 5.4 10.3 - - + +
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Residues in contact with GLU5013 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5011k LEU 2.8 8.4 + - - +
5012k PRO* 1.3 62.2 - - - +
5014k ALA* 1.3 55.5 + - - +
5015k TYR 2.7 5.0 + - - -
5016k ALA* 2.3 45.4 + - - +
5017k ILE* 4.5 0.3 - - - +
5061z VAL* 5.9 3.4 - - + -
5062z VAL* 5.4 19.2 - - + +
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Residues in contact with ALA5014 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5012k PRO 3.0 3.6 + - - +
5013k GLU* 1.3 76.2 - - - +
5015k TYR* 1.3 59.5 + - + +
5016k ALA 3.2 0.9 - - - -
5017k ILE* 3.5 20.3 - - - +
5018k PHE* 5.0 3.8 - - - -
5002z THR* 5.1 7.9 - - + -
5005z PHE* 4.2 27.6 - - + -
5006z GLN* 4.7 12.3 - - + +
5061z VAL* 4.0 30.9 - - + +
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Residues in contact with TYR5015 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5112c PHE* 3.1 42.8 - + - -
5011k LEU* 4.1 22.3 - - + +
5012k PRO* 2.6 46.4 + - + +
5014k ALA* 1.3 71.9 - - + +
5016k ALA* 1.3 51.6 + - - +
5017k ILE 2.8 6.6 + - - -
5018k PHE* 2.4 56.9 + + + +
5019k ASP 3.6 3.6 + - - -
6052k BCR 5.3 11.7 - - + -
5005z PHE* 4.4 21.2 - + - -
5009z LEU* 5.5 2.7 - - + -
5054z VAL* 5.1 5.8 - - + +
5058z ASN* 3.1 30.0 + - - +
5061z VAL* 5.3 6.1 - - + -
6053z BCR 4.1 7.6 - - - +
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Residues in contact with ALA5016 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5011k LEU* 4.3 8.2 + - - +
5012k PRO 4.0 0.4 + - - -
5013k GLU* 2.3 43.3 + - - +
5014k ALA 3.2 0.2 - - - -
5015k TYR* 1.3 65.2 - - - +
5017k ILE* 1.3 65.7 + - + +
5018k PHE 3.2 0.2 - - - -
5019k ASP* 3.4 21.5 - - - +
5020k PRO* 3.9 3.8 - - - +
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Residues in contact with ILE5017 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5013k GLU 4.5 0.7 - - - +
5014k ALA* 3.5 23.6 - - - +
5015k TYR 2.8 0.4 + - - +
5016k ALA* 1.3 88.1 - - + +
5018k PHE* 1.3 78.1 + - + +
5020k PRO* 2.9 22.3 - - - +
5021k LEU 5.1 0.2 + - - -
5006z GLN* 4.4 20.6 - - + +
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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