Contacts of the helix formed by residues 107 - 126 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F TYR* 5.0 0.9 - - - +
144F VAL* 5.8 0.9 - - + -
24G PHE* 3.7 42.7 - - + +
26G GLU* 6.1 0.2 - - - +
105G HIS 4.1 0.2 + - - -
106G MET* 1.3 77.8 - - - +
108G ALA* 1.3 69.0 + - - +
109G GLU* 4.2 11.9 - - + +
110G GLU* 2.8 27.6 + - + +
111G MET* 3.2 9.5 + - - +
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Residues in contact with ALA 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G MET 4.0 0.6 + - - -
107G ALA* 1.3 72.3 - - - +
109G GLU* 1.3 74.9 + - - +
111G MET* 3.0 19.2 + - - +
112G GLU* 3.2 11.0 + - - +
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Residues in contact with GLU 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F TYR* 3.5 15.2 - - + -
143F ASN* 4.6 15.9 - - + +
144F VAL* 3.2 41.8 - - + +
107G ALA* 3.3 6.4 - - + +
108G ALA* 1.3 89.2 + - + +
110G GLU* 1.3 57.0 + - - +
112G GLU* 3.2 18.1 + - + +
113G TRP 2.9 22.2 + - - -
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Residues in contact with GLU 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F TYR* 3.1 30.6 + - + +
24G PHE* 3.7 7.8 - - - -
80G LEU* 5.0 0.5 - - - +
83G ARG* 3.0 47.2 + - - +
84G LEU* 4.8 2.2 + - + +
87G ILE* 3.5 30.4 - - + +
106G MET* 3.3 10.8 - - + +
107G ALA* 2.8 34.9 + - + +
109G GLU* 1.3 74.8 - - - +
111G MET* 1.3 61.9 + - - +
113G TRP* 3.2 6.6 + - - +
114G PHE* 2.8 29.1 + - - +
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Residues in contact with MET 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G LEU* 4.6 1.6 - - + -
103G ARG* 3.4 52.9 - - + +
106G MET* 4.0 23.5 - - + +
107G ALA 3.2 6.2 + - - +
108G ALA* 3.0 12.4 + - - +
110G GLU* 1.3 78.6 - - - +
112G GLU* 1.3 58.2 + - - +
114G PHE* 3.3 11.8 + - - +
115G ASN* 2.8 57.0 + - - +
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Residues in contact with GLU 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F ASN* 5.2 0.9 - - - +
139F SER* 4.9 8.8 + - - -
140F TYR* 6.1 1.0 - - - -
143F ASN* 5.3 4.2 + - - -
108G ALA 3.2 7.0 + - - +
109G GLU* 3.3 22.4 - - - +
110G GLU 3.2 0.2 - - - -
111G MET* 1.3 80.1 - - - +
113G TRP* 1.3 57.1 + - - +
115G ASN* 3.3 8.5 + - - +
116G ASN* 2.9 51.3 + - - +
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Residues in contact with TRP 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F PHE* 3.8 34.8 - + - -
136F ASN* 2.9 56.6 + - - +
137F THR* 3.4 20.7 + - - +
140F TYR* 4.1 11.2 - - + -
84G LEU* 3.6 53.2 - - + +
87G ILE* 4.2 8.1 - - + -
88G ARG* 3.8 31.2 - - + -
109G GLU 2.9 13.8 + - - +
110G GLU 3.5 6.3 - - - +
112G GLU* 1.3 74.7 - - - +
114G PHE* 1.3 60.1 + + - +
116G ASN 3.1 1.2 + - - -
117G TYR* 2.8 50.0 + + + +
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Residues in contact with PHE 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G ILE* 3.5 39.3 - - + -
91G ARG* 3.7 28.7 - - + -
95G GLY 3.8 21.5 - - - -
96G SER 3.9 8.5 - - - -
98G LEU* 3.8 34.1 - - + -
106G MET* 4.1 4.3 - - + -
110G GLU 2.8 18.0 + - - +
111G MET* 3.4 11.2 - - - +
113G TRP* 1.3 84.2 - + - +
115G ASN* 1.3 67.8 + - - +
117G TYR* 3.2 9.1 + + - +
118G LYS* 2.9 47.5 + - + +
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Residues in contact with ASN 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G MET* 2.8 42.4 + - - +
112G GLU* 3.8 6.9 - - - +
114G PHE* 1.3 77.2 - - - +
116G ASN* 1.3 65.6 + - - +
118G LYS* 3.1 27.9 + - + +
119G ARG* 3.0 39.6 + - - +
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Residues in contact with ASN 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F ASN* 2.9 37.2 + - + +
112G GLU* 2.9 39.9 + - - +
115G ASN* 1.3 76.7 - - - +
117G TYR* 1.3 62.1 + - - +
119G ARG* 2.8 38.2 + - - +
120G SER* 3.1 27.5 + - - -
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Residues in contact with TYR 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F GLU* 2.8 35.0 + - - -
129F PHE* 3.9 15.8 - + - -
133F PHE* 3.9 23.1 - + - -
136F ASN* 3.8 5.6 - - - +
88G ARG* 3.1 21.3 + - + -
91G ARG* 4.1 23.3 - - + -
92G TRP* 3.0 32.2 + - - -
113G TRP* 2.8 34.3 + + + +
114G PHE* 3.4 9.6 - + - +
115G ASN 3.2 0.2 - - - -
116G ASN* 1.3 79.1 - - - +
118G LYS* 1.3 65.2 + - - +
120G SER* 3.2 6.3 + - - -
121G LEU* 3.0 28.9 + - + +
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Residues in contact with LYS 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G ARG* 4.2 23.0 + - - +
96G SER* 3.0 37.6 + - - +
97G ILE* 5.8 0.8 - - - +
114G PHE* 2.9 31.0 + - + +
115G ASN* 3.1 41.8 + - + +
117G TYR* 1.3 82.1 - - + +
119G ARG* 1.3 56.8 + - - +
121G LEU* 3.8 5.9 - - - +
122G ALA* 3.1 28.8 + - - +
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Residues in contact with ARG 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G ASN* 3.0 29.3 + - - +
116G ASN* 2.8 44.1 + - - +
117G TYR 3.1 0.2 - - - -
118G LYS* 1.3 75.8 - - - +
120G SER* 1.3 61.5 + - - +
122G ALA* 3.6 5.1 + - + +
123G THR* 2.8 33.6 + - - +
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Residues in contact with SER 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F PHE* 3.9 20.0 - - - +
132F GLU* 2.8 42.7 + - - +
133F PHE* 6.4 0.4 - - - -
116G ASN 3.1 15.4 + - - -
117G TYR* 3.2 11.0 + - - -
119G ARG* 1.3 73.9 - - - +
121G LEU* 1.3 59.9 + - - +
123G THR* 3.2 5.9 + - - -
124G TYR* 2.8 30.1 + - - +
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Residues in contact with LEU 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F LEU* 4.0 25.1 - - + -
129F PHE* 4.0 13.9 - - + -
91G ARG* 3.9 40.4 - - + +
92G TRP* 3.9 27.6 - - + +
117G TYR* 3.0 22.9 + - + +
118G LYS* 3.8 4.7 - - - +
120G SER* 1.3 76.6 - - - +
122G ALA* 1.3 54.8 + - - +
124G TYR* 2.9 6.8 + - + +
125G MET* 2.8 60.6 + - + +
137G THR* 4.5 3.1 - - - +
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Residues in contact with ALA 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G LYS 3.1 15.1 + - - +
119G ARG* 3.9 6.3 - - + +
121G LEU* 1.3 77.6 - - - +
123G THR* 1.3 65.0 + - - +
125G MET* 4.0 14.5 - - + +
126G ARG* 2.9 29.9 + - + +
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Residues in contact with THR 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F GLU* 5.2 10.3 - - - +
119G ARG* 2.8 24.3 + - - +
120G SER* 3.3 11.1 - - - -
122G ALA* 1.3 78.7 - - - +
124G TYR* 1.3 64.5 + - - +
126G ARG* 3.5 10.9 + - - +
127G SER* 3.4 15.1 + - - +
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Residues in contact with TYR 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F LEU* 3.8 18.3 + - + +
97F LEU* 3.8 38.1 - - + +
123F SER* 4.8 1.2 + - - -
125F GLU* 3.8 35.0 - - + +
126F GLU* 3.6 38.7 + - + +
129F PHE* 4.2 15.3 - - + -
120G SER 2.8 16.9 + - - +
121G LEU* 2.9 9.7 + - + +
123G THR* 1.3 74.3 - - - +
125G MET* 1.3 68.8 + - + +
127G SER* 2.8 22.2 + - - -
128G LEU* 3.5 34.2 - - + +
136G ILE* 4.3 9.9 - - + -
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Residues in contact with MET 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G ARG* 4.1 18.8 - - - +
121G LEU* 2.8 45.2 + - + +
122G ALA* 4.0 14.4 - - + +
124G TYR* 1.3 76.7 - - + +
126G ARG* 1.3 57.5 + - - +
127G SER 3.0 5.6 + - - -
128G LEU* 3.3 22.0 + - - +
132G GLU 4.7 0.7 - - - -
134G LEU 3.4 27.8 + - - +
135G ASP* 3.8 18.6 - - - +
136G ILE* 3.5 41.3 - - + -
137G THR* 4.1 6.3 - - - +
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Residues in contact with ARG 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G ALA* 2.9 19.8 + - - +
123G THR* 3.9 6.3 - - - +
124G TYR 3.3 0.2 - - - -
125G MET* 1.3 75.2 - - - +
127G SER* 1.3 58.2 + - - +
128G LEU 3.7 0.7 - - - -
129G GLY 4.9 1.7 - - - +
130G GLY 4.9 1.7 - - - +
131G ASP* 3.8 31.0 + - - +
132G GLU* 3.8 36.0 + - - +
133G GLY* 4.1 5.7 + - - -
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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
------------------------------------------------------------
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