Contacts of the helix formed by residues 103 - 114 (chain C) in PDB entry 3I5G
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 SER 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C ILE* 1.3 76.7 - - - +
104C SER* 1.3 58.2 + - - +
105C ALA* 3.0 14.9 + - - +
106C GLU* 3.0 43.7 + - - +
107C ILE* 3.1 12.3 + - - +
137C ASP* 6.0 0.2 - - - -
139C ASN* 3.2 24.4 - - - +
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Residues in contact with SER 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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102C ILE 3.2 3.0 + - - -
103C SER* 1.3 69.7 - - - +
105C ALA* 1.3 63.9 + - - +
107C ILE* 4.0 7.9 - - - -
108C ARG* 2.8 49.1 + - - +
127C PHE* 4.8 2.9 - - - -
134C GLU* 3.1 24.3 + - - +
139C ASN* 3.5 7.6 + - - -
140C ILE* 3.3 33.4 - - - +
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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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103C SER* 3.0 10.5 - - - +
104C SER* 1.3 82.7 + - - +
106C GLU* 1.3 58.2 + - + +
108C ARG* 3.9 6.0 - - - +
109C ASN* 3.0 34.1 + - - +
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Residues in contact with GLU 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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94C PHE* 4.4 26.5 - - + +
96C ARG* 2.5 42.9 + - - +
102C ILE* 4.2 9.9 - - + +
103C SER* 3.0 26.5 + - - +
105C ALA* 1.3 76.8 - - + +
107C ILE* 1.3 67.1 + - - +
108C ARG 3.2 1.1 - - - -
109C ASN* 2.8 12.2 + - + +
110C VAL* 2.7 28.3 + - + +
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Residues in contact with ILE 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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91C PHE* 3.8 25.1 - - + -
102C ILE* 3.4 35.9 - - + +
103C SER 3.1 13.2 + - - +
104C SER* 4.2 5.2 - - - +
106C GLU* 1.3 74.3 - - - +
108C ARG* 1.3 59.6 + - - +
110C VAL* 2.9 14.1 + - + +
111C LEU* 2.8 42.4 + - + +
127C PHE* 4.8 6.7 - - + -
140C ILE* 4.1 23.6 - - + -
142C TYR* 4.5 13.2 - - + -
145C LEU* 4.2 17.3 - - + -
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Residues in contact with ARG 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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104C SER* 2.8 35.2 + - - +
105C ALA* 3.9 5.6 - - - +
106C GLU 3.2 0.6 - - - -
107C ILE* 1.3 76.8 - - - +
109C ASN* 1.3 60.9 + - - +
111C LEU* 4.4 7.6 - - - -
112C LYS* 3.0 41.9 + - + +
120C GLU* 5.0 4.4 + - - -
123C CYS* 3.8 22.3 + - - +
124C ASN* 3.0 28.2 + - - +
127C PHE* 3.2 53.7 - - + +
134C GLU* 5.8 1.4 + - - -
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Residues in contact with ASN 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 20.6 + - - +
106C GLU* 2.8 16.7 + - + +
108C ARG* 1.3 72.9 - - - +
110C VAL* 1.3 59.5 + - - +
112C LYS* 3.2 1.7 + - - -
113C MET* 2.7 65.9 + - + +
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Residues in contact with VAL 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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784A ILE* 3.8 38.8 - - + -
788A GLN* 4.1 0.3 + - - -
91C PHE* 6.0 4.3 - - + -
94C PHE* 3.6 39.5 - - + -
106C GLU* 2.7 19.4 + - + +
107C ILE* 3.1 14.8 - - + +
109C ASN* 1.3 74.5 - - + +
111C LEU* 1.3 67.2 + - + +
114C LEU* 2.8 43.3 + - + +
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Residues in contact with LEU 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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784A ILE* 5.3 1.3 - - + -
787A PHE* 4.1 25.6 - - + -
788A GLN* 3.2 27.4 + - + +
791A ILE* 3.9 21.8 - - + -
91C PHE* 5.6 2.7 - - + -
107C ILE* 2.8 35.9 + - + +
108C ARG* 4.0 0.7 - - - +
110C VAL* 1.3 84.0 - - + +
112C LYS* 1.3 57.0 + - - +
118C ILE* 2.9 29.8 + - + +
123C CYS* 3.8 27.4 - - - -
126C ILE* 5.1 4.3 - - + -
127C PHE* 4.9 12.8 - - + -
145C LEU* 5.3 2.9 - - + -
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Residues in contact with LYS 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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108C ARG* 3.0 26.9 + - + +
109C ASN* 4.2 1.6 - - - +
111C LEU* 1.3 76.9 - - - +
113C MET* 1.3 78.5 + - + +
117C ARG* 3.3 30.9 + - - +
118C ILE 3.5 21.4 - - - +
119C THR 4.6 1.3 - - - +
120C GLU* 2.7 41.9 + - - +
123C CYS* 3.7 22.2 - - + -
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Residues in contact with MET 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 ASN* 2.7 44.7 + - - +
112C LYS* 1.3 105.8 - - + +
114C LEU* 1.3 70.4 + - + +
117C ARG* 3.1 35.5 + - - +
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Residues in contact with LEU 114 (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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780A LEU* 6.1 1.6 - - + -
784A ILE* 3.8 30.1 - - + -
788A GLN* 2.9 17.8 + - - -
94C PHE* 4.1 18.8 - - + -
110C VAL* 2.8 28.6 + - + +
113C MET* 1.3 85.9 - - + +
115C GLY* 1.3 73.0 + - - +
117C ARG* 3.2 7.8 + - - -
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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