Contacts of the helix formed by residues 79 - 93 (chain D) in PDB entry 3GHG
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 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D GLU 3.6 19.5 + - - +
76D TYR* 3.5 10.1 + - - +
78D LYS* 1.3 78.7 - - - +
80D ASN* 1.3 60.3 + - - +
81D LYS 3.4 0.2 - - - -
82D ASP* 3.5 28.3 + - - +
83D SER* 3.7 8.3 + - - -
54F THR* 4.4 21.0 + - - +
58F LYS* 5.5 13.1 + - - +
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Residues in contact with ASN 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TYR* 2.8 31.3 + - + +
77D GLN* 3.6 20.4 + - - +
79D ASN* 1.3 73.5 - - - +
81D LYS* 1.3 61.6 + - - +
82D ASP 3.1 4.9 - - - -
83D SER* 2.9 23.6 + - - -
84D HIS* 3.0 27.9 + - - +
107E VAL* 5.6 5.5 - - - +
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Residues in contact with LYS 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D GLN 3.5 18.4 - - - +
78D LYS* 3.6 13.8 + - + +
79D ASN 3.4 0.6 - - - -
80D ASN* 1.3 80.7 - - - +
82D ASP* 1.3 61.7 + - - +
84D HIS* 4.2 8.4 - - + +
85D SER* 2.8 25.3 + - - -
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Residues in contact with ASP 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D LYS 3.0 20.2 - - - +
79D ASN* 3.6 22.1 - - - +
80D ASN 3.1 0.8 - - - -
81D LYS* 1.3 80.2 - - - +
83D SER* 1.3 59.0 + - - +
85D SER* 3.6 4.0 - - - -
86D LEU* 3.3 36.5 + - + +
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Residues in contact with SER 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ASN 3.7 6.3 + - - -
80D ASN* 2.9 30.0 + - - -
82D ASP* 1.3 76.9 - - - +
84D HIS* 1.3 58.2 + - - +
85D SER 3.1 1.8 - - - -
86D LEU* 3.2 10.7 + - - +
87D THR* 2.9 35.2 + - - -
114E SER* 5.7 0.5 + - - -
57F VAL* 4.9 18.6 - - - -
61F ILE* 6.2 0.7 - - - -
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Residues in contact with HIS 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ASN* 3.0 25.6 + - - +
81D LYS* 4.7 8.3 - - + +
83D SER* 1.3 81.6 + - - +
85D SER* 1.3 58.2 + - - +
87D THR* 4.0 9.2 - - + -
88D THR* 3.0 37.3 + - - -
114E SER* 5.7 4.9 - - - -
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Residues in contact with SER 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LYS 2.8 20.8 + - - -
82D ASP* 3.6 11.0 - - - -
83D SER 3.1 0.6 - - - -
84D HIS* 1.3 77.0 - - - +
86D LEU* 1.3 64.9 + - - +
87D THR 3.2 0.2 - - - -
88D THR* 3.5 3.3 + - - -
89D ASN* 2.9 42.5 + - - +
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Residues in contact with LEU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ASP* 3.3 19.4 + - + +
83D SER* 3.2 10.8 + - - +
85D SER* 1.3 82.8 - - - +
87D THR* 1.3 57.2 + - - +
89D ASN* 4.1 13.5 - - - +
90D ILE* 3.1 37.9 + - + +
61F ILE* 3.0 57.7 - - + -
64F ILE* 5.7 0.7 - - + -
65F GLN* 3.7 15.3 - - + +
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Residues in contact with THR 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D SER* 2.9 18.2 + - - -
84D HIS* 4.1 10.9 - - + -
85D SER 3.2 0.4 - - - -
86D LEU* 1.3 76.1 - - - +
88D THR* 1.3 55.0 + - - +
89D ASN 3.3 0.2 - - - -
90D ILE* 3.6 5.6 - - + +
91D MET* 2.7 46.7 + - + +
114E SER* 5.4 3.9 + - - +
118E MET* 5.6 6.6 - - + +
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Residues in contact with THR 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D HIS* 3.0 29.6 + - - -
85D SER* 4.1 3.8 - - - -
87D THR* 1.3 76.3 - - - +
89D ASN* 1.3 64.4 + - - +
91D MET* 3.7 9.8 - - + +
92D GLU* 3.1 40.3 + - + +
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Residues in contact with ASN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D SER* 2.9 34.2 + - - +
86D LEU* 4.1 15.7 - - - +
88D THR* 1.3 81.2 - - - +
90D ILE* 1.3 58.4 - - + +
92D GLU* 4.9 1.8 - - - -
93D ILE* 2.9 44.5 + - + +
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Residues in contact with ILE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D LEU* 3.1 27.1 + - + +
87D THR* 3.9 5.6 - - - +
89D ASN* 1.3 72.9 - - + +
91D MET* 1.3 63.5 + - + +
92D GLU 3.2 1.2 + - - -
93D ILE* 4.0 15.3 - - + -
94D LEU* 3.1 40.8 + - + +
118E MET* 5.7 9.0 - - + -
61F ILE* 4.5 7.6 - - + -
64F ILE* 3.7 42.8 - - + +
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Residues in contact with MET 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D THR* 2.7 36.0 + - + +
88D THR* 3.7 13.2 - - + +
90D ILE* 1.3 73.7 - - + +
92D GLU* 1.3 56.6 + - + +
94D LEU* 4.8 2.1 - - - +
95D ARG* 3.6 27.7 + - - +
121E LEU* 6.4 2.5 - - - -
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Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D THR* 3.1 27.1 + - - +
89D ASN* 4.3 2.7 - - - +
90D ILE 3.2 0.2 - - - -
91D MET* 1.3 78.5 - - + +
93D ILE* 1.3 58.4 + - + +
94D LEU 3.1 4.9 - - - -
95D ARG* 2.7 36.6 + - - +
96D GLY* 3.3 21.7 + - - -
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Residues in contact with ILE 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ASN* 2.9 36.1 + - + +
90D ILE* 4.0 20.2 - - + -
92D GLU* 1.3 76.8 - - + +
94D LEU* 1.3 72.8 + - + +
96D GLY* 4.3 2.7 - - - -
97D ASP* 3.7 23.2 + - - +
64F ILE* 5.9 2.7 - - + +
68F TYR* 3.9 24.5 - - + +
69F ASN 6.0 1.6 - - - -
70F PRO* 6.3 3.1 - - + -
72F GLU* 4.4 11.8 - - - +
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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