Contacts of the helix formed by residues 101 - 114 (chain Q) in PDB entry 2J28
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 ASP 101 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97Q ILE 3.6 0.8 + - - +
98Q ALA 3.1 7.9 + - - -
99Q VAL 3.1 1.8 + - - -
100Q PHE* 1.3 84.9 - - + +
102Q LYS* 1.3 67.3 + - - +
103Q VAL* 3.0 32.0 - - - +
104Q ALA* 3.0 19.2 + - + +
105Q PHE* 2.8 31.9 + - + -
45R GLU* 5.4 7.4 - - + +
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Residues in contact with LYS 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J HIS* 5.8 4.5 - - + +
67Q ALA* 3.9 29.0 - - + +
70Q GLN* 3.0 32.8 - - - +
98Q ALA* 3.4 13.5 + - + +
99Q VAL* 4.7 8.8 + - - +
101Q ASP* 1.3 71.6 - - - +
103Q VAL* 1.3 63.8 + - + +
105Q PHE* 2.8 6.2 + - + +
106Q THR* 2.5 56.6 + - + +
109Q VAL* 5.0 2.8 - - - +
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Residues in contact with VAL 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q ASP* 3.0 29.4 - - - +
102Q LYS* 1.3 80.9 - - + +
104Q ALA* 1.3 63.7 + - + +
106Q THR* 3.4 17.2 - - - +
107Q ALA* 4.1 7.3 + - - +
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Residues in contact with ALA 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q ASP* 3.0 29.6 + - + +
103Q VAL* 1.3 81.6 - - + +
105Q PHE* 1.3 65.8 + - + +
107Q ALA* 3.5 16.6 - - - +
108Q LEU 4.1 1.2 + - - -
111Q LYS* 5.2 0.5 + - - -
44R GLY 3.2 15.2 - - - +
45R GLU* 4.1 28.7 - - + +
50R GLY* 5.4 5.4 - - - +
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Residues in contact with PHE 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Q PHE* 5.5 0.2 - - - -
94Q LEU* 3.9 38.6 - - + -
97Q ILE* 3.7 20.2 - - + -
98Q ALA* 3.2 47.8 - - + +
101Q ASP* 2.8 23.4 + - + +
102Q LYS* 2.8 12.7 + - - +
104Q ALA* 1.3 78.3 - - + +
106Q THR* 1.3 60.8 + - - +
107Q ALA 2.9 5.8 - - - -
108Q LEU* 2.9 33.9 + - + +
109Q VAL* 3.5 7.4 + - - +
43R ASN* 5.5 3.6 - - - -
44R GLY 4.5 14.6 - - - -
45R GLU* 4.6 15.3 - - + -
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Residues in contact with THR 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Q GLN* 3.4 24.8 + - - -
102Q LYS* 2.5 51.7 + - + +
103Q VAL* 3.4 16.4 - - - +
105Q PHE* 1.3 72.9 - - - +
107Q ALA* 1.3 64.1 + - + +
109Q VAL* 3.1 27.5 - - - +
110Q GLU* 3.7 12.5 + - - +
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Residues in contact with ALA 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q VAL 4.2 7.6 - - - +
104Q ALA* 3.5 14.4 - - - +
106Q THR* 1.3 80.3 - - + +
108Q LEU* 1.3 57.0 + - - +
109Q VAL 3.0 2.0 - - - -
110Q GLU* 2.7 41.7 + - + +
111Q LYS* 3.4 17.9 - - - +
50R GLY* 5.1 13.0 - - - -
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Residues in contact with LEU 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Q PHE* 4.3 10.8 - - + -
82Q LEU* 3.5 13.7 - - + -
88Q GLU* 3.5 17.7 - - - +
91Q ARG* 5.2 1.3 - - + -
94Q LEU* 4.4 14.6 - - + -
104Q ALA 4.1 1.5 + - - +
105Q PHE* 2.9 29.1 + - + +
107Q ALA* 1.3 77.7 - - - +
109Q VAL* 1.3 61.3 + - - +
110Q GLU 3.3 0.3 + - - -
111Q LYS* 3.3 26.1 + - + +
112Q ALA* 3.2 19.9 + - - +
44R GLY 5.3 2.2 - - - +
53R PHE* 3.2 54.1 - - + -
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Residues in contact with VAL 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Q ALA* 5.0 8.3 - - - +
70Q GLN* 3.5 26.2 - - - +
73Q ILE* 4.9 9.6 - - + -
78Q PHE* 3.5 35.7 - - + -
102Q LYS* 5.0 2.2 - - - +
105Q PHE 3.7 10.3 - - - +
106Q THR* 3.1 21.3 - - - +
108Q LEU* 1.3 79.1 - - - +
110Q GLU* 1.3 50.2 + - - +
112Q ALA* 3.6 1.3 - - - +
113Q LYS* 2.6 59.8 + - + +
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Residues in contact with GLU 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Q GLN* 5.4 0.5 - - - +
106Q THR* 3.9 12.0 + - - +
107Q ALA* 2.7 33.1 + - + +
109Q VAL* 1.3 69.2 - - - +
111Q LYS* 1.3 65.7 + - + +
113Q LYS* 3.2 28.6 + - - +
114Q ALA* 3.1 21.1 + - - +
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Residues in contact with LYS 111 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85Q ALA* 4.7 8.7 - - + +
88Q GLU* 4.2 14.4 - - - +
104Q ALA 5.2 0.2 + - - -
107Q ALA* 3.4 16.6 - - - +
108Q LEU* 3.3 47.1 + - + +
110Q GLU* 1.3 76.2 - - + +
112Q ALA* 1.3 65.2 + - - +
114Q ALA* 3.1 21.2 + - - +
44R GLY* 4.1 11.1 + - - -
50R GLY* 4.8 2.9 + - - -
51R VAL 3.9 5.4 + - - +
52R PRO* 3.0 55.5 - - + +
53R PHE 3.9 5.1 - - - +
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Residues in contact with ALA 112 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Q PHE* 3.7 23.6 - - + +
81Q GLY* 3.6 15.8 - - - -
82Q LEU* 3.5 42.8 - - + +
85Q ALA* 4.8 0.4 - - - -
108Q LEU 3.2 9.8 + - - +
109Q VAL* 3.7 6.3 - - + +
111Q LYS* 1.3 78.7 - - - +
113Q LYS* 1.3 64.7 + - - +
114Q ALA 3.0 1.9 + - - -
115Q ALA* 3.2 11.3 + - - +
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Residues in contact with LYS 113 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Q GLN* 4.4 3.0 + - - +
71Q ASN* 3.2 43.3 - - - +
73Q ILE* 4.7 15.4 - - + +
109Q VAL* 2.6 40.9 + - + +
110Q GLU* 3.2 31.1 + - - +
112Q ALA* 1.3 73.5 - - - +
114Q ALA* 1.3 54.9 + - - +
115Q ALA* 2.8 11.3 + - - +
116Q LEU* 4.7 6.2 - - - +
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Residues in contact with ALA 114 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q GLU 3.1 9.1 + - - +
111Q LYS* 3.4 14.2 - - - +
112Q ALA 3.0 3.8 + - - -
113Q LYS* 1.3 74.5 - - - +
115Q ALA* 1.3 62.0 + - - +
116Q LEU* 3.1 14.5 + - - +
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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