Contacts of the helix formed by residues 102 - 112 (chain E) in PDB entry 3PHW
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 THR 102 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E GLU* 2.6 30.5 + - - +
101E SER* 1.3 71.9 - - - +
103E LEU* 1.3 60.0 + - - +
105E ALA* 3.7 1.1 - - - -
106E SER* 3.0 24.1 + - - -
118E ILE* 3.6 23.5 - - + +
131E ILE* 4.4 9.2 - - + -
133E PHE* 3.5 29.3 - - + -
42F ARG* 5.5 0.7 - - - -
71F LEU 4.0 2.6 + - - +
72F ARG* 3.6 1.9 - - - -
73F LEU* 3.0 43.2 + - + +
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E TYR* 4.2 5.6 - - + -
76E GLU* 3.9 22.9 - - + +
78E GLU* 3.3 17.6 + - + -
79E ALA* 3.8 26.9 - - + +
82E VAL* 3.5 31.4 - - + -
89E TYR* 4.0 20.6 - - + +
101E SER* 3.0 4.9 + - - +
102E THR* 1.3 77.1 - - - +
104E GLU* 1.3 65.5 + - - +
106E SER* 3.4 4.7 + - - -
107E MET* 3.2 33.8 + - + +
72F ARG* 3.5 18.8 - - - +
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Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PHE* 3.8 16.4 - - + -
42E TYR* 3.6 20.9 - - - +
65E THR* 3.6 17.7 - - + -
89E TYR* 2.6 37.2 + - - +
93E MET* 4.5 2.3 - - - +
99E TRP 4.5 2.8 - - - +
100E GLY* 3.4 3.4 - - - -
101E SER* 2.6 49.0 + - - +
103E LEU* 1.3 78.3 - - - +
105E ALA* 1.3 56.3 + - - +
107E MET* 3.8 6.4 - - + +
108E LEU* 2.7 43.9 + - + +
72F ARG* 5.3 2.3 + - - -
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Residues in contact with ALA 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PHE* 3.8 16.9 - - + -
101E SER 3.3 8.3 + - - +
102E THR 3.7 7.0 - - - +
104E GLU* 1.3 76.9 - - - +
106E SER* 1.3 57.6 + - - +
108E LEU* 4.5 0.2 - - - -
109E ALA* 2.9 32.4 + - - +
116E ILE* 3.5 34.6 - - + +
118E ILE* 4.2 7.4 - - + -
133E PHE* 4.0 16.2 - - + +
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Residues in contact with SER 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN* 3.3 16.6 + - - +
76E GLU* 2.7 27.8 + - - -
78E GLU* 5.8 1.3 - - - -
102E THR 3.0 13.6 + - - -
103E LEU* 3.6 9.2 - - - -
105E ALA* 1.3 78.7 - - - +
107E MET* 1.3 62.0 + - - +
109E ALA* 3.7 2.6 + - - +
110E LYS* 3.1 33.5 + - - +
133E PHE* 3.6 24.1 - - - +
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Residues in contact with MET 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E THR* 4.6 5.8 - - + -
68E ALA* 3.6 17.3 - - + +
69E ALA* 3.8 17.5 - - + -
72E TYR* 4.1 6.1 - - + -
73E TYR* 3.8 30.7 - - + -
76E GLU* 3.7 25.1 - - + +
89E TYR* 3.3 36.3 - - + +
103E LEU* 3.2 28.0 + - + +
104E GLU* 3.9 9.4 - - + +
106E SER* 1.3 76.6 - - - +
108E LEU* 1.3 61.4 + - + +
110E LYS* 3.2 8.2 + - - +
111E GLU* 2.9 26.0 + - - +
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Residues in contact with LEU 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PHE* 4.0 22.7 - - + -
45E ILE* 4.7 9.0 - - + -
61E ILE* 3.9 19.1 - - + +
64E LEU* 3.9 17.9 - - + +
65E THR* 3.4 46.7 - - + +
68E ALA* 4.9 1.6 - - + -
104E GLU* 2.7 28.8 + - + +
105E ALA* 4.2 2.0 - - - +
107E MET* 1.3 70.6 - - - +
109E ALA* 1.3 60.2 + - - +
111E GLU* 4.1 3.4 - - + -
112E MET* 2.8 50.9 + - + +
116E ILE* 4.2 9.0 - - + -
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Residues in contact with ALA 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ALA 2.9 21.1 + - - +
106E SER 3.9 4.9 - - - +
108E LEU* 1.3 76.4 - - - +
110E LYS* 1.3 58.9 + - + +
113E GLY* 3.1 7.3 + - - -
114E ILE* 3.0 50.6 + - - +
116E ILE* 3.9 6.4 - - + +
133E PHE* 3.7 25.1 - - + +
134E GLY* 4.8 1.6 - - - +
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Residues in contact with LYS 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E TYR* 3.7 50.8 + - + +
76E GLU* 2.6 31.1 + - - -
106E SER* 3.1 24.5 + - - +
107E MET 3.2 3.6 + - - +
108E LEU 3.1 0.4 - - - -
109E ALA* 1.3 78.1 - - + +
111E GLU* 1.3 67.0 + - - +
113E GLY* 3.6 7.7 + - - -
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Residues in contact with GLU 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E LEU* 3.5 25.0 - - + +
67E SER* 2.9 31.1 + - - -
68E ALA* 3.5 30.3 - - + -
71E LYS* 3.1 30.7 + - - +
72E TYR* 4.1 3.2 - - - -
107E MET 2.9 7.9 + - - +
108E LEU* 3.2 6.0 + - - +
110E LYS* 1.3 80.3 - - - +
112E MET* 1.3 67.5 + - + +
113E GLY 3.4 0.3 + - - -
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Residues in contact with MET 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ILE* 4.6 10.8 - - - -
49E THR* 3.9 36.8 - - + +
60E TYR* 5.6 1.8 - - + -
61E ILE* 4.5 5.6 - - + -
64E LEU* 3.8 29.8 - - + -
108E LEU* 2.8 43.7 + - + +
111E GLU* 1.3 74.4 - - + +
113E GLY* 1.3 63.2 + - - +
114E ILE* 3.6 27.2 - - + +
116E ILE* 5.9 0.2 - - - -
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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