Contacts of the helix formed by residues 106 - 116 (chain G) in PDB entry 3ECS
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 LEU 106 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102G ARG 3.9 13.9 - - - +
103G ARG* 3.0 17.2 + - + +
105G SER* 1.3 89.7 - - - +
107G SER* 1.3 64.7 + - - +
108G ARG 3.5 2.2 - - - -
109G ASN* 3.3 13.6 + - + +
110G LYS* 3.1 41.1 + - + +
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Residues in contact with SER 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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103G ARG 4.0 2.0 + - - -
104G ILE* 3.3 26.8 + - - +
106G LEU* 1.3 75.5 - - - +
108G ARG* 1.3 67.7 + - - +
109G ASN 3.1 0.5 + - - -
110G LYS* 3.2 3.9 + - - +
111G ILE* 3.1 28.8 + - - +
231G GLU* 3.8 18.8 - - - +
232G SER* 5.3 0.3 + - - -
233G PHE* 4.5 3.6 - - - -
287G ASP* 3.3 37.7 + - - +
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Residues in contact with ARG 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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19G ASP 3.4 12.2 + - - -
20G MSE 5.5 0.2 - - - -
21G ALA* 4.0 15.2 - - - +
24G VAL* 5.8 2.6 - - - +
104G ILE 4.9 0.6 + - - -
105G SER 5.5 1.3 - - - -
106G LEU 3.5 1.2 - - - +
107G SER* 1.3 78.6 - - - +
109G ASN* 1.3 58.2 + - - +
111G ILE* 3.3 9.7 + - - +
112G ALA* 2.9 28.9 + - - +
132G ARG* 3.0 50.8 - - - +
133G VAL* 4.3 15.7 - - + +
136G ARG* 3.9 35.0 + - + +
231G GLU* 2.9 25.8 + - - +
233G PHE* 5.2 1.8 - - - -
507G SO4 3.3 8.2 + - - -
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Residues in contact with ASN 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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106G LEU* 3.3 14.4 + - + +
107G SER 3.1 0.8 - - - -
108G ARG* 1.3 75.7 - - - +
110G LYS* 1.3 66.3 + - - +
111G ILE 3.0 1.6 - - - -
112G ALA* 3.3 2.8 + - - +
113G ASP* 3.0 39.9 + - - +
136G ARG* 3.6 21.9 + - - +
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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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103G ARG 4.6 3.8 + - - -
106G LEU* 3.1 48.5 + - + +
107G SER* 3.2 7.6 + - - +
109G ASN* 1.3 74.9 - - - +
111G ILE* 1.3 57.6 + - - +
113G ASP* 3.3 10.2 - - - +
114G LEU* 2.9 35.6 + - + +
287G ASP* 3.3 40.0 - - + +
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Residues in contact with ILE 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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107G SER 3.3 18.2 - - - +
108G ARG 3.3 6.1 - - - +
109G ASN 3.0 0.4 - - - -
110G LYS* 1.3 73.2 - - - +
112G ALA* 1.3 65.1 + - - +
113G ASP 2.7 6.2 + - - -
114G LEU* 2.8 18.9 + - - +
115G CYS* 3.0 11.6 + - - +
133G VAL* 3.8 10.3 - - + -
137G VAL* 4.1 4.9 - - + -
229G VAL* 3.3 31.0 - - + -
230G ALA 3.7 31.2 - - - +
231G GLU* 3.8 12.1 - - + +
285G PHE* 3.7 10.1 - - + +
286G THR* 3.5 7.9 - - - -
287G ASP 3.5 23.3 - - - +
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Residues in contact with ALA 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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108G ARG 2.9 11.2 + - - +
109G ASN* 3.3 5.4 + - - +
111G ILE* 1.3 74.3 - - - +
113G ASP* 1.3 61.9 + - - +
115G CYS* 3.9 2.1 - - - +
116G HIS* 3.6 18.0 + - - +
136G ARG* 3.5 29.2 - - + +
137G VAL* 3.9 25.5 - - + +
140G ALA* 3.8 29.0 - - + +
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Residues in contact with ASP 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 ASN* 3.0 31.3 + - - +
110G LYS* 3.3 11.2 - - - +
111G ILE 2.7 1.4 + - - -
112G ALA* 1.3 77.9 - - - +
114G LEU* 1.3 60.4 + - + +
115G CYS 2.8 8.1 + - - -
116G HIS* 2.7 37.6 + - + +
140G ALA* 5.8 1.9 - - - +
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Residues in contact with LEU 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 LYS* 2.9 23.3 + - + +
111G ILE* 2.8 11.2 + - - +
113G ASP* 1.3 72.1 - - + +
115G CYS* 1.3 58.8 + - - +
117G THR* 4.9 3.5 + - - -
118G PHE* 4.1 6.6 - - - -
285G PHE* 3.4 27.2 - - + -
286G THR 2.8 34.3 - - - +
287G ASP* 4.8 2.9 - - - +
289G GLY* 3.5 24.5 - - - +
290G VAL* 4.2 12.0 - - + +
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Residues in contact with CYS 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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111G ILE* 3.0 10.9 + - - +
112G ALA 4.1 1.3 - - - +
113G ASP 2.8 4.2 - - - -
114G LEU* 1.3 78.5 - - - +
116G HIS* 1.3 65.2 + - - +
117G THR 2.8 5.1 + - - -
118G PHE* 3.1 15.7 + - + +
119G ILE* 3.7 11.6 + - + +
137G VAL* 3.5 27.1 - - + -
194G ILE* 6.4 1.1 - - - -
229G VAL* 3.9 15.5 - - - -
285G PHE* 3.3 50.0 - - - -
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Residues in contact with HIS 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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112G ALA 3.6 9.6 + - - +
113G ASP* 2.7 41.9 + - + +
115G CYS* 1.3 75.9 - - - +
117G THR* 1.3 76.8 + - - +
119G ILE* 3.6 4.7 - - - +
137G VAL 5.8 1.1 - - - -
140G ALA* 4.6 14.4 - - + +
141G ALA* 5.3 10.1 - - - -
144G ALA* 5.7 2.9 - - + -
146G LYS* 3.3 31.4 - - - +
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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