Contacts of the helix formed by residues 69 - 76 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A HIS* 3.8 27.0 - - + +
37A GLN 4.4 2.7 + - - +
38A GLU 3.7 12.1 - - - +
39A GLN* 3.5 10.1 - - - +
40A GLY* 3.4 37.5 - - - +
67A LYS 3.9 2.2 - - - +
68A ALA* 1.3 73.5 - - - +
70A GLU* 1.3 61.7 + - - +
72A LYS* 2.9 28.1 + - - +
73A TRP* 3.7 24.1 - - + +
94A PHE* 4.5 1.1 - - - -
97A GLU* 4.8 3.4 - - - +
98A GLN* 3.3 31.4 - - - +
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Residues in contact with GLU 70 (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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37A GLN* 4.6 4.3 - - - +
40A GLY* 3.0 9.7 - - - -
41A HIS* 2.7 34.2 + - - +
44A LEU* 3.7 24.2 - - + -
62A PHE* 3.8 10.0 - - + -
68A ALA* 3.3 22.7 - - - +
69A ILE* 1.3 77.3 + - - +
71A MET* 1.3 64.4 + - - +
72A LYS 3.1 0.2 - - - -
73A TRP* 3.1 48.7 + - + +
74A PHE* 3.2 17.5 + - + -
145A TRP* 4.2 10.4 + - - -
147A ARG* 6.6 0.4 - - - -
300A SAH 5.3 1.7 - - - +
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Residues in contact with MET 71 (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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62A PHE* 3.2 40.4 - - + -
65A CYS* 3.7 31.4 - - + -
66A GLY 4.3 2.5 - - - +
68A ALA 3.1 22.8 + - - +
69A ILE 3.1 1.2 - - - -
70A GLU* 1.3 78.6 - - - +
72A LYS* 1.3 61.2 + - - +
74A PHE 3.4 0.7 + - - -
75A ALA* 3.2 20.3 + - - +
81A VAL* 3.7 22.1 - - + +
83A GLY* 4.7 0.2 - - - -
94A PHE* 3.8 31.0 - - + -
123A ILE* 4.4 4.3 - - + +
125A LEU* 3.7 30.5 - - + -
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Residues in contact with LYS 72 (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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69A ILE 2.9 13.0 + - - +
71A MET* 1.3 79.0 - - - +
73A TRP* 1.3 59.8 + - + +
75A ALA* 4.5 4.0 - - + +
76A ASP* 3.0 62.5 + - - +
94A PHE* 4.2 3.3 - - + -
98A GLN* 3.6 46.3 + - + +
100A LEU* 4.1 32.5 - - + -
123A ILE* 4.5 7.0 - - + -
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Residues in contact with TRP 73 (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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39A GLN 3.9 9.2 - - - -
40A GLY* 4.1 2.9 - - - -
41A HIS 3.8 26.9 - - - -
44A LEU* 4.3 7.0 - - + -
45A LYS* 4.1 29.6 - - + -
48A LEU* 4.2 20.6 - - + -
69A ILE* 3.7 37.8 + - + +
70A GLU* 3.1 39.9 + - + +
72A LYS* 1.3 81.9 - - + +
74A PHE* 1.3 62.6 + + + +
76A ASP* 3.8 3.6 + - - +
77A ARG* 3.0 47.7 + - - +
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Residues in contact with PHE 74 (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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44A LEU* 4.1 19.5 - - + -
48A LEU* 3.4 30.1 - - + -
51A PHE* 3.8 31.4 - + - -
52A LEU* 3.8 23.1 - - + -
60A VAL* 3.9 21.8 - - + -
62A PHE* 3.4 29.2 - + - -
70A GLU* 3.2 23.9 + - + -
71A MET 3.9 0.4 - - - +
72A LYS 3.3 0.4 - - - -
73A TRP* 1.3 78.3 - - + +
75A ALA* 1.3 66.3 + - - +
77A ARG* 3.0 11.4 + - - +
78A GLY 3.4 0.3 + - - -
79A HIS* 3.2 28.8 + + + +
81A VAL* 3.6 17.9 - - + -
145A TRP* 4.8 1.8 - - + -
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Residues in contact with ALA 75 (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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71A MET 3.2 10.5 + - - +
72A LYS* 4.1 6.5 - - + +
74A PHE* 1.3 78.2 - - - +
76A ASP* 1.3 63.2 + - - +
77A ARG 3.1 1.2 + - - -
78A GLY* 3.1 11.8 + - - -
79A HIS 3.4 13.4 + - - +
81A VAL* 3.8 3.1 - - + +
122A SER* 4.1 18.3 + - - -
123A ILE* 3.7 34.5 - - + -
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Residues in contact with ASP 76 (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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72A LYS* 3.0 58.4 + - - +
73A TRP* 3.9 8.6 - - - +
74A PHE 3.2 0.2 - - - -
75A ALA* 1.3 78.2 - - - +
77A ARG* 1.3 64.8 + - + +
78A GLY 3.3 1.4 + - - -
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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