Contacts of the helix formed by residues 102 - 113 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78G GLU* 2.5 34.6 + - - +
101G SER* 1.3 70.7 - - - +
103G LEU* 1.3 64.1 + - - +
105G ALA* 3.7 7.4 - - - +
106G SER* 3.0 24.3 + - - -
118G ILE* 3.5 24.7 - - + -
131G ILE* 4.9 2.7 - - + -
133G PHE* 3.6 19.6 - - + -
42H ARG* 5.8 0.2 - - - -
71H LEU 4.4 4.9 - - - +
72H ARG* 3.5 1.9 - - - -
73H LEU* 3.1 43.1 + - + +
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Residues in contact with LEU 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G TYR* 3.9 25.4 - - + -
76G GLU* 3.8 34.1 - - + +
78G GLU* 3.6 15.5 + - + -
79G ALA* 4.1 14.8 - - + +
82G VAL* 4.0 21.3 - - + -
89G TYR* 4.0 15.7 - - + +
101G SER* 3.1 12.2 + - - +
102G THR* 1.3 82.1 + - - +
104G GLU* 1.3 63.8 + - - +
106G SER* 3.3 2.6 + - - -
107G MET* 3.2 30.2 + - + +
72H ARG* 3.7 8.7 - - - +
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Residues in contact with GLU 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G PHE* 3.7 18.2 - - + -
42G TYR* 3.4 23.4 + - - +
65G THR* 3.7 15.9 - - + -
89G TYR* 2.9 37.2 + - - +
93G MET* 4.5 2.9 - - + +
99G TRP 5.0 3.3 - - - +
100G GLY* 4.2 2.2 - - - -
101G SER* 2.6 48.8 + - - +
103G LEU* 1.3 78.6 - - - +
105G ALA* 1.3 54.8 + - - +
107G MET* 3.2 8.3 + - - +
108G LEU* 2.7 40.3 + - + +
72H ARG* 5.4 1.7 + - - -
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Residues in contact with ALA 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G PHE* 3.6 16.4 - - + -
101G SER 3.1 16.0 + - - +
102G THR 3.7 5.4 - - - +
103G LEU 3.4 0.2 - - - -
104G GLU* 1.3 76.0 - - - +
106G SER* 1.3 58.3 + - - +
108G LEU* 4.5 0.2 - - - -
109G ALA* 3.0 31.2 + - - +
116G ILE* 3.4 20.8 - - + +
118G ILE* 4.0 22.9 - - + -
133G PHE* 4.0 11.7 - - + +
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Residues in contact with SER 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G GLN* 3.5 12.7 + - - +
76G GLU* 2.9 26.7 + - - -
78G GLU* 5.7 2.0 - - - -
102G THR 3.0 17.8 + - - -
103G LEU* 3.6 6.3 - - - -
104G GLU 3.2 0.2 - - - -
105G ALA* 1.3 77.7 - - - +
107G MET* 1.3 61.5 + - - +
109G ALA* 3.6 3.6 + - - +
110G LYS* 3.4 29.6 + - - +
133G PHE* 3.7 25.6 - - - -
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Residues in contact with MET 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G THR* 4.7 6.5 - - + +
68G ALA* 3.6 15.2 - - + +
69G ALA* 3.8 16.6 - - + +
72G TYR* 4.1 8.7 - - + -
73G TYR* 3.6 35.2 - - + -
76G GLU* 3.5 24.5 - - + +
89G TYR* 3.2 38.1 - - + +
103G LEU* 3.2 26.7 + - + +
104G GLU* 3.8 7.0 - - - +
106G SER* 1.3 75.8 - - - +
108G LEU* 1.3 59.7 + - + +
110G LYS* 3.3 5.5 + - - +
111G GLU* 3.0 27.4 + - - +
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Residues in contact with LEU 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G PHE* 4.0 22.0 - - + -
45G ILE* 4.6 7.6 - - + -
61G ILE* 3.8 19.5 - - + +
64G LEU* 3.9 19.7 - - + +
65G THR* 3.2 45.8 - - + +
68G ALA* 4.9 0.2 - - + -
104G GLU 2.7 23.9 + - - +
105G ALA* 4.0 2.9 - - - +
107G MET* 1.3 71.2 - - + +
109G ALA* 1.3 58.4 + - - +
111G GLU* 4.2 2.5 - - + -
112G MET* 2.7 55.2 + - + +
116G ILE* 4.1 9.0 - - + -
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Residues in contact with ALA 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G ALA 3.0 19.0 + - - +
106G SER 3.7 6.3 - - - +
107G MET 3.3 0.4 - - - -
108G LEU* 1.3 76.2 - - - +
110G LYS* 1.3 60.4 + - + +
113G GLY* 3.1 8.0 + - - -
114G ILE* 3.1 45.1 + - - +
116G ILE* 3.9 10.0 - - + +
133G PHE* 3.7 26.2 - - + +
134G GLY* 4.7 1.3 - - - +
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Residues in contact with LYS 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G GLN* 5.7 0.4 - - - +
72G TYR* 3.5 50.2 + - + +
76G GLU* 2.6 31.5 + - - -
106G SER* 3.4 20.1 + - - +
107G MET 3.3 4.8 + - - +
108G LEU 3.1 0.6 - - - -
109G ALA* 1.3 78.4 - - + +
111G GLU* 1.3 65.3 + - - +
113G GLY* 3.5 9.5 + - - -
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Residues in contact with GLU 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G LEU* 3.7 36.0 - - + +
67G SER* 3.0 26.3 + - - -
68G ALA* 3.4 23.5 - - + -
71G LYS* 3.2 32.9 + - - +
72G TYR* 3.8 10.1 + - + -
107G MET 3.0 8.1 + - - +
108G LEU* 3.9 4.9 - - - +
110G LYS* 1.3 78.5 - - - +
112G MET* 1.3 60.0 + - + +
113G GLY 3.6 0.2 + - - -
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Residues in contact with MET 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G ILE* 4.3 14.1 - - - -
49G THR* 4.0 31.6 - - + +
50G MET* 6.3 0.2 - - + -
61G ILE* 4.4 3.6 - - + -
64G LEU* 4.2 29.4 - - + -
108G LEU* 2.7 48.5 + - + +
111G GLU* 1.3 74.7 - - + +
113G GLY* 1.3 60.4 + - - +
114G ILE* 3.9 30.4 - - + +
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Residues in contact with GLY 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G ALA 3.1 10.6 + - - -
110G LYS 3.5 6.6 + - - -
111G GLU 3.3 3.6 + - - -
112G MET* 1.3 80.0 - - - +
114G ILE* 1.3 62.3 + - - +
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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