Contacts of the helix formed by residues 42 - 50 (chain A) in PDB entry 3NTV
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 VAL 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A SER 5.4 1.3 - - - +
39A SER* 3.5 19.7 - - - +
40A ILE 3.1 0.2 + - - -
41A GLU* 1.4 77.2 - - + +
43A LEU* 1.4 59.7 + - - +
45A GLU* 3.2 31.8 - - + +
46A PHE* 4.1 1.4 + - - +
118A TYR* 4.9 10.1 - - - +
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Residues in contact with LEU 43 (chain A).
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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40A ILE* 3.0 20.2 + - + +
42A VAL* 1.4 73.0 - - - +
44A ARG* 1.4 63.5 + - - +
45A GLU 3.1 2.7 - - - -
46A PHE* 3.2 19.6 + - + +
47A ALA* 3.1 18.0 + - - +
54A ILE* 4.9 0.7 - - - -
82A ILE* 3.7 23.4 - - + +
84A TYR* 4.5 7.2 - - + -
87A MSE 3.5 32.1 - - + -
114A ASN* 3.5 29.4 - - - +
118A TYR* 3.9 29.8 - - + +
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE 4.5 0.4 + - - -
41A GLU* 2.8 38.9 + - + +
43A LEU* 1.4 76.0 - - - +
45A GLU* 1.3 70.2 + - - +
47A ALA* 3.2 4.2 + - - +
48A GLU* 3.1 36.9 + - - +
54A ILE* 3.5 30.4 + - + +
55A VAL 2.9 28.9 + - - -
56A ASP* 3.8 6.7 + - - +
57A ARG* 3.4 32.9 - - - +
84A TYR* 2.8 27.3 + - + -
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Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLU* 3.0 26.2 - - - +
42A VAL* 3.2 23.5 - - + +
44A ARG* 1.3 79.7 - - - +
46A PHE* 1.4 64.3 + - - +
48A GLU* 3.1 29.7 - - - +
49A VAL* 3.3 30.1 + - + +
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Residues in contact with PHE 46 (chain A).
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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42A VAL 4.1 1.2 + - - +
43A LEU* 3.2 24.5 + - + +
45A GLU* 1.4 79.8 - - - +
47A ALA* 1.4 64.2 + - - +
49A VAL* 3.5 2.1 + - - +
50A ASN* 2.9 58.6 + - - +
52A VAL* 4.3 6.1 - - + -
82A ILE* 4.0 33.4 - - + -
110A TYR* 3.9 36.3 - + + -
114A ASN* 6.0 1.1 - - - -
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Residues in contact with ALA 47 (chain A).
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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43A LEU 3.1 9.9 + - - +
44A ARG 3.2 9.2 + - - +
46A PHE* 1.4 79.0 - - - +
48A GLU* 1.4 60.7 + - - +
51A GLU* 3.4 3.3 + - - -
52A VAL* 2.9 53.7 + - + +
54A ILE* 3.6 36.3 - - + -
82A ILE* 4.5 2.0 - - + -
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Residues in contact with GLU 48 (chain A).
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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44A ARG* 3.1 21.9 + - - +
45A GLU* 3.1 43.5 - - - +
47A ALA* 1.4 76.5 - - - +
49A VAL* 1.3 64.6 + - + +
50A ASN 3.6 0.2 + - - -
51A GLU* 3.7 8.8 + - - +
52A VAL 5.1 0.2 - - - -
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Residues in contact with VAL 49 (chain A).
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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45A GLU* 3.3 20.1 + - + +
46A PHE* 3.9 4.0 - - - +
48A GLU* 1.3 79.3 - - + +
50A ASN* 1.4 72.7 + - - +
51A GLU* 3.7 6.9 + - - +
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Residues in contact with ASN 50 (chain A).
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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46A PHE* 2.9 56.2 + - + +
48A GLU 3.4 0.2 - - - -
49A VAL* 1.4 88.7 + - - +
51A GLU* 1.4 74.2 + - - +
52A VAL* 3.2 19.0 + - + +
110A TYR* 5.2 5.4 + - - +
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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