Contacts of the helix formed by residues 74 - 80 (chain o) in PDB entry 4PJO
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 PRO 74 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13n PHE* 3.8 26.9 - - + +
14n ALA 4.3 8.7 - - - +
15n PRO* 5.1 4.5 - - + -
16n ARG 5.8 0.4 - - - +
13o ALA* 4.1 7.9 - - + -
16o HIS* 3.8 24.7 - - + -
17o ILE 3.5 23.6 - - - +
18o VAL* 4.3 0.9 - - + -
73o LEU* 1.3 88.6 - - + +
75o ASP* 1.3 66.1 + - - +
76o MET 3.1 1.6 - - - +
77o LEU* 3.0 36.0 + - + +
69p LEU* 3.8 2.6 - - - +
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Residues in contact with ASP 75 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14n ALA 4.7 4.8 + - - -
16n ARG* 2.9 45.7 + - - +
73o LEU 4.1 2.9 - - - +
74o PRO* 1.3 71.4 - - - +
76o MET* 1.3 62.7 + - - +
78o LYS* 2.9 38.7 + - + +
67p LEU 5.1 0.3 - - - +
69p LEU* 3.4 30.5 + - + +
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Residues in contact with MET 76 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38m TYR* 5.6 5.5 - - - -
41m TRP* 4.5 13.0 - - - +
12n LEU* 3.4 55.5 + - + +
13n PHE* 3.3 38.1 - - + -
14n ALA 5.7 0.4 + - - -
74o PRO* 3.0 1.6 + - - +
75o ASP* 1.3 76.4 - - - +
77o LEU* 1.3 56.6 + - - +
79o ASN* 2.8 53.8 + - - +
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Residues in contact with LEU 77 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38m TYR* 5.9 0.7 - - - +
13n PHE* 4.5 17.7 - - + -
9o VAL* 4.1 14.2 - - + +
12o GLU* 3.5 45.1 - - + +
13o ALA* 3.4 30.7 - - + +
16o HIS* 5.9 0.4 - - + +
73o LEU* 3.7 20.2 - - + -
74o PRO* 3.0 21.7 + - + +
75o ASP 3.0 0.4 + - - -
76o MET* 1.3 77.4 - - - +
78o LYS* 1.3 56.6 + - - +
79o ASN 3.0 0.4 - - - -
80o ALA* 2.9 32.4 + - + +
83o LEU* 4.6 5.0 - - - +
69p LEU* 3.8 11.9 - - + -
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Residues in contact with LYS 78 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75o ASP* 2.9 32.5 + - + +
77o LEU* 1.3 77.1 - - - +
79o ASN* 1.3 76.5 + - - +
80o ALA 3.3 2.0 + - - -
83o LEU* 3.7 33.9 - - + +
32p LYS* 5.2 3.2 + - + -
43p CYS* 3.8 29.6 - - - -
44p ASP* 3.4 33.3 + - - -
69p LEU* 4.1 9.7 - - + +
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Residues in contact with ASN 79 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37m TYR* 3.8 17.7 + - - -
38m TYR* 4.4 8.1 - - + -
41m TRP* 3.0 51.3 - - + +
76o MET* 2.8 45.8 + - - +
78o LYS* 1.3 98.6 - - - +
80o ALA* 1.3 65.6 + - - +
83o LEU 5.1 0.9 - - - -
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Residues in contact with ALA 80 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8m TYR* 5.0 2.0 - - - +
37m TYR* 4.1 1.2 + - - -
38m TYR* 4.1 13.9 + - - +
9o VAL* 5.5 5.4 - - + -
12o GLU* 5.0 11.2 - - + -
76o MET 4.1 0.4 + - - -
77o LEU* 2.9 23.1 + - + +
78o LYS 3.3 0.4 - - - -
79o ASN* 1.3 82.3 - - - +
81o PRO* 1.4 76.7 - - + +
82o MET* 3.5 16.1 + - + -
83o LEU* 3.1 22.0 + - + +
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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