Contacts of the helix formed by residues 107 - 129 (chain C) in PDB entry 2Q9Q
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 ALA 107 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B TYR* 5.1 0.4 - - - +
144B VAL* 6.5 0.2 - - + -
24C PHE* 3.9 35.5 - - + +
26C GLU* 5.7 3.6 - - - +
105C HIS 4.1 0.8 + - - -
106C MET* 1.3 76.2 - - - +
108C ALA* 1.3 68.3 + - - +
109C GLU* 3.5 13.9 - - + +
110C GLU* 2.9 32.3 + - + +
111C MET* 3.0 12.4 + - - +
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C MET 3.9 0.8 + - - -
107C ALA* 1.3 71.7 - - - +
109C GLU* 1.3 71.9 + - - +
111C MET* 3.2 11.5 + - - +
112C GLU* 3.0 21.2 + - - +
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Residues in contact with GLU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B TYR* 3.5 28.3 - - + -
143B ASN* 5.7 6.5 - - + -
144B VAL* 3.7 20.3 - - + +
107C ALA* 3.5 11.9 - - + +
108C ALA* 1.3 88.2 + - + +
110C GLU* 1.3 59.8 + - - +
112C GLU* 3.2 14.4 + - - +
113C TRP 3.0 22.5 + - - -
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Residues in contact with GLU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B TYR* 3.2 28.6 + - + +
24C PHE* 3.6 9.8 - - - -
83C ARG* 2.5 63.3 + - - +
84C LEU* 4.7 2.6 - - + +
87C ILE* 3.6 24.2 - - + +
106C MET* 3.3 10.4 - - + +
107C ALA* 2.9 29.6 + - + +
109C GLU* 1.3 76.6 - - - +
111C MET* 1.3 57.9 + - - +
113C TRP* 3.1 6.5 + - - +
114C PHE* 2.9 28.4 + - - +
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Residues in contact with MET 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 4.2 9.4 - - + -
103C ARG* 3.8 36.1 - - - +
106C MET* 3.8 13.1 - - + +
107C ALA 3.0 11.2 + - - +
108C ALA* 3.3 12.8 - - - +
110C GLU* 1.3 76.1 - - - +
112C GLU* 1.3 57.4 + - - +
114C PHE* 3.4 37.9 + - + +
115C ASN* 2.9 50.4 + - - +
118C LYS* 5.9 0.2 - - - +
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ALA 3.0 11.4 + - - +
109C GLU* 3.5 16.8 - - - +
110C GLU 3.2 0.2 - - - -
111C MET* 1.3 75.5 - - - +
113C TRP* 1.3 59.8 + - - +
115C ASN* 3.3 8.7 + - + +
116C ASN* 2.9 47.6 + - - +
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Residues in contact with TRP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.6 37.9 - + - -
136B ASN* 3.0 54.8 + - - +
137B THR* 3.1 22.1 + - - +
140B TYR* 3.8 16.4 - - + -
84C LEU* 3.7 52.0 - - + +
85C LEU* 6.5 0.2 - - + -
87C ILE* 4.3 7.9 - - + -
88C ARG* 3.9 28.7 - - + -
109C GLU 3.0 13.4 + - - +
110C GLU* 3.1 9.4 + - - +
112C GLU* 1.3 75.5 - - - +
114C PHE* 1.3 65.4 + - - +
116C ASN* 3.3 0.6 + - - +
117C TYR* 2.9 43.1 + + + +
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Residues in contact with PHE 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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87C ILE* 3.8 29.4 - - + -
88C ARG* 5.4 0.2 - - - -
91C ARG* 3.6 39.3 - - + -
95C GLY 3.8 13.7 - - - -
96C SER 3.6 18.6 - - - -
98C LEU* 3.7 35.4 - - + -
106C MET* 4.3 1.3 - - + -
110C GLU 2.9 12.3 + - - +
111C MET* 3.4 31.2 - - + +
113C TRP* 1.3 84.7 - + - +
115C ASN* 1.3 61.8 + - - +
117C TYR* 3.1 9.7 + + - +
118C LYS* 2.8 37.3 + - + +
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Residues in contact with ASN 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 MET* 2.9 45.0 + - - +
112C GLU* 3.3 7.6 + - + +
114C PHE* 1.3 74.1 - - - +
116C ASN* 1.3 68.7 + - - +
118C LYS* 3.6 31.3 + - - +
119C ARG* 2.9 27.5 + - - +
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Residues in contact with ASN 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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136B ASN* 2.8 37.1 + - + +
112C GLU* 2.9 39.4 + - - +
113C TRP* 4.5 0.2 - - - +
115C ASN* 1.3 76.6 - - - +
117C TYR* 1.3 57.9 + - - +
119C ARG* 3.4 35.2 + - - +
120C SER* 3.0 32.3 + - - -
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Residues in contact with TYR 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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101B GLU* 2.7 38.2 + - - -
129B PHE* 3.9 17.1 - + - -
133B PHE* 3.9 22.7 - + - -
136B ASN* 3.9 6.0 - - - +
88C ARG* 3.1 17.4 + - + -
91C ARG* 4.1 23.1 - - + -
92C TRP* 2.9 30.9 + - - -
113C TRP* 2.9 31.3 + + + +
114C PHE* 3.2 12.8 - + - +
116C ASN* 1.3 75.7 - - - +
118C LYS* 1.3 65.5 + - + +
120C SER* 3.1 7.7 + - - -
121C LEU* 2.9 32.1 + - + +
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Residues in contact with LYS 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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91C ARG* 3.8 23.3 + - + +
96C SER* 2.6 46.7 + - - +
97C ILE* 4.1 11.7 - - - +
111C MET* 5.9 0.4 - - - +
114C PHE* 2.8 28.2 + - + +
115C ASN* 3.6 29.2 + - - +
117C TYR* 1.3 79.5 - - + +
119C ARG* 1.3 61.3 + - + +
121C LEU* 3.4 6.4 + - - +
122C ALA* 2.9 29.6 + - - +
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Residues in contact with ARG 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 ASN 2.9 18.7 + - - +
116C ASN* 3.4 30.3 + - - +
118C LYS* 1.3 79.3 - - + +
120C SER* 1.3 63.6 + - - +
122C ALA* 3.5 7.2 + - - +
123C THR* 3.1 30.9 + - - +
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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
----------------------------------------------------------
129B PHE* 3.9 15.5 - - - -
132B GLU* 2.7 45.3 + - - +
116C ASN 3.0 17.2 + - - -
117C TYR* 3.1 7.2 + - - -
119C ARG* 1.3 77.3 + - - +
121C LEU* 1.3 60.3 + - - +
123C THR* 3.3 5.0 + - - -
124C TYR* 2.9 27.7 + - - +
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Residues in contact with LEU 121 (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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97B LEU* 3.9 26.9 - - + -
129B PHE* 3.8 16.5 - - + -
91C ARG* 4.0 34.8 - - + +
92C TRP* 4.0 27.6 - - + -
117C TYR* 2.9 21.0 + - + +
118C LYS* 3.8 5.2 - - - +
120C SER* 1.3 74.4 - - - +
122C ALA* 1.3 60.8 + - - +
124C TYR* 3.2 2.2 + - + -
125C MET* 2.9 65.4 + - + +
137C THR* 4.4 3.1 - - - +
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Residues in contact with ALA 122 (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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118C LYS 2.9 17.9 + - - +
119C ARG* 3.6 8.1 - - - +
121C LEU* 1.3 77.0 - - - +
123C THR* 1.3 58.6 + - - +
125C MET* 3.6 14.4 + - + +
126C ARG* 3.0 31.1 + - - +
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Residues in contact with THR 123 (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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132B GLU* 5.2 7.2 - - - +
119C ARG* 3.1 17.6 + - - +
120C SER* 3.6 10.7 - - - -
121C LEU 3.2 0.2 - - - -
122C ALA* 1.3 76.4 - - - +
124C TYR* 1.3 68.3 + - - +
126C ARG* 3.4 9.9 + - - +
127C SER* 3.2 22.5 + - - -
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Residues in contact with TYR 124 (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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93B LEU* 3.7 20.8 + - + +
97B LEU* 3.9 32.8 - - + +
123B SER* 4.8 1.2 + - - -
125B GLU* 3.8 35.4 - - + +
126B GLU* 3.7 34.9 + - + +
129B PHE* 4.1 19.7 - + + -
120C SER 2.9 16.5 + - - +
121C LEU* 3.2 4.2 + - + +
123C THR* 1.3 78.4 - - - +
125C MET* 1.3 71.4 + - + +
127C SER* 2.7 23.8 + - - -
128C LEU* 3.3 41.8 + - + +
136C ILE* 4.2 6.1 - - + -
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Residues in contact with MET 125 (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 ARG* 4.2 17.0 - - - +
121C LEU* 2.9 48.7 + - + +
122C ALA* 4.0 12.3 - - + +
124C TYR* 1.3 75.5 - - + +
126C ARG* 1.3 55.5 + - - +
128C LEU* 3.3 14.2 - - - +
133C GLY 2.6 29.7 - - - +
134C LEU 3.3 10.1 - - - +
135C ASP* 3.4 31.9 - - + +
136C ILE* 3.5 31.4 - - + -
137C THR* 4.2 5.6 - - - +
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Residues in contact with ARG 126 (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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122C ALA 3.0 19.8 + - - +
123C THR* 3.9 8.5 - - - +
124C TYR 3.2 0.2 - - - -
125C MET* 1.3 76.3 - - - +
127C SER* 1.3 64.6 - - - +
128C LEU 3.2 0.7 - - - -
129C GLY 4.0 0.3 + - - -
130C GLY 3.8 6.1 - - - +
131C ASP* 3.1 31.0 + - - +
132C GLU* 3.0 35.8 + - + +
133C GLY 3.7 15.3 + - - +
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Residues in contact with SER 127 (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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125B GLU* 3.1 37.4 - - - +
123C THR* 3.2 14.0 + - - -
124C TYR* 2.7 19.5 + - - -
126C ARG* 1.3 76.7 - - - +
128C LEU* 1.3 65.4 + - - +
129C GLY 3.5 0.4 + - - -
130C GLY 4.5 6.9 + - - +
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Residues in contact with LEU 128 (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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51B VAL* 5.2 9.0 - - + +
52B GLU* 5.4 3.6 - - - +
55B MET* 3.3 22.0 - - + +
93B LEU* 3.7 30.1 - - + -
125B GLU* 5.6 3.1 - - + -
124C TYR* 3.5 52.0 - - + +
125C MET* 3.3 21.5 - - - +
126C ARG 3.2 0.2 - - - -
127C SER* 1.3 82.9 + - - +
129C GLY* 1.3 57.7 + - - +
130C GLY 4.2 1.1 + - - -
133C GLY 3.4 3.8 - - - +
134C LEU* 4.0 11.4 - - + +
136C ILE* 4.0 11.0 - - + -
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Residues in contact with GLY 129 (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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55B MET* 3.0 21.8 - - - -
59B GLU* 4.6 5.8 - - - -
127C SER 3.5 0.8 - - - -
128C LEU* 1.3 73.9 - - - +
130C GLY* 1.3 67.7 + - - -
132C GLU 3.1 2.6 + - - -
133C GLY* 2.5 47.4 + - - +
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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
------------------------------------------------------------
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