Contacts of the helix formed by residues 102 - 113 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C GLU* 2.6 33.2 + - - +
101C SER* 1.3 69.7 - - - +
103C LEU* 1.3 63.1 + - - +
105C ALA* 3.5 8.7 - - - +
106C SER* 3.0 24.6 + - - -
118C ILE* 3.7 23.0 - - + +
131C ILE* 4.6 4.5 - - + -
133C PHE* 3.8 22.0 - - + -
42D ARG* 5.5 0.7 - - - +
70D VAL* 6.4 0.2 - - + -
71D LEU 4.3 5.4 - - - +
72D ARG* 3.6 1.4 - - - -
73D LEU* 3.0 45.2 + - + +
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C TYR* 4.0 10.5 - - + -
76C GLU* 3.9 28.5 - - + +
78C GLU* 3.3 17.7 + - + +
79C ALA* 4.1 17.7 - - + +
82C VAL* 3.6 26.5 - - + -
89C TYR* 3.8 27.4 - - + +
101C SER* 3.1 12.9 + - - +
102C THR* 1.3 79.9 - - - +
104C GLU* 1.3 65.0 + - - +
106C SER* 3.3 4.2 + - - -
107C MET* 3.3 28.5 + - + +
72D ARG* 3.5 9.4 - - - +
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE* 3.7 19.3 - - + -
42C TYR* 3.3 24.5 - - - +
65C THR* 3.7 15.0 - - + +
89C TYR* 2.5 39.3 + - - +
93C MET* 4.4 2.3 - - - +
99C TRP 4.6 2.8 - - - +
100C GLY* 3.4 2.6 - - - -
101C SER* 2.5 47.0 + - - +
103C LEU* 1.3 81.5 - - - +
105C ALA* 1.3 57.7 + - - +
107C MET* 3.3 8.7 + - - +
108C LEU* 2.9 34.8 + - + +
72D ARG* 5.4 2.1 + - - -
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE* 3.7 19.7 - - + -
101C SER 3.0 12.2 + - - +
102C THR* 3.5 13.9 - - - +
103C LEU 3.2 0.2 - - - -
104C GLU* 1.3 78.4 - - - +
106C SER* 1.3 62.6 + - - +
109C ALA* 3.0 25.1 + - - +
116C ILE* 3.6 19.9 - - + +
118C ILE* 4.2 7.2 - - + -
133C PHE* 4.1 20.0 - - + +
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLN* 3.4 13.7 + - - +
76C GLU* 2.9 27.5 + - - -
78C GLU* 6.0 1.1 - - - -
102C THR 3.0 13.6 + - - -
103C LEU* 3.7 5.8 - - - -
105C ALA* 1.3 79.8 - - - +
107C MET* 1.3 61.9 + - - +
109C ALA* 3.4 10.0 + - - +
110C LYS* 3.5 22.0 + - - +
133C PHE* 3.5 28.5 - - - +
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Residues in contact with MET 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C THR* 4.4 7.0 - - + -
68C ALA* 3.5 15.7 - - + +
69C ALA* 3.7 32.8 - - + -
72C TYR* 3.9 11.5 - - + -
73C TYR* 3.8 21.1 - - - -
76C GLU* 3.6 27.8 - - + +
89C TYR* 3.6 26.0 - - + +
103C LEU* 3.3 27.1 + - + +
104C GLU* 4.0 9.0 - - - +
106C SER* 1.3 77.3 - - - +
108C LEU* 1.3 57.9 + - + +
110C LYS* 3.4 4.4 + - - +
111C GLU* 3.0 27.4 + - - +
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE* 3.9 10.5 - - + -
45C ILE* 3.6 26.5 - - + -
61C ILE* 3.8 10.8 - - + +
64C LEU* 3.8 29.8 - - + +
65C THR* 3.3 34.5 - - + +
104C GLU* 2.9 21.3 + - + +
105C ALA 3.9 2.9 - - - +
107C MET* 1.3 74.8 - - - +
109C ALA* 1.3 59.7 + - - +
111C GLU* 4.2 3.6 - - + -
112C MET* 2.7 57.4 + - + +
116C ILE* 4.2 10.1 - - + -
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ALA 3.0 18.3 + - - +
106C SER 3.6 6.1 - - - +
107C MET 3.4 0.4 - - - -
108C LEU* 1.3 76.3 - - - +
110C LYS* 1.3 58.3 + - + +
113C GLY* 3.1 8.0 + - - -
114C ILE* 3.1 49.7 + - - +
116C ILE* 4.1 5.5 - - + +
133C PHE* 3.6 26.7 - - + +
134C GLY* 5.1 1.6 - - - -
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Residues in contact with LYS 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLN* 5.2 9.3 - - - +
17A TYR* 3.9 9.4 - - - +
135A ASP* 3.1 41.6 - - - +
72C TYR* 3.6 40.7 + - + -
76C GLU* 2.7 33.4 + - - -
106C SER* 3.5 17.6 + - - +
107C MET 3.4 3.7 + - - +
108C LEU 3.2 0.4 - - - -
109C ALA* 1.3 77.6 - - + +
111C GLU* 1.3 65.3 + - - +
113C GLY* 3.5 8.7 + - - -
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Residues in contact with GLU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C LEU* 3.6 35.4 - - + +
67C SER* 4.0 10.0 - - - -
68C ALA* 3.6 22.5 - - + -
71C LYS* 2.8 41.2 + - - -
72C TYR* 3.9 3.8 - - + -
107C MET 3.0 17.2 + - - +
108C LEU* 3.9 5.8 - - + +
110C LYS* 1.3 79.1 - - - +
112C MET* 1.3 61.2 + - + +
113C GLY 3.5 0.2 + - - -
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Residues in contact with MET 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 4.2 14.4 - - + -
49C THR* 3.8 38.8 - - + +
61C ILE* 4.7 2.9 - - + -
64C LEU* 3.9 29.4 - - + -
108C LEU* 2.7 46.2 + - + +
111C GLU* 1.3 75.0 - - + +
113C GLY* 1.3 65.0 + - - +
114C ILE* 3.3 27.5 - - + +
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Residues in contact with GLY 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ALA 3.1 9.9 + - - -
110C LYS* 3.5 6.9 + - - -
111C GLU 3.3 4.2 + - - -
112C MET* 1.3 78.7 - - - +
114C ILE* 1.3 60.6 + - - +
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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