Contacts of the helix formed by residues 84 - 93 (chain A) in PDB entry 4RG7
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 LYS 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR* 5.3 6.3 - - + +
79A CYS* 2.7 34.8 + - + +
82A LEU* 3.3 5.6 - - + +
83A SER* 1.3 72.4 - - - +
85A LEU* 1.3 57.3 + - - +
86A ALA 3.4 2.0 - - - -
87A GLU* 3.3 15.5 + - + +
88A GLY* 2.9 24.6 + - - -
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Residues in contact with LEU 85 (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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80A VAL* 5.5 3.8 - - - +
83A SER* 3.3 9.6 + - - +
84A LYS* 1.3 73.8 - - - +
86A ALA* 1.3 65.1 + - - +
88A GLY* 3.4 2.3 + - - +
89A GLU* 3.1 22.2 + - - +
124A VAL* 4.0 29.1 - - + +
127A LYS* 6.3 1.6 - - + -
128A THR* 4.1 22.9 - - + -
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Residues in contact with ALA 86 (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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84A LYS 3.4 0.6 - - - -
85A LEU* 1.3 77.4 - - - +
87A GLU* 1.3 62.5 + - - +
89A GLU* 3.5 14.5 - - - +
90A GLN* 3.5 29.4 + - - +
128A THR* 5.4 2.6 - - - +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 4.2 13.7 + - - +
79A CYS* 2.9 32.3 - - - +
84A LYS* 3.3 15.4 + - + +
86A ALA* 1.3 77.7 - - - +
88A GLY* 1.3 79.4 + - - +
90A GLN* 2.8 40.3 + - + +
91A ILE* 3.1 36.2 + - + +
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Residues in contact with GLY 88 (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 ALA* 4.1 13.9 - - - +
79A CYS* 4.4 7.9 - - - -
80A VAL* 5.2 5.8 - - - -
84A LYS 2.9 10.1 + - - -
85A LEU* 3.4 6.0 + - - -
87A GLU* 1.3 90.3 + - - +
89A GLU* 1.3 62.4 + - - +
91A ILE* 3.6 3.6 + - - +
92A LEU* 3.5 25.8 + - - +
124A VAL* 5.6 3.6 - - - -
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Residues in contact with GLU 89 (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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85A LEU 3.1 11.5 + - - +
86A ALA* 3.5 15.4 - - - +
87A GLU 3.1 0.2 - - - -
88A GLY* 1.3 74.7 - - - +
90A GLN* 1.3 58.2 + - - +
92A LEU* 3.0 2.8 + - - +
93A SER* 2.5 49.0 + - - -
95A GLY* 4.0 18.1 - - - -
96A VAL* 4.6 11.8 + - - +
121A LEU* 4.3 13.0 - - + -
124A VAL* 5.2 6.8 - - + +
125A TYR* 3.6 32.0 + - + +
128A THR* 5.7 0.7 + - - -
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Residues in contact with GLN 90 (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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86A ALA* 3.5 19.6 + - - +
87A GLU* 2.8 26.9 + - + +
89A GLU* 1.3 74.4 - - + +
91A ILE* 1.3 65.1 + - + +
94A GLY* 3.2 17.9 + - - -
95A GLY 4.1 9.4 - - - +
96A VAL* 4.7 26.8 - - + +
97A PHE* 5.2 10.1 - - + +
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Residues in contact with ILE 91 (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* 3.7 36.7 - - + +
75A LEU* 3.8 25.8 - - + -
76A ALA* 3.8 14.1 - - + +
79A CYS* 4.5 0.2 - - - -
87A GLU* 3.1 40.9 + - + +
88A GLY 4.0 5.2 - - - +
90A GLN* 1.3 80.1 - - + +
92A LEU* 1.3 64.0 + - - +
94A GLY* 4.4 1.0 + - - -
109A GLU* 5.6 2.4 - - - +
110A PHE* 5.4 1.0 - - - -
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Residues in contact with LEU 92 (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 4.3 8.3 - - - +
73A TYR* 4.5 6.3 - - + -
76A ALA* 3.8 16.6 - - + -
88A GLY 3.5 13.4 + - - +
89A GLU 3.0 4.8 + - - +
91A ILE* 1.3 83.3 - - + +
93A SER* 1.3 65.0 + - - +
94A GLY 3.6 0.2 + - - -
101A LYS* 5.1 1.7 - - - +
106A ILE* 4.5 11.2 - - + +
109A GLU* 4.6 10.6 - - - +
110A PHE* 3.5 37.9 - - + -
117A THR* 3.8 20.2 - - - +
120A LEU* 3.9 22.0 - - + -
121A LEU* 3.8 32.3 - - + +
124A VAL* 5.9 1.1 - - + -
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Residues in contact with SER 93 (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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89A GLU* 2.5 24.1 + - - -
92A LEU* 1.3 75.6 - - - +
94A GLY* 1.3 56.6 + - - +
95A GLY* 3.1 21.1 - - - -
100A GLN* 4.0 10.4 - - - +
101A LYS* 3.0 40.1 + - - +
106A ILE* 5.0 5.3 - - - +
121A LEU* 4.3 11.2 - - - -
125A TYR* 3.5 24.0 + - - -
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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