Contacts of the helix formed by residues 106 - 120 (chain C) in PDB entry 3Q37
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 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C ARG* 4.4 0.2 - - - -
104C GLY 3.2 15.7 + - - +
105C GLU* 1.3 73.8 - - - +
107C ASN* 1.3 67.3 + - - +
108C GLU* 3.5 16.7 + - - +
109C ILE* 3.0 32.2 + - + +
110C VAL* 2.9 24.9 + - - +
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Residues in contact with ASN 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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100C ARG* 3.0 25.9 + - - +
106C THR* 1.3 73.8 - - - +
108C GLU* 1.3 74.2 + - - +
110C VAL* 3.4 2.1 + - - +
111C ALA* 2.9 32.1 + - - +
146C THR* 3.7 28.7 + - - +
147C GLN* 3.6 24.8 + - - +
150C ALA* 3.9 16.7 - - + +
151C VAL* 5.3 1.2 - - - +
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Residues in contact with GLU 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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106C THR* 3.1 13.2 + - - +
107C ASN* 1.3 93.0 + - - +
109C ILE* 1.3 64.8 + - + +
111C ALA* 3.4 6.2 + - - +
112C ASP* 3.0 35.6 + - - +
150C ALA* 4.8 6.9 - - + +
154C LYS* 5.0 4.6 + - - +
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Residues in contact with ILE 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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104C GLY 3.8 20.0 - - - +
105C GLU* 4.5 13.7 - - + -
106C THR* 3.0 28.2 + - + +
108C GLU* 1.3 77.5 - - + +
110C VAL* 1.3 63.3 + - - +
112C ASP* 3.4 9.0 + - - +
113C LYS* 3.3 45.3 + - - +
102D TYR 6.2 0.4 - - - +
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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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94C LEU* 4.5 3.1 - - + +
95C GLY* 3.8 31.9 - - - +
100C ARG* 3.7 31.4 - - - +
105C GLU* 4.1 18.6 - - + +
106C THR 2.9 20.6 + - - +
107C ASN 3.7 4.0 - - - +
109C ILE* 1.3 77.1 - - - +
111C ALA* 1.3 63.2 + - - +
113C LYS* 3.1 11.4 + - - +
114C VAL* 2.9 39.4 + - + +
126C VAL* 4.7 2.9 - - + -
151C VAL* 4.5 8.5 - - + -
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Residues in contact with ALA 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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107C ASN 2.9 21.3 + - - +
108C GLU* 3.7 5.8 - - - +
110C VAL* 1.3 73.2 - - - +
112C ASP* 1.3 63.4 + - - +
114C VAL* 3.3 2.2 + - - +
115C ALA* 3.1 25.1 + - - +
150C ALA* 3.3 34.3 - - + +
151C VAL* 3.7 16.1 - - + +
154C LYS* 4.2 14.6 - - + +
155C LEU* 5.5 0.2 - - - +
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Residues in contact with ASP 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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70C THR* 4.0 11.5 + - + +
108C GLU* 3.0 27.2 + - - +
109C ILE* 3.5 9.4 - - - +
111C ALA* 1.3 78.4 - - - +
113C LYS* 1.3 60.6 + - + +
115C ALA* 3.5 5.0 + - - +
116C ALA* 3.2 22.7 + - - +
154C LYS* 3.0 27.4 + - - +
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Residues in contact with LYS 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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67C ASN* 3.2 10.3 + - - +
68C ALA 3.0 29.0 + - - +
69C ILE* 4.2 14.5 - - - +
70C THR* 3.7 21.3 - - - +
81C LEU* 3.7 8.6 - - + +
94C LEU* 3.8 21.4 - - + +
105C GLU* 2.7 35.8 + - - +
109C ILE* 3.3 29.3 - - + +
110C VAL* 3.1 10.4 + - - +
112C ASP* 1.3 74.4 - - + +
114C VAL* 1.3 67.8 + - - +
116C ALA* 3.4 1.2 + - - -
117C ALA* 2.9 24.6 + - - +
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Residues in contact with VAL 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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94C LEU* 3.9 20.2 - - + -
110C VAL* 2.9 37.3 + - + +
111C ALA 3.3 4.5 + - - +
113C LYS* 1.3 76.6 - - - +
115C ALA* 1.3 63.3 + - - +
117C ALA* 3.2 2.9 + - - +
118C VAL* 3.0 30.8 + - + +
124C VAL* 4.2 6.3 - - + -
126C VAL* 3.9 29.8 - - + -
151C VAL* 3.7 25.4 - - + -
155C LEU* 4.4 11.0 - - + -
163C VAL* 5.2 1.3 - - + -
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Residues in contact with ALA 115 (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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111C ALA 3.1 16.4 + - - +
112C ASP* 3.8 5.2 - - - +
114C VAL* 1.3 79.0 - - - +
116C ALA* 1.3 61.7 + - - +
118C VAL* 3.3 4.0 - - - +
119C ALA* 3.1 26.0 + - - +
154C LYS* 3.9 29.4 - - + +
155C LEU* 3.7 16.1 - - + +
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Residues in contact with ALA 116 (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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70C THR* 3.4 35.0 - - + +
71C ARG* 5.0 5.8 - - - +
81C LEU* 3.8 14.1 - - + +
112C ASP 3.2 9.2 + - - +
113C LYS 3.8 0.4 - - - +
114C VAL 3.3 0.2 - - - -
115C ALA* 1.3 79.1 - - - +
117C ALA* 1.3 61.9 + - - +
119C ALA* 3.4 6.8 + - - +
120C SER* 3.0 24.4 + - - -
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Residues in contact with ALA 117 (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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81C LEU* 3.5 23.0 - - + +
92C VAL* 4.2 3.1 - - + -
94C LEU* 4.2 2.0 - - + -
113C LYS 2.9 17.9 + - - +
114C VAL 3.2 1.3 + - - +
116C ALA* 1.3 77.6 - - - +
118C VAL* 1.3 63.2 + - - +
120C SER* 3.0 13.6 + - - -
122C PHE* 3.0 32.9 + - + +
124C VAL* 3.4 25.4 - - + -
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Residues in contact with VAL 118 (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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114C VAL* 3.0 16.2 + - + +
115C ALA 3.3 11.7 - - - +
117C ALA* 1.3 74.9 - - - +
119C ALA* 1.3 62.7 + - + +
121C GLY 3.5 4.6 + - - -
122C PHE 3.7 13.0 - - - +
124C VAL* 3.7 18.8 - - + -
155C LEU* 3.8 21.3 - - + -
159C ALA* 3.9 17.0 - - + -
162C ARG* 3.0 47.6 + - + +
163C VAL* 4.2 17.3 - - + -
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Residues in contact with ALA 119 (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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115C ALA 3.1 21.2 + - - +
116C ALA* 3.6 8.3 - - - +
117C ALA 3.1 0.2 - - - -
118C VAL* 1.3 80.0 - - + +
120C SER* 1.3 56.9 + - - +
121C GLY 3.5 0.8 + - - -
162C ARG* 5.1 0.7 - - - +
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Residues in contact with SER 120 (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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81C LEU* 4.6 5.9 - - - +
85C LYS* 3.1 44.4 + - - +
116C ALA 3.0 15.7 + - - -
117C ALA* 3.0 7.1 + - - -
119C ALA* 1.3 80.0 - - - +
121C GLY* 1.3 57.4 + - - -
122C PHE* 3.4 20.6 + - - -
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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