Contacts of the helix formed by residues 68 - 77 (chain V) in PDB entry 4ADV
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 ASP 68 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66V GLU* 3.0 18.6 + - - +
67V LEU* 1.3 76.1 - - - +
69V ARG* 1.3 58.1 + - - +
70V ASP* 2.8 46.1 + - - +
71V LEU* 3.1 25.7 + - + +
72V ALA* 3.0 28.6 + - - +
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Residues in contact with ARG 69 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67V LEU 3.2 9.5 + - - +
68V ASP* 1.3 72.6 + - - +
70V ASP* 1.3 64.1 + - - +
72V ALA* 3.4 1.8 + - - +
73V ALA* 3.2 24.3 + - - +
89V GLN* 3.4 52.1 + - + +
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Residues in contact with ASP 70 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68V ASP* 2.8 16.8 + - - +
69V ARG* 1.3 80.8 + - - +
71V LEU* 1.3 63.9 + - + +
73V ALA* 3.5 10.1 + - - +
74V ARG* 3.4 19.5 + - - +
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Residues in contact with LEU 71 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19V PHE* 3.7 35.7 - - + -
47V GLY* 3.6 25.7 - - - +
48V LEU* 3.6 24.2 - - + +
66V GLU* 4.6 8.1 - - + +
68V ASP* 3.1 30.1 + - + +
70V ASP* 1.3 77.3 - - + +
72V ALA* 1.3 64.4 + - - +
74V ARG* 3.2 19.3 + - - +
75V LEU* 3.2 25.8 + - - +
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Residues in contact with ALA 72 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66V GLU* 4.1 14.1 - - + +
68V ASP 3.0 17.2 + - - +
69V ARG 3.7 0.9 - - - +
70V ASP 3.3 0.4 - - - -
71V LEU* 1.3 75.3 - - - +
73V ALA* 1.3 62.4 + - - +
75V LEU* 3.3 12.0 + - - +
76V GLN* 3.3 21.5 + - - +
87V ILE* 4.1 13.6 - - + +
89V GLN* 3.7 38.4 - - + +
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Residues in contact with ALA 73 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69V ARG 3.2 16.9 + - - +
70V ASP* 3.7 7.6 - - - +
71V LEU 3.2 0.2 - - - -
72V ALA* 1.3 78.3 - - - +
74V ARG* 1.3 60.3 + - + +
76V GLN* 3.5 17.8 + - - +
77V THR* 3.5 17.7 + - - +
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Residues in contact with ARG 74 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47V GLY 5.3 1.0 + - - -
48V LEU* 3.6 33.8 + - - +
49V ALA* 6.2 0.2 - - - +
70V ASP 3.4 17.0 - - - +
71V LEU* 3.2 23.5 + - - +
72V ALA 3.2 0.6 - - - -
73V ALA* 1.3 76.4 - - + +
75V LEU* 1.3 65.5 + - + +
77V THR* 3.5 15.7 + - - -
78V HIS* 3.5 10.7 + - - +
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Residues in contact with LEU 75 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46V PRO* 3.5 37.7 - - + -
47V GLY 4.6 8.1 - - - +
48V LEU 5.4 0.2 - - - -
49V ALA* 3.8 28.9 - - + -
52V THR* 4.7 2.0 - - - +
64V VAL* 4.1 15.3 - - + -
66V GLU* 4.8 2.5 - - + -
71V LEU 3.2 15.2 + - - +
72V ALA* 3.3 15.0 + - - +
74V ARG* 1.3 74.8 - - + +
76V GLN* 1.3 66.5 + - - +
78V HIS* 3.0 22.3 + - + +
81V LEU* 4.7 7.4 - - + -
82V GLY* 3.8 9.4 + - - -
85V LEU* 3.6 22.8 - - + +
87V ILE* 4.3 3.8 - - + -
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Residues in contact with GLN 76 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72V ALA 3.3 10.0 + - - +
73V ALA* 3.7 13.8 - - - +
74V ARG 3.4 0.4 - - - -
75V LEU* 1.3 79.9 - - - +
77V THR* 1.3 64.0 + - + +
78V HIS 3.6 0.7 + - - +
82V GLY* 3.6 18.7 - - - +
87V ILE* 4.1 21.7 - - + +
89V GLN* 5.4 7.9 - - - +
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Residues in contact with THR 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73V ALA 3.5 13.0 + - - +
74V ARG* 3.5 14.1 + - - -
75V LEU 3.2 0.2 - - - -
76V GLN* 1.3 80.5 - - + +
78V HIS* 1.3 64.0 + - - +
79V PRO* 3.2 8.8 - - - +
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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