Contacts of the helix formed by residues 70 - 80 (chain A) in PDB entry 2G43
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 70 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLY 3.0 12.2 + - - -
60A ARG* 2.7 26.2 - - - +
61A ARG* 2.7 43.1 + - - +
68A GLY 3.6 0.8 - - - -
69A ASN* 1.3 78.1 - - - +
71A HIS* 1.3 57.0 + - - +
72A ALA 3.3 3.4 - - - -
73A VAL* 2.8 34.0 - - + +
74A GLU* 2.9 27.7 + - + +
77A ARG* 5.2 7.2 + - - +
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Residues in contact with HIS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ZN 2.0 39.1 - - - -
38A CYS* 3.4 10.5 - - - -
40A LYS* 3.8 30.8 + - + +
41A CYS* 3.4 20.2 - - + -
57A LEU* 3.7 12.4 - - + +
58A CYS* 3.3 5.6 + - - -
69A ASN* 3.1 18.1 + - + +
70A ASN* 1.3 78.1 - - - +
72A ALA* 1.3 62.7 + - - +
74A GLU* 3.7 21.0 - - - +
75A HIS* 3.0 23.7 + - - +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 4.4 11.9 - - + +
50A ASN* 5.8 0.9 + - - -
57A LEU* 3.5 27.9 - - + +
58A CYS 3.1 19.5 + - - +
59A GLY* 5.0 2.2 - - - -
60A ARG 5.8 0.2 - - - +
71A HIS* 1.3 78.0 - - - +
73A VAL* 1.3 57.5 + - - +
75A HIS* 3.1 6.1 + - - +
76A TYR* 2.9 25.5 + - - +
100A TYR* 3.1 25.3 + - + +
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Residues in contact with VAL 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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58A CYS 4.8 0.2 + - - -
60A ARG* 4.3 23.5 - - + +
70A ASN* 2.8 53.8 - - + +
72A ALA* 1.3 75.8 - - - +
74A GLU* 1.3 68.4 + - + +
76A TYR* 3.0 7.6 + - + +
77A ARG* 3.0 49.6 + - + +
100A TYR* 3.9 28.4 + - + -
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 5.9 1.5 - - - +
69A ASN 3.9 4.0 - - - +
70A ASN* 2.9 42.5 + - + +
71A HIS* 3.7 22.0 + - - +
73A VAL* 1.3 76.0 - - - +
75A HIS* 1.3 61.7 + - - +
77A ARG* 3.3 32.9 + - - +
78A GLU* 3.3 21.8 + - - +
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Residues in contact with HIS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 4.1 19.2 + - - +
50A ASN* 4.4 14.4 - - + -
53A ASP* 2.7 30.5 + - - -
55A SER* 3.3 23.6 + - - -
57A LEU* 3.3 22.4 - - + +
71A HIS 3.0 6.3 + - - +
72A ALA* 3.2 9.9 - - - +
73A VAL 3.1 0.2 - - - -
74A GLU* 1.3 78.0 - - - +
76A TYR* 1.3 63.0 + - - +
78A GLU* 3.1 7.9 + - - +
79A THR* 3.0 50.6 + - + +
81A TYR* 4.5 0.2 - - - -
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Residues in contact with TYR 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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50A ASN* 5.6 0.7 - - - +
72A ALA 2.9 12.8 + - - +
73A VAL* 3.0 13.4 + - + +
75A HIS* 1.3 78.7 - - - +
77A ARG* 1.3 71.2 + - + +
79A THR* 4.0 5.4 - - - -
80A GLY* 2.8 50.5 + - - -
81A TYR 3.4 22.7 - - - +
82A PRO* 4.1 7.6 - - + -
100A TYR* 3.5 51.4 - + + -
101A ASP* 3.7 23.0 + - + +
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Residues in contact with ARG 77 (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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60A ARG* 5.3 4.2 - - - +
70A ASN* 5.2 6.1 + - - -
73A VAL* 3.0 43.3 + - + +
74A GLU* 3.6 29.7 - - - +
75A HIS 3.3 0.2 - - - -
76A TYR* 1.3 86.2 - - + +
78A GLU* 1.3 60.8 + - + +
80A GLY 5.0 0.5 + - - -
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Residues in contact with GLU 78 (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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74A GLU* 3.3 15.0 - - - +
75A HIS* 3.1 9.3 + - - +
76A TYR 3.0 0.6 - - - -
77A ARG* 1.3 83.2 - - + +
79A THR* 1.3 63.5 + - + +
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Residues in contact with THR 79 (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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75A HIS* 3.0 44.2 + - + +
76A TYR* 3.9 3.6 + - - -
78A GLU* 1.3 83.8 - - + +
80A GLY* 1.3 62.6 + - - +
81A TYR* 3.2 52.7 + - + +
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Residues in contact with GLY 80 (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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76A TYR* 2.8 35.8 + - - -
77A ARG 4.8 0.4 + - - -
78A GLU 3.8 0.4 - - - -
79A THR* 1.3 72.7 - - - +
81A TYR* 1.3 61.0 + - - +
82A PRO* 3.0 15.6 - - - +
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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