Contacts of the helix formed by residues 106 - 123 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104X GLU 3.5 4.7 + - - +
105X LEU* 1.3 77.5 - - - +
107X ALA* 1.3 64.7 + - - +
108X SER* 3.3 9.3 + - - -
109X GLN* 3.1 38.3 + - - +
110X ARG* 3.1 22.8 + - - +
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Residues in contact with ALA 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106X THR* 1.3 75.5 - - - +
108X SER* 1.3 62.7 + - - +
110X ARG* 3.5 25.9 + - - +
111X GLU* 3.4 19.2 + - - +
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Residues in contact with SER 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106X THR* 3.3 10.8 + - - -
107X ALA* 1.3 75.9 - - - +
109X GLN* 1.3 65.0 + - - +
111X GLU* 3.3 6.4 + - - +
112X ALA* 2.9 32.0 + - - +
115X ARG* 4.6 2.3 + - - +
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Residues in contact with GLN 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75W HIS* 3.4 28.2 + - - +
76W ALA* 3.5 24.1 + - - +
77W LYS* 5.2 4.4 - - - +
104X GLU 4.4 1.4 - - - +
105X LEU* 3.4 18.8 - - + +
106X THR* 3.1 42.8 + - - +
108X SER* 1.3 83.4 + - - +
110X ARG* 1.3 57.3 + - - +
112X ALA* 3.9 6.8 - - - +
113X ALA* 3.0 29.3 + - - +
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Residues in contact with ARG 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72W TYR* 4.0 9.7 - - + -
88W TYR* 2.8 54.0 + - + -
105X LEU* 3.7 28.1 + - + +
106X THR 3.1 11.3 + - - +
107X ALA* 3.5 30.3 + - - +
109X GLN* 1.3 77.6 - - - +
111X GLU* 1.3 57.3 + - - +
113X ALA* 3.5 4.4 - - - +
114X GLU* 3.0 51.0 + - - +
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Residues in contact with GLU 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152U ASN* 4.7 14.3 + - - +
107X ALA 3.4 8.1 + - - +
108X SER* 3.3 8.8 + - - +
110X ARG* 1.3 77.0 - - - +
112X ALA* 1.3 57.2 + - - +
113X ALA 3.1 1.3 - - - -
114X GLU* 2.9 29.1 + - - +
115X ARG* 2.8 63.3 + - - +
118X ARG* 4.2 10.4 + - - -
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Residues in contact with ALA 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75W HIS* 3.4 22.4 + - + -
108X SER 2.9 18.0 + - - +
109X GLN* 3.9 8.1 - - - +
111X GLU* 1.3 75.0 - - - +
113X ALA* 1.3 60.9 + - - +
115X ARG* 3.6 24.3 + - - +
116X ALA* 3.5 13.3 + - - +
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Residues in contact with ALA 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71W THR* 4.2 6.1 - - + +
72W TYR* 3.9 22.4 - - + -
75W HIS* 3.4 29.1 - - + +
105X LEU* 4.7 0.2 - - + -
109X GLN 3.0 18.6 + - - +
110X ARG 3.5 4.9 - - - +
112X ALA* 1.3 76.8 - - - +
114X GLU* 1.3 63.7 + - - +
116X ALA* 3.0 15.2 + - - +
117X MET* 3.3 21.0 + - + +
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Residues in contact with GLU 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150U HIS* 5.5 3.3 - - - +
152U ASN* 5.8 0.2 - - - +
72W TYR* 3.6 24.6 + - + +
92W ARG* 3.7 28.3 + - - +
110X ARG* 3.0 41.4 + - - +
111X GLU* 2.9 30.0 + - - +
113X ALA* 1.3 72.8 - - - +
115X ARG* 1.3 60.6 + - - +
117X MET* 3.6 12.9 + - - -
118X ARG* 3.8 18.9 + - - +
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Residues in contact with ARG 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X SER* 4.6 2.0 + - - +
111X GLU* 2.8 37.9 + - - +
112X ALA* 3.6 34.7 + - - +
114X GLU* 1.3 70.8 - - - +
116X ALA* 1.3 65.8 + - - +
118X ARG* 3.2 41.1 + - - +
119X GLN* 3.4 10.4 - - - +
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Residues in contact with ALA 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71W THR* 5.1 3.4 - - + -
75W HIS* 3.8 20.9 - - + +
112X ALA 3.5 12.5 + - - +
113X ALA 3.0 10.1 + - - +
115X ARG* 1.3 78.5 - - - +
117X MET* 1.3 56.2 + - - +
119X GLN* 3.0 35.7 - - + +
120X ARG* 4.2 1.6 + - - +
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Residues in contact with MET 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68W ASP* 3.4 30.1 - - - +
71W THR* 3.7 18.8 - - + -
72W TYR* 3.6 38.4 - - + +
92W ARG* 3.2 32.1 - - - +
113X ALA 3.3 17.2 + - - +
114X GLU* 3.8 4.9 - - - +
115X ARG 3.2 0.6 - - - -
116X ALA* 1.3 72.7 - - - +
118X ARG* 1.3 51.0 - - - +
119X GLN 3.1 5.6 - - - -
120X ARG* 3.2 41.6 - - - +
121X ASP* 2.7 38.2 + - - +
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Residues in contact with ARG 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104U GLN* 5.1 8.4 + - - -
150U HIS 5.9 1.6 + - - -
151U ILE* 6.0 1.4 - - - +
152U ASN* 3.7 29.3 + - - +
92W ARG* 4.4 4.4 - - - +
111X GLU* 4.2 7.9 + - - -
114X GLU* 3.8 16.8 + - - +
115X ARG* 3.2 45.3 + - - +
117X MET* 1.3 74.3 - - - +
119X GLN* 1.3 66.3 + - - +
121X ASP* 3.4 16.6 - - + +
122X ARG* 3.1 64.3 + - - +
123X GLU 4.2 0.3 + - - -
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Residues in contact with GLN 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115X ARG 3.4 19.2 - - - +
116X ALA* 3.0 21.6 + - - +
117X MET 3.1 0.2 - - - -
118X ARG* 1.3 79.7 - - - +
120X ARG* 1.3 52.6 + - - +
123X GLU* 2.7 47.8 + - - +
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Residues in contact with ARG 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67W ARG* 3.4 37.9 + - - +
68W ASP* 2.8 27.9 + - - -
71W THR* 3.1 29.6 + - - +
116X ALA 5.1 0.9 - - - +
117X MET* 3.2 35.5 + - - +
119X GLN* 1.3 78.0 - - - +
121X ASP* 1.3 72.4 + - - +
123X GLU* 3.8 15.1 - - - +
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Residues in contact with ASP 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92W ARG* 2.9 34.5 + - - -
117X MET 2.7 27.5 + - - +
118X ARG* 3.4 13.5 - - + +
119X GLN 3.2 0.6 - - - -
120X ARG* 1.3 90.7 + - - +
122X ARG* 1.3 69.3 + - + +
123X GLU 4.4 2.4 - - - +
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Residues in contact with ARG 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103U GLY 4.6 8.4 + - - -
104U GLN* 3.7 30.7 + - - +
118X ARG* 3.1 46.9 + - - +
121X ASP* 1.3 81.8 - - + +
123X GLU* 1.3 65.3 + - - +
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Residues in contact with GLU 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118X ARG 4.2 0.4 + - - -
119X GLN* 2.7 38.9 + - - +
120X ARG* 3.8 13.7 - - - +
121X ASP 3.3 2.7 - - - +
122X ARG* 1.3 83.5 - - - +
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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