Contacts of the helix formed by residues 100 - 109 (chain J) in PDB entry 3BBX
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 VAL 100 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74J TYR* 3.3 36.1 - - + -
76J HIS* 4.2 8.7 - - - +
93J ILE* 3.4 30.5 - - + -
97J PRO* 5.1 0.2 - - + -
98J GLU* 2.5 21.6 + - + +
99J ARG* 1.3 78.3 - - - +
101J ILE* 1.3 75.2 + - + +
102J GLU* 2.5 30.3 + - - +
103J ILE* 2.6 25.3 + - - +
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Residues in contact with ILE 101 (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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59J ALA 5.6 0.9 - - - +
62J VAL* 4.0 27.4 - - + -
72J LYS* 5.1 0.9 - - - +
74J TYR* 3.6 22.2 + - + +
90J GLU* 4.0 22.9 - - + +
93J ILE* 5.0 7.0 - - + +
94J ALA* 4.6 13.5 - - + -
97J PRO* 4.0 18.2 - - + -
100J VAL* 1.3 98.1 - - + +
102J GLU* 1.3 72.4 + - - +
103J ILE 2.9 0.2 - - - -
104J ALA* 2.6 39.9 + - - +
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Residues in contact with GLU 102 (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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28J LEU* 5.7 3.5 - - - +
32J LEU* 5.0 10.2 - - - +
56J VAL* 5.5 5.1 - - + +
59J ALA* 4.7 14.1 - - + -
97J PRO* 2.4 42.9 - - + +
98J GLU* 2.6 22.6 - - - +
100J VAL 2.5 14.6 + - - +
101J ILE* 1.3 93.4 - - + +
103J ILE* 1.3 71.9 + - + +
104J ALA* 3.0 5.9 + - - +
105J VAL* 4.2 8.5 + - - +
124J VAL* 3.0 39.7 - - + +
125J TYR 4.6 0.2 - - - +
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Residues in contact with ILE 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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98J GLU 3.1 11.9 - - - +
99J ARG* 3.5 19.1 - - + -
100J VAL* 2.6 41.8 + - - +
101J ILE 4.1 1.1 - - - -
102J GLU* 1.3 81.7 - - + +
104J ALA* 1.3 54.3 + - - -
105J VAL* 2.9 18.2 + - + +
106J LYS* 3.2 30.3 + - + +
107J GLY 4.6 0.5 + - - -
119J PHE 6.4 0.2 - - - -
120J ARG* 4.8 21.3 - - + +
122J LEU* 5.2 4.0 - - + -
124J VAL* 3.5 20.9 - - + -
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Residues in contact with ALA 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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26J GLY* 6.0 4.7 - - - -
29J ALA* 4.7 14.6 - - + -
72J LYS* 5.3 9.2 - - - +
101J ILE* 2.6 27.9 + - - +
102J GLU 3.0 3.3 - - - +
103J ILE* 1.3 71.6 - - - +
105J VAL* 1.3 59.1 + - - +
106J LYS 3.4 0.2 - - - -
107J GLY* 3.8 7.3 + - - -
108J MET* 3.8 19.3 + - + +
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Residues in contact with VAL 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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29J ALA* 4.6 8.8 - - + +
32J LEU* 4.5 9.9 - - + +
33J ALA* 3.7 35.7 - - + +
36J LEU* 4.2 10.5 - - + -
102J GLU 4.2 5.5 + - - +
103J ILE* 2.9 14.8 - - + -
104J ALA* 1.3 78.1 - - - +
106J LYS* 1.3 62.4 + - + +
108J MET* 2.7 26.6 + - - -
109J LEU* 3.0 26.2 + - + +
119J PHE 5.1 7.0 - - - +
120J ARG* 6.3 0.2 - - - -
122J LEU* 4.3 20.6 - - + -
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Residues in contact with LYS 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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2041B U 5.4 5.9 + - - -
99J ARG* 5.4 13.2 - - + +
103J ILE* 3.2 27.0 + - + +
105J VAL* 1.3 83.8 - - + +
107J GLY* 1.3 61.0 + - - +
108J MET 3.1 0.7 + - - -
109J LEU* 3.2 21.8 + - - +
111J LYS* 3.9 13.8 - - + +
116J ARG* 5.4 12.1 - - - +
119J PHE* 5.9 12.1 - - + +
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Residues in contact with GLY 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 ILE 4.6 0.6 + - - -
104J ALA 3.8 6.6 + - - -
105J VAL 3.2 0.8 - - - -
106J LYS* 1.3 79.0 - - - +
108J MET* 1.3 61.3 + - - +
109J LEU 3.4 0.9 - - - -
111J LYS* 4.1 22.2 + - - +
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Residues in contact with MET 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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1006B C 5.3 9.9 - - - -
1138B G 5.3 14.6 - - - +
1139B G 6.5 0.9 - - - -
26J GLY 4.3 6.7 - - - +
29J ALA* 3.4 32.5 - - + -
30J THR* 4.0 30.5 - - + -
33J ALA* 4.1 13.3 - - + +
37J ARG* 5.9 0.3 + - - -
104J ALA* 3.8 13.5 - - + +
105J VAL* 2.7 16.2 + - - +
107J GLY* 1.3 81.0 - - - +
109J LEU* 1.3 62.1 + - - +
110J PRO* 4.7 0.3 - - - +
111J LYS* 5.7 0.2 - - - -
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Residues in contact with LEU 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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33J ALA* 4.0 24.5 - - + +
36J LEU* 4.8 9.0 - - + +
37J ARG* 5.5 2.0 - - + +
105J VAL* 3.0 33.4 + - + +
106J LYS* 3.2 13.9 + - - +
108J MET* 1.3 81.2 - - - +
110J PRO* 1.3 70.5 - - + +
111J LYS* 2.7 38.6 + - - +
115J GLY 4.0 12.6 - - - +
118J MET* 4.2 13.5 - - + -
119J PHE* 3.8 31.9 - - + +
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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