Contacts of the helix formed by residues 70 - 80 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLY 3.0 12.6 + - - -
60B ARG* 3.0 15.2 - - - +
61B ARG* 2.7 44.1 + - - +
68B GLY 3.6 0.4 - - - -
69B ASN* 1.3 77.8 - - - +
71B HIS* 1.3 62.0 + - - +
72B ALA 3.4 2.2 - - - -
73B VAL* 3.3 15.3 - - + +
74B GLU* 2.8 38.1 + - + +
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Residues in contact with HIS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B CYS* 3.9 8.1 - - - -
40B LYS* 3.6 32.9 + - + +
41B CYS* 3.7 18.8 - - + -
57B LEU* 3.6 10.2 - - + +
58B CYS* 3.3 7.4 + - - -
69B ASN* 3.2 19.7 + - + -
70B ASN* 1.3 77.8 - - - +
72B ALA* 1.3 62.7 + - - +
74B GLU* 3.5 20.7 + - - +
75B HIS* 3.1 22.3 + - - +
131B ZN 2.1 38.7 - - - -
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TRP* 4.2 10.5 - - + +
50B ASN* 5.5 1.2 + - - -
57B LEU* 3.5 27.7 - - + +
58B CYS 2.9 18.6 + - - +
71B HIS* 1.3 76.3 - - - +
73B VAL* 1.3 61.1 + - - +
75B HIS* 3.2 5.7 + - - +
76B TYR* 3.1 17.0 + - - +
100B TYR* 3.1 26.5 + - + +
134B UNX 3.7 6.1 - - - +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 4.4 17.5 - - + +
70B ASN* 3.3 36.3 - - + +
72B ALA* 1.3 77.8 - - - +
74B GLU* 1.3 71.0 + - + +
76B TYR* 3.2 7.6 + - + +
77B ARG* 3.0 21.9 + - + +
100B TYR* 3.6 30.3 + - + -
134B UNX 3.8 6.7 + - - +
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Residues in contact with GLU 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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69B ASN 4.6 1.1 - - - +
70B ASN* 2.8 35.7 + - + +
71B HIS* 3.8 23.3 + - + +
73B VAL* 1.3 78.1 - - + +
75B HIS* 1.3 61.8 + - - +
77B ARG* 3.3 13.8 + - - +
78B GLU* 3.1 24.4 + - - +
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Residues in contact with HIS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 5.4 7.8 + - - +
50B ASN* 4.2 15.9 - - + -
53B ASP* 2.5 29.5 + - - -
55B SER* 3.4 24.4 + - - -
57B LEU* 3.4 22.8 - - + +
71B HIS 3.1 5.5 + - - +
72B ALA 3.3 9.9 - - - +
73B VAL 3.1 0.4 - - - -
74B GLU* 1.3 75.6 - - - +
76B TYR* 1.3 59.8 + - - +
78B GLU* 3.1 13.7 + - - +
79B THR* 2.8 59.0 + - + +
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Residues in contact with TYR 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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50B ASN* 5.4 0.8 - - - +
72B ALA 3.1 10.0 + - - +
73B VAL* 3.2 13.9 + - + +
75B HIS* 1.3 78.1 - - - +
77B ARG* 1.3 65.3 + - + +
79B THR* 4.1 5.2 - - - -
80B GLY* 2.7 50.4 + - - -
81B TYR 3.3 23.6 - - - +
82B PRO* 4.1 2.7 - - + -
100B TYR* 3.4 55.1 + + + -
101B ASP* 3.4 34.9 + - - -
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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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73B VAL* 3.0 13.9 + - + +
74B GLU* 3.4 15.9 + - - +
75B HIS 3.3 0.4 - - - -
76B TYR* 1.3 84.0 - - + +
78B GLU* 1.3 61.8 + - - +
80B GLY* 4.8 0.3 + - - -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 5.7 2.6 + - - -
74B GLU 3.1 15.6 + - - +
75B HIS* 3.6 13.5 + - - +
76B TYR 3.0 0.4 - - - -
77B ARG* 1.3 82.3 - - - +
79B THR* 1.3 69.4 + - + +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 2.8 52.1 + - + +
76B TYR* 4.1 0.3 - - - -
78B GLU* 1.3 86.3 - - + +
80B GLY* 1.3 63.7 + - - +
81B TYR* 3.1 51.9 + - + +
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 2.7 38.0 + - - -
77B ARG 4.7 0.8 + - - -
78B GLU 3.8 0.4 - - - -
79B THR* 1.3 72.5 + - - +
81B TYR* 1.3 60.4 + - - +
82B PRO* 3.0 15.1 - - - +
101B ASP* 4.5 2.8 - - - +
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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