Contacts of the helix formed by residues 102 - 113 (chain J) in PDB entry 5A15
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 GLU 102 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81J LEU* 4.1 7.4 - - + +
100J PHE* 3.2 29.6 - - + -
101J PRO* 1.3 82.3 - - + +
103J LYS* 1.3 63.6 + - - +
104J GLY 3.4 2.0 - - - +
105J ARG* 3.6 37.4 + - - +
106J LEU* 3.6 14.4 + - - +
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Residues in contact with LYS 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J LEU* 4.0 17.3 - - + -
100J PHE* 3.4 35.0 - - + +
101J PRO 3.7 2.2 + - - -
102J GLU* 1.3 74.4 - - - +
104J GLY* 1.3 66.2 + - - +
105J ARG 3.5 0.2 + - - -
106J LEU* 3.5 6.4 + - - +
107J LYS* 3.5 17.7 + - - +
122J LEU* 4.6 17.9 - - + +
124J PRO* 6.4 0.4 - - - +
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Residues in contact with GLY 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J GLU* 3.4 0.8 - - - +
103J LYS* 1.3 78.6 - - - +
105J ARG* 1.3 62.8 + - - +
107J LYS* 3.3 10.5 + - - +
108J ARG* 3.2 18.7 + - - +
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Residues in contact with ARG 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J ASP* 4.4 15.8 + - - -
81J LEU* 3.7 21.2 - - + +
102J GLU* 3.6 31.5 + - - +
103J LYS 3.3 0.4 - - - -
104J GLY* 1.3 73.5 - - - +
106J LEU* 1.3 60.8 + - - +
108J ARG* 2.8 12.5 + - - +
109J GLU* 2.8 32.6 + - + +
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Residues in contact with LEU 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81J LEU* 3.6 32.9 - - + +
84J TYR* 3.9 22.7 - - + -
85J ILE* 3.4 32.1 - - + +
94J VAL* 4.9 3.6 - - + -
96J LEU* 4.3 17.0 - - + -
100J PHE* 4.6 7.0 - - + -
102J GLU 3.6 10.5 + - - +
103J LYS 3.5 8.9 + - - +
104J GLY 3.4 0.6 - - - -
105J ARG* 1.3 78.1 - - - +
107J LYS* 1.3 56.7 + - - +
109J GLU* 3.2 5.0 + - + +
110J ALA* 2.9 27.9 + - - +
118J LEU* 5.2 2.5 - - + -
122J LEU* 3.6 28.3 - - + -
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Residues in contact with LYS 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J LYS 3.5 6.8 + - - +
104J GLY* 3.3 13.4 + - - +
106J LEU* 1.3 79.5 - - - +
108J ARG* 1.3 56.9 + - - +
110J ALA* 3.3 4.5 + - - +
111J GLU* 3.0 37.8 + - - +
119J VAL* 4.0 9.3 - - + +
122J LEU* 3.5 35.1 - - + +
123J THR* 5.5 1.8 - - - +
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Residues in contact with ARG 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77J ARG* 3.8 32.0 - - - +
104J GLY 3.2 7.6 + - - +
105J ARG* 2.8 18.9 + - + +
107J LYS* 1.3 77.4 - - - +
109J GLU* 1.3 66.7 + - - +
111J GLU* 3.2 21.4 + - - +
112J TYR* 3.1 25.2 + - - +
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Residues in contact with GLU 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77J ARG* 2.8 52.7 + - - +
78J ASP* 4.6 11.9 + - - +
81J LEU* 3.9 28.1 - - + +
85J ILE* 4.1 16.4 - - + -
105J ARG* 2.8 19.8 + - - +
106J LEU* 3.2 9.2 + - - +
108J ARG* 1.3 76.8 + - - +
110J ALA* 1.3 60.4 + - - +
112J TYR* 3.1 2.1 + - - +
113J PHE* 2.8 42.7 + - + -
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Residues in contact with ALA 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J ILE* 4.0 7.8 - - - +
106J LEU 2.9 11.4 + - - +
107J LYS* 3.4 11.7 - - - +
108J ARG 3.3 0.2 - - - -
109J GLU* 1.3 75.1 - - - +
111J GLU* 1.3 57.6 + - - +
113J PHE 3.5 1.1 + - - +
114J GLN 2.8 8.5 + - - -
115J LEU* 2.8 32.0 + - - +
118J LEU* 3.5 38.4 - - + -
119J VAL* 3.8 15.0 - - + +
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Residues in contact with GLU 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J LYS* 3.0 23.3 + - - +
108J ARG* 3.3 24.2 + - - +
109J GLU 3.2 0.2 - - - -
110J ALA* 1.3 74.8 - - - +
112J TYR* 1.3 65.1 + - - +
114J GLN* 3.0 19.3 + - - +
119J VAL* 3.6 28.0 - - + +
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Residues in contact with TYR 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J LEU* 3.3 37.5 - - + +
54J MET* 6.0 0.9 - - - -
75J ILE* 5.1 4.0 - - + +
76J ASP* 5.5 1.9 + - - +
77J ARG* 3.3 70.3 - - + +
108J ARG* 3.1 12.5 + - - +
109J GLU 3.1 5.4 + - - +
111J GLU* 1.3 77.9 - - - +
113J PHE* 1.3 71.8 + + - +
114J GLN* 3.2 13.7 + - - +
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Residues in contact with PHE 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J SER* 4.1 0.2 - - - -
50J LEU* 3.2 29.2 + - + -
51J LEU* 3.9 29.7 + - + -
54J MET* 6.2 0.4 - - - -
75J ILE* 4.1 16.8 - - + -
77J ARG* 4.1 19.1 - - + -
82J PHE* 3.6 38.1 - + + -
85J ILE* 4.0 21.3 - - + -
109J GLU* 2.8 45.3 + - - +
112J TYR* 1.3 82.2 - + - +
114J GLN* 1.3 72.4 + - - +
115J LEU* 3.9 24.1 - - + +
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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