Contacts of the helix formed by residues 69 - 79 (chain E) in PDB entry 4GOO
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 ARG 69 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ILE* 3.0 34.4 + - + +
68E MET* 1.3 90.4 - - + +
70E THR* 1.3 63.4 + - - -
71E ASP 3.4 1.7 + - - -
72E GLU* 2.6 49.3 + - - +
73E TYR* 3.1 19.8 + - - +
105E PHE* 3.5 39.2 - - + +
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Residues in contact with THR 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ILE 4.4 0.7 - - - -
66E VAL* 3.0 25.1 - - - +
67E LYS 3.7 14.4 - - - +
68E MET 3.5 2.3 + - - -
69E ARG* 1.3 74.2 - - - +
71E ASP* 1.3 65.4 + - - +
73E TYR* 3.6 3.1 - - - +
74E VAL* 2.9 28.1 + - - +
148E LEU 5.5 0.7 + - - -
149E TYR* 3.9 20.3 - - - -
152E ALA* 4.0 18.8 - - + +
156E GLN* 5.4 2.5 - - - +
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Residues in contact with ASP 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ARG 3.6 0.2 - - - -
70E THR* 1.3 77.3 + - - +
72E GLU* 1.3 63.4 + - - +
74E VAL 4.6 0.2 - - - +
75E GLN* 3.1 44.1 + - - +
149E TYR* 3.3 32.7 + - - -
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Residues in contact with GLU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ARG* 2.6 57.6 + - - +
70E THR 3.4 0.4 - - - -
71E ASP* 1.3 77.0 - - - +
73E TYR* 1.3 64.5 + - - +
75E GLN* 4.1 3.5 - - - +
76E ALA* 3.2 22.1 + - + +
105E PHE* 3.5 19.0 - - + -
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Residues in contact with TYR 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 5.2 0.3 - - - -
62E LEU* 3.5 12.3 - - + +
65E ILE* 3.8 29.8 - - + +
66E VAL* 4.0 15.0 - - + -
69E ARG 3.1 17.9 + - - +
70E THR* 3.6 3.8 - - - +
72E GLU* 1.3 74.6 - - - +
74E VAL* 1.3 75.0 + - + +
75E GLN 3.1 0.7 + - - -
76E ALA* 3.1 4.2 + - - +
77E ALA* 2.9 32.4 + - + +
105E PHE* 3.8 9.8 - + + -
108E ALA* 3.0 42.4 + - + -
109E VAL* 3.6 17.9 - - + -
112E LEU* 3.2 23.7 - - + +
148E LEU* 3.8 33.0 - - + -
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Residues in contact with VAL 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E VAL* 6.5 0.2 - - + -
70E THR* 2.9 22.6 + - - +
71E ASP 4.2 2.0 - - - +
73E TYR* 1.3 84.0 - - + +
75E GLN* 1.3 69.2 + - - +
77E ALA* 3.3 2.4 + - - -
78E ARG* 3.1 24.4 + - - +
143E PHE* 3.7 15.7 - - + -
145E GLU* 4.0 19.1 - - + +
148E LEU* 4.2 26.7 - - + -
149E TYR* 3.7 40.8 - - + +
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Residues in contact with GLN 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ASP* 3.1 41.8 + - - +
72E GLU* 4.1 3.6 - - - +
74E VAL* 1.3 82.2 - - - +
76E ALA* 1.3 61.9 + - - +
78E ARG* 2.7 50.3 + - - +
79E GLU* 3.8 10.8 + - - +
145E GLU* 5.0 0.2 - - - +
149E TYR* 4.2 11.6 + - - -
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Residues in contact with ALA 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E GLU* 3.2 15.8 + - + +
73E TYR 3.1 3.7 + - - +
75E GLN* 1.3 78.0 - - - +
77E ALA* 1.3 60.9 + - - +
79E GLU* 3.3 22.3 - - - +
80E LEU* 3.9 9.4 - - - +
105E PHE* 4.1 21.5 - - + -
109E VAL* 4.3 10.0 - - + +
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Residues in contact with ALA 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E TYR* 2.9 44.1 + - + +
74E VAL* 3.9 2.5 - - - +
76E ALA* 1.3 68.6 - - - +
78E ARG* 1.3 64.2 + - - +
79E GLU 2.9 6.7 + - - -
80E LEU* 2.9 20.3 + - - +
81E PHE* 3.8 9.6 - - + -
109E VAL* 4.3 16.3 - - + +
112E LEU* 4.4 7.2 - - + -
143E PHE* 3.7 17.5 - - + -
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Residues in contact with ARG 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E VAL* 3.1 9.4 + - - +
75E GLN* 2.7 57.4 + - - +
77E ALA* 1.3 75.9 - - - +
79E GLU* 1.3 60.9 + - - +
81E PHE* 3.3 18.0 + - + +
82E VAL* 4.6 3.5 - - - +
143E PHE* 3.6 30.7 - - + -
145E GLU* 2.4 42.1 + - - -
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Residues in contact with GLU 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E GLN 3.8 10.3 + - - +
76E ALA* 3.3 18.8 - - - +
78E ARG* 1.3 80.1 + - - +
80E LEU* 1.3 66.0 + - + +
81E PHE 3.2 0.2 - - - -
82E VAL* 3.4 23.4 - - - +
85E THR* 5.3 0.5 - - - +
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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