Contacts of the helix formed by residues 69 - 77 (chain B) in PDB entry 3BGD
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 ILE 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B HIS* 4.0 22.6 - - + +
37B GLN 4.2 3.0 + - - +
38B GLU 3.7 15.3 - - - +
39B GLN* 3.6 11.9 - - - +
40B GLY* 3.6 34.3 - - - +
67B LYS 3.9 2.2 - - - +
68B ALA* 1.3 72.3 - - - +
70B GLU* 1.3 61.2 + - - +
72B LYS* 3.0 28.2 + - - +
73B TRP* 3.7 25.3 + - + +
94B PHE* 4.6 0.7 - - - -
97B GLU* 5.0 2.9 - - - +
98B GLN* 3.7 29.1 - - - +
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLN* 4.7 4.3 - - - +
40B GLY* 3.2 8.6 - - - -
41B HIS* 2.7 33.2 + - + +
44B LEU* 3.7 23.8 - - + -
62B PHE* 4.0 9.9 - - + -
68B ALA* 3.0 24.0 + - - +
69B ILE* 1.3 78.4 + - - +
71B MET* 1.3 64.8 + - - +
72B LYS 3.1 0.2 - - - -
73B TRP* 3.0 48.8 + - + +
74B PHE* 3.2 18.1 + - + -
145B TRP* 4.0 11.0 + - - -
147B ARG* 5.6 1.9 - - - +
300B SAH 5.4 1.4 - - - +
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Residues in contact with MET 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PHE* 3.5 39.0 - - + -
65B CYS* 3.8 28.7 - - + -
66B GLY 4.4 2.0 - - - +
68B ALA* 3.7 15.5 - - + +
69B ILE 3.1 0.8 + - - -
70B GLU* 1.3 78.4 - - - +
72B LYS* 1.3 60.7 + - - +
74B PHE* 3.5 1.1 + - - -
75B ALA* 3.1 23.2 + - - +
81B VAL* 3.6 21.4 - - + +
83B GLY* 4.6 0.7 - - - -
94B PHE* 3.7 37.0 - - + -
123B ILE* 4.2 3.7 - - + +
125B LEU* 3.7 34.1 - - + -
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ILE 3.0 13.8 + - - +
71B MET* 1.3 77.1 - - - +
73B TRP* 1.3 67.0 + - + +
75B ALA* 4.5 5.2 - - + -
76B ASP* 2.9 61.0 + - - +
94B PHE* 4.2 2.4 - - + -
98B GLN* 3.7 46.2 + - + +
100B LEU* 3.6 38.8 - - + -
123B ILE* 4.5 5.2 - - + -
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Residues in contact with TRP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN 3.9 3.4 - - - -
40B GLY* 4.0 1.3 - - - -
41B HIS 3.7 23.3 - - - -
44B LEU* 4.1 13.5 - - + -
45B LYS* 3.5 42.4 - - + -
48B LEU* 4.1 24.0 - - + -
69B ILE* 3.7 43.1 - - + +
70B GLU* 3.0 34.8 + - + +
72B LYS* 1.3 80.6 - - + +
74B PHE* 1.3 62.2 + + + +
76B ASP* 3.5 3.8 + - - -
77B ARG* 2.7 49.5 + - - +
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 4.0 20.2 - - + -
48B LEU* 3.5 26.0 - - + -
51B PHE* 3.7 33.4 - + - -
52B LEU* 3.9 21.5 - - + -
60B VAL* 3.8 28.3 - - + -
62B PHE* 3.5 25.4 - + - -
70B GLU* 3.2 23.5 + - + -
71B MET 3.9 1.3 - - - +
72B LYS 3.3 0.2 - - - -
73B TRP* 1.3 77.9 - - + +
75B ALA* 1.3 66.5 + - - +
76B ASP 3.1 0.2 - - - -
77B ARG* 3.1 11.8 + - - +
79B HIS* 3.1 31.5 + - + +
81B VAL* 3.7 17.3 - - + -
145B TRP* 4.8 2.2 - - + -
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B MET 3.1 15.3 + - - +
72B LYS* 4.0 5.6 - - + +
74B PHE* 1.3 79.5 - - - +
76B ASP* 1.3 64.8 + - - +
77B ARG 3.2 0.5 + - - -
78B GLY* 3.3 10.4 + - - -
79B HIS 3.5 12.1 - - - +
81B VAL* 3.8 4.6 - - + +
122B SER* 4.1 19.2 + - - -
123B ILE* 3.7 29.6 - - + -
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LYS* 2.9 58.4 + - - +
73B TRP* 3.7 8.9 - - - +
74B PHE 3.1 0.4 - - - -
75B ALA* 1.3 79.1 - - - +
77B ARG* 1.3 66.1 + - - +
78B GLY 3.3 2.4 + - - -
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 3.9 25.6 - - - +
49B ASP* 5.1 8.7 + - - -
52B LEU* 4.3 18.8 - - - -
56B SER* 5.9 0.3 - - - -
57B GLY 5.2 1.0 + - - -
73B TRP* 2.7 44.5 + - - +
74B PHE 3.1 9.1 + - - +
76B ASP* 1.3 86.5 + - + +
78B GLY* 1.3 58.1 + - - +
79B HIS* 3.4 24.2 + - + +
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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