Contacts of the helix formed by residues 65 - 70 (chain R) in PDB entry 3MQT
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 ASN 65 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R SER 2.8 23.3 + - - -
55R GLU* 3.6 4.4 - - - +
56R ILE* 2.9 42.4 + - - +
58R ASN* 2.9 17.0 + - - +
64R ASN* 1.3 74.5 - - - +
66R ILE* 1.3 64.7 + - - +
67R LYS* 2.8 43.2 + - - +
68R GLU* 3.2 32.8 + - - +
69R ALA 4.2 1.2 + - - -
88R THR* 5.1 1.7 + - - -
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Residues in contact with ILE 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R PHE* 5.1 2.2 - - + -
53R PHE* 4.7 17.0 + - + +
54R SER* 4.3 25.1 - - - -
56R ILE* 5.0 1.8 - - - +
64R ASN 3.2 3.2 + - - -
65R ASN* 1.3 74.8 + - - +
67R LYS* 1.3 69.1 + - + +
69R ALA* 3.2 19.0 + - - +
70R VAL* 4.3 1.4 + - - +
85R MET* 3.8 20.7 - - + +
88R THR* 5.3 0.2 - - - -
89R THR* 4.0 24.0 - - + +
101R ALA* 4.2 7.4 - - + -
102R ILE* 3.4 43.7 - - + +
105R ILE* 4.0 21.7 - - + +
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Residues in contact with LYS 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R VAL* 2.9 51.6 + - + +
11R GLU* 4.6 6.1 - - - +
12R PHE 5.1 0.4 - - - +
54R SER* 3.2 37.0 + - - +
55R GLU* 4.2 17.6 + - - +
65R ASN* 2.8 18.7 + - - +
66R ILE* 1.3 77.0 - - + +
68R GLU* 1.3 56.9 + - + +
69R ALA 3.0 0.2 - - - -
70R VAL* 2.9 27.5 + - - +
71R ILE* 3.1 24.8 + - + +
105R ILE* 5.3 1.6 - - - -
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Residues in contact with GLU 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58R ASN* 3.0 36.9 + - - +
64R ASN* 5.2 4.4 - - + +
65R ASN* 3.2 23.4 + - - +
66R ILE 3.2 1.0 - - - -
67R LYS* 1.3 77.9 - - + +
69R ALA* 1.3 60.5 + - - +
70R VAL 3.1 1.3 + - - -
71R ILE* 4.1 19.9 - - + +
73R ARG* 5.3 3.3 + - - -
84R ARG* 5.4 0.3 - - - -
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Residues in contact with ALA 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R ASN 4.2 1.2 + - - -
66R ILE 3.2 14.0 + - - +
67R LYS 3.0 1.2 - - - -
68R GLU* 1.3 78.1 - - - +
70R VAL* 1.3 61.4 + - - +
73R ARG* 3.8 2.3 - - - +
84R ARG* 2.9 42.3 + - + +
85R MET* 3.7 28.7 - - + +
88R THR* 3.7 24.5 - - - +
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Residues in contact with VAL 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R ILE* 3.2 26.6 - - + +
10R VAL* 3.8 24.7 - - + -
31R VAL* 5.5 0.2 - - + -
66R ILE 4.8 0.7 - - - +
67R LYS* 2.9 16.7 + - - +
69R ALA* 1.3 85.2 - - - +
71R ILE* 1.3 68.2 + - - +
72R GLY 3.2 0.3 + - - -
73R ARG* 2.9 25.0 + - + +
81R ASN* 4.5 16.8 - - + +
85R MET* 4.0 32.5 - - + -
105R ILE* 4.4 11.9 - - + -
109R LEU* 4.5 6.5 - - + -
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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