Contacts of the helix formed by residues 106 - 124 (chain T) in PDB entry 5C3I
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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103T GLU* 5.7 4.5 - - - +
104T GLU 4.3 7.0 - - - +
105T LEU* 1.3 78.4 - - - +
107T ALA* 1.3 66.4 + - - +
108T SER* 3.7 8.0 + - - -
109T GLN* 3.2 35.9 + - - +
110T ARG* 3.2 20.8 + - - +
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Residues in contact with ALA 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106T THR* 1.3 76.4 - - - +
108T SER* 1.3 58.6 + - - +
110T ARG* 3.9 3.1 - - - +
111T GLU* 3.1 27.4 + - - +
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Residues in contact with SER 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106T THR* 3.7 8.8 + - - -
107T ALA* 1.3 76.8 - - - +
109T GLN* 1.3 63.5 + - - +
111T GLU* 3.5 7.4 - - - +
112T ALA* 2.9 32.1 + - - +
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Residues in contact with GLN 109 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75S HIS* 3.4 32.9 + - - +
76S ALA* 3.5 23.2 + - - +
77S LYS* 3.7 17.8 - - - +
104T GLU 4.0 4.3 - - - +
105T LEU* 3.6 16.1 - - + -
106T THR* 3.2 38.7 + - - +
107T ALA 3.3 0.6 - - - -
108T SER* 1.3 83.5 + - - +
110T ARG* 1.3 61.3 + - - +
112T ALA* 4.1 3.3 - - - +
113T ALA* 3.1 24.3 + - - +
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Residues in contact with ARG 110 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150Q HIS* 3.3 38.3 + - - -
72S TYR* 4.0 16.2 + - + -
88S TYR* 3.3 52.1 + - + +
91S LYS* 4.8 12.9 - - - +
105T LEU* 3.7 17.6 - - + +
106T THR 3.2 18.4 + - - +
107T ALA* 3.9 4.0 - - - +
109T GLN* 1.3 73.4 - - - +
111T GLU* 1.3 65.0 - - - +
113T ALA* 3.4 3.3 + - - +
114T GLU* 3.1 41.1 + - - +
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Residues in contact with GLU 111 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152Q ASN* 3.9 23.3 + - - +
154Q GLU 4.6 4.2 - - - +
155Q ASP* 5.2 8.7 - - - -
107T ALA 3.1 18.9 + - - +
108T SER* 3.5 9.4 - - - +
110T ARG* 1.3 75.8 - - - +
112T ALA* 1.3 63.6 + - - +
113T ALA 3.2 1.0 + - - -
114T GLU* 3.2 17.3 + - - +
115T ARG* 3.2 37.7 + - - +
118T ARG* 5.3 1.2 + - - -
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Residues in contact with ALA 112 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75S HIS* 3.6 19.0 + - + -
108T SER 2.9 21.3 + - - +
109T GLN* 4.1 4.5 - - - +
111T GLU* 1.3 72.5 - - - +
113T ALA* 1.3 61.5 + - - +
115T ARG* 3.6 29.8 + - - +
116T ALA* 3.2 17.2 + - - +
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Residues in contact with ALA 113 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71S THR* 4.9 1.3 - - + +
72S TYR* 3.8 27.1 - - + -
75S HIS* 3.6 28.3 - - + +
105T LEU* 4.8 0.2 - - + -
109T GLN 3.1 19.5 + - - +
110T ARG 3.4 6.1 - - - +
111T GLU 3.1 0.2 - - - -
112T ALA* 1.3 76.1 - - - +
114T GLU* 1.3 56.7 + - - +
116T ALA* 2.9 7.3 + - - +
117T MET* 2.9 33.8 + - + +
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Residues in contact with GLU 114 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150Q HIS* 3.2 37.6 + - - +
151Q ILE* 4.9 0.2 - - - -
152Q ASN* 4.6 2.1 + - - -
72S TYR* 3.7 20.7 + - + +
92S ARG* 4.6 9.1 + - - +
110T ARG* 3.1 35.8 + - - +
111T GLU* 3.2 7.1 + - - +
113T ALA* 1.3 78.9 - - - +
115T ARG* 1.3 56.5 + - - +
117T MET* 3.5 11.9 + - + +
118T ARG* 3.1 61.8 + - - +
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Residues in contact with ARG 115 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152Q ASN* 6.0 2.5 - - - +
111T GLU* 3.2 29.5 + - - +
112T ALA* 3.6 34.3 + - - +
113T ALA 3.2 0.8 - - - -
114T GLU* 1.3 73.2 - - - +
116T ALA* 1.3 64.2 + - - +
118T ARG* 3.5 20.5 + - - +
119T GLN* 3.3 20.8 + - - +
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Residues in contact with ALA 116 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71S THR* 5.2 3.4 - - + -
75S HIS* 3.5 31.4 - - + +
112T ALA 3.2 6.8 + - - +
113T ALA 2.9 9.7 + - - +
115T ARG* 1.3 78.2 - - - +
117T MET* 1.3 57.2 + - - +
119T GLN* 3.2 23.3 - - - +
120T ARG* 3.6 9.4 - - - +
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Residues in contact with MET 117 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68S ASP* 3.3 41.1 - - - +
71S THR* 3.7 22.4 - - + +
72S TYR* 3.5 40.8 - - + +
92S ARG* 3.4 26.5 - - - +
113T ALA* 2.9 11.4 + - + +
114T GLU* 3.8 17.7 - - - +
115T ARG 3.3 0.4 - - - -
116T ALA* 1.3 76.3 - - - +
118T ARG* 1.3 59.3 + - - +
120T ARG* 3.2 21.9 - - - +
121T ASP* 3.0 33.3 + - - +
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Residues in contact with ARG 118 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q GLN* 3.3 24.0 + - - +
150Q HIS 5.3 0.8 + - - -
151Q ILE* 3.9 3.6 - - - +
152Q ASN* 3.0 48.6 - - - +
92S ARG* 4.3 8.9 - - - +
111T GLU* 5.3 1.2 + - - -
114T GLU* 3.1 56.4 + - - +
115T ARG* 3.7 22.4 - - - +
116T ALA 3.4 0.2 - - - -
117T MET* 1.3 73.6 - - - +
119T GLN* 1.3 56.0 + - - +
121T ASP* 3.0 9.3 + - + +
122T ARG* 2.6 60.5 + - + +
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Residues in contact with GLN 119 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115T ARG 3.3 11.0 + - - +
116T ALA* 3.2 15.9 - - - +
118T ARG* 1.3 78.3 - - - +
120T ARG* 1.3 57.6 + - - +
122T ARG* 3.3 30.1 + - - +
123T GLU* 2.9 38.4 + - - +
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Residues in contact with ARG 120 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67S ARG* 3.5 38.0 - - - +
68S ASP* 2.6 30.9 + - - -
71S THR* 4.4 5.9 + - - -
92S ARG* 3.5 11.9 - - - +
93S GLN* 5.5 1.8 - - - +
116T ALA 3.6 11.7 - - - +
117T MET* 3.2 27.5 + - - +
119T GLN* 1.3 76.0 - - - +
121T ASP* 1.3 88.9 + - - +
123T GLU* 3.2 26.7 + - + +
124T ALA* 3.5 7.8 + - - +
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Residues in contact with ASP 121 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92S ARG* 3.5 20.3 + - - -
117T MET 3.1 9.3 + - - +
118T ARG* 3.0 13.6 + - + +
120T ARG* 1.3 110.3 + - - +
122T ARG* 1.3 63.4 + - - +
124T ALA* 3.9 13.4 + - - +
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Residues in contact with ARG 122 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118T ARG* 2.6 41.8 + - + +
119T GLN* 3.5 29.3 + - - +
121T ASP* 1.3 71.9 - - - +
123T GLU* 1.3 67.7 + - - +
124T ALA 3.0 8.7 + - - -
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Residues in contact with GLU 123 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119T GLN* 2.9 29.4 + - - +
120T ARG* 3.2 17.4 - - - +
122T ARG* 1.3 75.6 - - - +
124T ALA* 1.3 62.5 + - - +
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Residues in contact with ALA 124 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120T ARG 3.5 6.2 + - - +
121T ASP* 4.1 11.7 - - - +
122T ARG 3.0 8.5 + - - -
123T GLU* 1.3 84.6 - - - +
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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