Contacts of the helix formed by residues 105 - 117 (chain G) in PDB entry 1DSX
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 PRO 105 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99F ARG* 3.2 35.4 - - + +
102F VAL* 6.4 2.7 - - + -
100G ARG* 4.2 5.2 - - - +
103G ASN 3.8 7.4 - - - +
104G VAL* 1.3 94.1 - - + +
106G LEU* 1.3 64.2 + - - +
107G ASP* 3.3 4.2 + - - +
108G ILE* 3.3 16.0 + - + -
109G PHE* 3.0 19.1 + - - +
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Residues in contact with LEU 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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100G ARG* 3.6 37.1 - - + +
104G VAL 3.5 1.2 + - - -
105G PRO* 1.3 72.1 - - - +
107G ASP* 1.3 57.4 + - - +
109G PHE* 3.4 6.6 + - + -
110G SER* 2.9 45.9 + - - +
113G ILE* 6.4 0.4 - - + -
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Residues in contact with ASP 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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97F ARG* 4.5 9.7 + - - -
99F ARG* 2.2 52.9 + - - -
105G PRO* 3.4 5.4 - - - +
106G LEU* 1.3 74.9 + - - +
108G ILE* 1.3 72.3 + - - +
110G SER* 3.4 6.0 + - - -
111G GLU* 3.2 22.5 + - - +
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Residues in contact with ILE 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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90F TYR* 3.5 50.2 + - + +
99F ARG* 4.0 27.1 - - + +
81G ASN* 4.2 13.2 - - + +
84G SER* 4.2 7.6 - - - +
104G VAL* 3.7 17.0 - - + -
105G PRO* 3.6 22.0 - - + +
107G ASP* 1.3 91.3 + - - +
109G PHE* 1.3 63.8 + - - +
111G GLU* 3.2 15.8 + - - +
112G GLU* 3.2 14.2 + - + +
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Residues in contact with PHE 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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84G SER* 3.5 43.3 - - - -
87G ALA* 3.4 26.0 - - + -
88G ILE* 4.4 13.5 - - + -
98G LEU* 4.8 10.3 - - + -
99G ARG 3.8 6.7 - - - -
100G ARG* 3.9 30.3 - - + -
101G PRO* 3.7 11.9 - - + -
104G VAL* 4.1 5.8 - - + -
105G PRO 3.0 16.1 + - - +
106G LEU* 3.9 11.0 - - + +
108G ILE* 1.3 76.4 - - - +
110G SER* 1.3 61.7 + - - +
112G GLU* 3.0 5.1 + - + +
113G ILE* 3.0 54.0 + - + +
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Residues in contact with SER 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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106G LEU* 2.9 35.1 + - - +
107G ASP* 3.9 5.8 - - - -
108G ILE 3.4 0.2 - - - -
109G PHE* 1.3 72.1 - - - +
111G GLU* 1.3 62.0 + - - +
113G ILE* 3.4 14.8 + - - +
114G ARG* 3.1 34.5 + - - +
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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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90F TYR* 5.2 6.3 - - - +
97F ARG* 5.8 3.4 + - - -
80G ARG* 4.5 11.9 - - - +
107G ASP 3.2 12.2 + - - +
108G ILE* 3.2 12.9 + - - +
110G SER* 1.3 76.2 - - - +
112G GLU* 1.3 62.5 + - - +
114G ARG* 2.7 41.9 + - - +
115G PHE* 3.0 28.9 + - - +
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Residues in contact with GLU 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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90F TYR* 5.0 8.1 + - - -
80G ARG* 2.7 52.3 + - - +
81G ASN* 4.2 19.0 + - + +
84G SER* 3.6 32.7 - - - +
88G ILE* 4.7 6.1 - - + -
108G ILE* 3.2 11.7 + - + +
109G PHE* 3.0 8.3 + - + +
111G GLU* 1.3 80.8 - - - +
113G ILE* 1.3 62.4 + - - +
115G PHE* 3.2 3.3 + - - -
116G TYR* 2.9 47.0 + - + -
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Residues in contact with ILE 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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88G ILE* 4.5 10.5 - - + -
98G LEU* 4.4 28.3 - - + -
106G LEU* 6.4 0.4 - - + -
109G PHE* 3.0 50.9 + - + +
110G SER* 3.7 15.9 - - - +
111G GLU 3.3 0.2 - - - -
112G GLU* 1.3 74.2 - - - +
114G ARG* 1.3 67.4 + - + +
116G TYR* 3.4 1.0 + - - -
117G GLU 3.0 17.2 + - - -
118G LEU* 3.2 30.7 + - + +
119G GLY* 4.2 11.6 + - - +
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Residues in contact with ARG 114 (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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110G SER* 3.1 19.3 + - - +
111G GLU* 2.7 45.2 + - - +
113G ILE* 1.3 78.6 - - + +
115G PHE* 1.3 63.6 + - - +
117G GLU* 3.0 21.3 + - - +
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Residues in contact with PHE 115 (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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58G LEU* 3.5 29.9 - - + +
68G TYR* 3.5 34.5 - + - -
78G PHE* 3.6 19.1 - + - -
80G ARG* 3.3 55.6 - - - +
111G GLU 3.0 17.5 + - - +
112G GLU 3.2 3.3 + - - +
114G ARG* 1.3 77.7 - - - +
116G TYR* 1.3 76.8 + + - +
117G GLU* 3.3 8.1 + - - +
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Residues in contact with TYR 116 (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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39G ILE* 3.7 13.3 - - - +
57G THR* 3.6 5.5 - - - -
58G LEU* 3.0 28.5 + - + +
59G LEU* 4.1 21.8 - - + -
78G PHE* 4.1 14.7 - + - +
80G ARG* 3.7 16.1 - - - +
81G ASN 5.3 1.0 + - - -
84G SER* 6.1 0.4 - - - -
85G PHE* 3.6 35.0 - + - -
88G ILE* 4.0 18.6 - - + -
92G TYR* 4.6 2.7 + - - +
112G GLU* 2.9 54.3 + - + +
113G ILE 4.2 1.3 - - - +
115G PHE* 1.3 96.2 - + - +
117G GLU* 1.3 66.9 + - - +
118G LEU* 3.3 18.6 + - + +
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Residues in contact with GLU 117 (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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56G GLU* 3.9 6.9 - - - +
57G THR* 3.4 17.1 - - - +
58G LEU* 4.0 14.9 + - - +
64G LYS* 2.6 44.6 + - - +
113G ILE 3.0 1.9 + - - -
114G ARG* 3.0 21.4 + - - +
115G PHE 3.7 8.3 - - - +
116G TYR* 1.3 80.7 - - - +
118G LEU* 1.3 65.0 - - - +
119G GLY 3.7 0.7 - - - -
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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