Contacts of the helix formed by residues 66 - 74 (chain R) in PDB entry 1G4Y
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 66 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64R ASP* 3.2 21.8 - - + +
65R PHE* 1.3 98.3 - - + +
67R GLU* 1.3 60.5 + - + +
69R LEU* 3.2 21.7 + - + +
70R THR* 3.9 9.4 + - - +
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Residues in contact with GLU 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R VAL* 3.3 26.7 - - - +
57R ALA* 2.6 38.5 + - + +
58R ASP* 3.3 2.6 - - - +
60R ASN* 5.1 0.3 + - - -
62R THR 3.3 3.8 - - - +
63R ILE* 3.4 8.0 - - + -
64R ASP* 2.7 52.9 + - - +
66R PRO* 1.3 72.8 - - + +
68R PHE* 1.3 58.3 + - - +
69R LEU 2.9 11.0 + - - -
70R THR* 3.3 24.9 + - + -
71R MET* 3.7 3.8 + - - +
1002R CA 2.2 30.4 - - - -
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Residues in contact with PHE 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 4.5 11.2 - - + -
484B ALA* 4.0 16.2 - - + -
12R PHE* 3.7 28.0 - + + -
15R ALA* 4.2 2.9 - - + -
16R PHE* 3.7 24.0 - + + -
19R PHE* 3.5 38.4 - + - -
27R ILE* 4.6 10.5 - - + -
55R VAL* 5.7 0.2 - - - -
63R ILE* 3.9 13.6 - - + +
64R ASP 3.0 10.5 + - - +
65R PHE* 2.9 22.6 + + - +
67R GLU* 1.3 76.4 - - - +
69R LEU* 1.3 60.1 + - + +
71R MET* 4.4 11.4 - - - -
72R MET* 3.1 43.2 + - + +
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Residues in contact with LEU 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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9R ILE* 4.9 18.2 - - + -
12R PHE* 4.4 26.2 - - + -
65R PHE* 2.8 55.4 - - + +
66R PRO* 3.4 11.0 - - + +
67R GLU 2.9 0.8 - - - -
68R PHE* 1.3 87.8 - - + +
70R THR* 1.3 61.6 + - + +
71R MET 3.2 1.3 - - - -
72R MET* 3.4 5.4 + - + +
73R ALA* 2.9 30.1 + - - +
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Residues in contact with THR 70 (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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55R VAL* 3.4 22.2 - - + +
66R PRO 3.9 13.2 - - - +
67R GLU* 3.3 10.1 + - - +
69R LEU* 1.3 75.4 - - + +
71R MET* 1.3 64.3 + - - +
73R ALA* 3.8 5.6 - - - +
74R ARG* 2.8 50.9 + - - +
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Residues in contact with MET 71 (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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477B ALA* 3.5 43.7 - - + +
480B LEU* 3.6 32.8 - - + -
481B VAL* 4.0 5.5 - - + +
51R MET* 4.3 12.3 - - + +
55R VAL* 3.7 31.6 - - + -
63R ILE* 5.4 3.4 - - - -
67R GLU 3.7 6.8 + - - +
68R PHE* 4.5 10.1 - - - +
69R LEU 3.2 0.2 - - - -
70R THR* 1.3 84.9 + - - +
72R MET* 1.3 72.2 + - + +
74R ARG* 4.0 4.6 + - - +
75R LYS* 3.1 28.4 - - + +
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Residues in contact with MET 72 (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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480B LEU 4.6 1.1 - - - -
481B VAL* 3.2 50.9 - - + +
484B ALA* 3.7 24.2 - - + -
12R PHE* 3.9 35.4 - - + -
68R PHE* 3.1 40.4 - - + +
69R LEU* 3.4 7.6 + - + +
70R THR 3.1 0.2 - - - -
71R MET* 1.3 95.3 - - + +
73R ALA* 1.3 67.3 + - - +
74R ARG 3.0 1.8 - - - -
75R LYS* 2.7 17.7 + - - -
76R MET* 3.2 19.1 + - - +
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Residues in contact with ALA 73 (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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3R GLN* 5.3 14.8 - - - +
69R LEU 2.9 18.4 + - - +
70R THR* 3.8 7.6 - - - +
72R MET* 1.3 77.6 - - - +
74R ARG* 1.3 60.3 + - + +
75R LYS 3.1 5.4 + - - -
76R MET* 3.9 14.9 + - - +
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Residues in contact with ARG 74 (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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54R GLU* 5.5 5.5 + - - +
55R VAL* 5.6 3.6 - - - +
70R THR* 2.8 40.3 + - - +
71R MET* 4.1 9.2 - - - +
72R MET 3.0 1.0 + - - -
73R ALA* 1.3 77.7 - - + +
75R LYS* 1.3 67.9 + - + +
76R MET 4.1 0.2 - - - -
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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