Contacts of the helix formed by residues 68 - 76 (chain A) in PDB entry 2G4C
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 ALA 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLU* 1.3 71.9 - - - +
69A LEU* 1.3 60.1 + - - +
70A LEU 3.6 0.2 - - - -
71A GLU* 3.6 28.9 - - + +
72A ILE* 3.6 22.7 - - - +
354A PHE* 3.8 12.2 - - + -
370A LYS* 5.7 6.1 + - - +
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Residues in contact with LEU 69 (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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67A GLU* 3.4 11.1 - - + -
68A ALA* 1.3 74.6 - - - +
70A LEU* 1.3 58.2 + - + +
71A GLU 2.8 6.4 + - - -
72A ILE* 3.0 6.8 + - + +
73A CYS* 2.7 55.2 + - - -
350A LEU* 3.3 31.9 - - + +
351A TYR* 3.4 43.3 - - + -
354A PHE* 3.6 36.6 - - + -
372A LEU* 4.6 13.0 - - + -
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Residues in contact with LEU 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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67A GLU* 3.7 13.0 + - - +
68A ALA* 4.5 0.4 - - - +
69A LEU* 1.3 91.4 - - + +
71A GLU* 1.3 63.8 + - + +
73A CYS* 4.0 14.5 - - + +
74A GLN* 3.7 16.6 + - - +
79A LEU* 5.1 7.4 - - + +
86A LEU* 5.3 13.7 - - + +
87A SER 6.2 0.2 - - - -
88A ARG* 5.8 10.8 - - + -
91A LEU* 4.2 26.0 - - + -
347A LEU* 6.2 0.7 - - + -
351A TYR* 3.5 33.9 - - + +
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Residues in contact with GLU 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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67A GLU 5.2 0.7 - - - +
68A ALA* 3.6 34.5 - - + +
69A LEU 2.8 0.4 + - - -
70A LEU* 1.3 82.0 - - + +
72A ILE* 1.3 67.9 + - + +
74A GLN* 2.9 21.7 + - - +
75A ARG* 3.0 44.8 + - - +
83A LYS* 4.3 24.9 + - - -
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Residues in contact with ILE 72 (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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68A ALA 3.6 11.0 - - - +
69A LEU* 3.0 7.1 + - + +
71A GLU* 1.3 80.0 - - + +
73A CYS* 1.3 57.5 + - - +
74A GLN 3.0 1.0 + - - -
75A ARG* 3.0 11.3 + - - +
76A ARG* 2.8 36.2 + - + +
78A PHE* 5.7 0.4 - - + -
354A PHE* 3.4 41.1 - - + -
370A LYS* 3.8 26.9 - - + +
372A LEU* 3.8 18.6 - - + -
434A GLU* 3.5 43.7 - - + +
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Residues in contact with CYS 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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69A LEU* 2.7 45.8 + - - +
70A LEU* 4.0 9.9 - - - -
72A ILE* 1.3 76.8 - - - +
74A GLN* 1.3 56.8 + - - +
76A ARG 4.2 0.2 - - - -
78A PHE* 2.8 41.8 + - + -
79A LEU* 2.9 33.5 + - + +
350A LEU* 3.6 31.4 - - - -
372A LEU* 4.9 2.5 - - - -
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Residues in contact with GLN 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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70A LEU 3.7 13.3 + - - +
71A GLU* 2.9 17.5 + - - +
73A CYS* 1.3 76.9 - - - +
75A ARG* 1.3 78.8 + - - +
76A ARG 3.1 2.6 + - - -
77A HIS* 3.2 17.7 + - - -
79A LEU* 4.2 10.0 - - - +
81A GLY 4.2 17.7 - - - +
82A SER* 4.3 2.5 - - - +
83A LYS* 3.1 37.3 - - - +
86A LEU* 5.0 7.3 - - + +
195C ASN* 5.4 2.4 - - - +
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Residues in contact with ARG 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 GLU* 3.0 43.1 + - - +
72A ILE* 3.8 12.4 - - - +
74A GLN* 1.3 89.7 - - - +
76A ARG* 1.3 88.4 + - - +
77A HIS* 3.5 13.5 + - - -
370A LYS* 5.4 9.1 - - - +
434A GLU* 5.3 4.7 - - - +
198C ASP* 5.2 2.8 - - - +
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Residues in contact with ARG 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 ILE* 2.8 21.2 + - + +
75A ARG* 1.3 95.6 + - + +
77A HIS* 1.3 70.9 + - - +
78A PHE* 3.4 15.7 + - + -
102A LEU* 3.1 21.0 - - - +
431A LYS* 3.8 36.7 - - - +
434A GLU* 2.8 44.5 + - + +
435A MET* 3.9 36.5 - - + +
198C ASP* 5.6 3.2 + - - -
199C LEU* 5.9 0.4 - - - -
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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