Contacts of the helix formed by residues 115 - 135 (chain A) in PDB entry 3C7N
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.9 1.4 - - - +
71A ILE* 3.1 53.6 - - + +
72A ILE* 3.5 11.5 - - + +
73A GLY 4.9 0.9 - - - +
100A THR 3.6 12.0 + - - +
101A GLY* 4.5 0.2 - - - -
113A PHE 4.0 0.4 + - - -
114A SER* 1.3 71.1 - - - +
116A THR* 1.3 57.0 + - - +
118A LEU* 3.7 13.3 - - - +
119A ALA* 2.9 31.7 + - - +
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Residues in contact with THR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 3.9 10.3 - - - +
114A SER* 3.8 11.3 + - - -
115A ALA* 1.3 79.4 - - - +
117A GLN* 1.3 57.8 + - - +
120A ALA* 3.1 24.8 + - - +
156A ASN* 3.7 39.0 - - - +
159A ASP* 4.4 7.2 - - + -
160A ALA* 3.5 14.4 - - - +
163A ILE* 4.1 13.2 - - + -
542A LEU* 4.6 11.8 - - + +
550A LEU* 4.6 2.9 - - + -
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL 4.4 2.1 + - - +
113A PHE* 3.6 27.6 - - + -
114A SER* 2.8 34.0 + - - +
116A THR* 1.3 78.0 - - - +
118A LEU* 1.3 63.7 + - - +
119A ALA 3.3 0.2 - - - -
120A ALA* 3.4 8.3 + - + +
121A MET* 3.1 30.9 + - + +
163A ILE* 4.6 5.4 - - + -
550A LEU* 3.7 37.1 + - + +
553A LYS* 3.7 35.2 - - - +
554A GLU* 4.0 3.5 - - + +
557A MET* 4.9 3.7 - - + +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.7 12.8 - - + +
42A PHE* 3.8 21.3 - - + -
65A VAL* 4.1 14.1 - - + -
68A LEU* 4.0 13.8 - - + +
71A ILE* 3.9 24.5 - - + -
102A ALA* 3.9 16.6 - - + +
113A PHE* 3.7 25.8 - - + +
114A SER 2.8 20.7 + - - +
115A ALA* 3.7 4.0 - - - +
117A GLN* 1.3 76.0 - - - +
119A ALA* 1.3 59.6 + - - +
120A ALA 3.1 0.2 - - - -
121A MET* 3.1 41.4 + - + +
122A PHE 3.4 5.0 + - - -
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 5.6 4.0 - - + -
68A LEU* 4.1 21.5 - - + +
72A ILE* 4.0 7.9 - - + -
115A ALA 2.9 19.0 + - - +
116A THR 4.1 2.9 - - - +
118A LEU* 1.3 75.1 - - - +
120A ALA* 1.3 64.6 + - - +
122A PHE* 3.7 1.2 + - - +
123A ILE* 3.1 31.3 + - + +
157A ILE* 4.0 27.4 - - + -
160A ALA* 4.2 3.4 - - + -
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A THR 3.1 19.7 + - - +
117A GLN 3.5 7.2 - - - +
118A LEU 3.1 0.2 - - - -
119A ALA* 1.3 77.5 - - - +
121A MET* 1.3 62.4 + - - +
123A ILE* 3.6 1.0 + - - +
124A ASP* 3.1 20.1 + - - +
160A ALA* 3.5 15.9 - - - +
163A ILE* 3.2 41.5 - - + -
164A ALA* 3.1 13.0 - - - +
554A GLU* 4.0 2.6 - - - +
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Residues in contact with MET 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.9 12.3 - - + -
42A PHE* 3.4 29.2 - - + -
47A ARG* 2.7 33.2 - - - +
49A LEU* 3.6 15.2 - - + +
113A PHE* 3.7 28.0 - - + -
117A GLN 3.1 24.6 + - - +
118A LEU* 3.1 35.8 + - + +
120A ALA* 1.3 75.3 - - - +
122A PHE* 1.3 66.0 + - - +
124A ASP* 3.4 6.1 + - - +
125A LYS 3.3 14.0 + - - -
554A GLU* 3.1 15.9 - - - +
557A MET* 4.2 5.2 - - + -
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 5.0 1.6 - - + -
9A LEU* 4.8 15.0 - - + -
14A SER* 3.0 32.5 - - - -
36A THR* 4.2 6.3 - - + -
37A PRO 2.9 30.5 - - - -
38A SER* 3.4 10.8 - - - -
39A VAL 3.8 20.4 - - - -
40A VAL* 3.7 7.7 - - + +
49A LEU* 5.0 0.7 - - - -
50A GLY* 3.7 15.9 - - - -
68A LEU* 3.4 26.7 - - + -
118A LEU 3.4 2.8 + - - -
119A ALA 4.1 3.1 - - - +
120A ALA 3.5 0.2 - - - -
121A MET* 1.3 78.1 - - - +
123A ILE* 1.3 62.4 + - - +
125A LYS* 2.9 24.1 + - + +
126A VAL* 3.1 36.9 + - + +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 5.8 0.2 - - + -
7A LEU* 4.1 10.8 - - + -
9A LEU* 3.9 24.2 - - + -
119A ALA 3.1 19.2 + - - +
120A ALA* 3.7 3.8 - - - +
122A PHE* 1.3 76.3 - - + +
124A ASP* 1.3 57.4 + - - +
126A VAL* 3.2 10.8 - - + +
127A LYS* 2.8 27.4 + - - +
141A VAL* 6.2 0.2 - - + -
143A ILE* 3.8 28.0 - - + -
157A ILE* 4.5 2.7 - - + +
160A ALA* 4.3 7.2 - - + -
161A ALA* 4.2 22.0 - - + +
164A ALA* 3.8 10.5 - - + -
166A LEU* 3.7 25.4 - - + -
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Residues in contact with ASP 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 5.5 0.9 - - - +
49A LEU* 5.6 0.7 - - + -
120A ALA 3.1 11.5 + - - +
121A MET 3.4 10.5 - - - +
122A PHE 3.1 0.2 - - - -
123A ILE* 1.3 73.5 - - - +
125A LYS* 1.3 66.2 + - - +
127A LYS* 3.1 18.5 + - - +
128A ASP* 3.0 22.5 + - - +
163A ILE 4.3 0.3 - - - +
164A ALA* 3.3 28.2 - - - +
554A GLU* 3.1 34.6 - - - +
558A LEU* 4.0 30.8 - - + +
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLU* 3.5 35.4 + - - +
36A THR* 5.2 2.5 - - + -
49A LEU* 3.2 55.1 - - + +
50A GLY* 4.4 5.4 - - - +
51A GLU 5.1 0.7 - - - +
52A THR* 5.6 3.4 + - - -
121A MET 3.3 3.8 + - - +
122A PHE* 2.9 14.1 + - + +
124A ASP* 1.3 77.5 - - - +
126A VAL* 1.3 55.9 + - + +
128A ASP* 3.0 17.8 + - + +
129A THR* 2.7 40.0 + - - +
132A GLN* 6.1 1.2 - - - +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 4.1 16.8 - - + -
7A LEU* 4.5 13.7 - - + -
16A LEU* 3.9 23.1 - - + -
36A THR* 4.2 13.9 - - + +
122A PHE* 3.1 37.9 + - + +
123A ILE* 3.2 22.4 - - + +
125A LYS* 1.3 74.3 - - + +
127A LYS* 1.3 64.1 + - - +
129A THR* 3.4 9.2 - - - +
130A VAL* 2.9 34.5 + - - +
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Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 4.2 11.7 - - - -
123A ILE 2.8 20.6 + - - +
124A ASP* 3.1 17.9 + - - +
126A VAL* 1.3 75.4 - - - +
128A ASP* 1.3 52.5 + - + +
130A VAL* 3.4 3.8 + - - +
131A LYS* 2.8 68.6 + - + +
138A ILE* 4.5 10.3 - - + +
164A ALA 3.2 30.4 + - - +
165A GLY* 4.1 10.7 + - - -
166A LEU* 3.8 32.8 - - + -
558A LEU* 6.0 2.0 - - - +
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Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ASP 3.0 11.6 + - - +
125A LYS* 3.0 22.1 + - + +
127A LYS* 1.3 73.3 - - - +
129A THR* 1.3 66.6 + - - +
130A VAL 3.0 0.9 - - - -
131A LYS* 2.8 30.2 + - - +
132A GLN* 2.6 45.8 + - - +
558A LEU* 5.8 3.3 - - + +
562A LYS* 4.0 26.5 + - - +
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Residues in contact with THR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.3 27.1 - - + -
27A VAL* 3.9 12.3 - - + -
28A VAL 4.3 0.9 - - - +
29A ASN* 4.0 26.0 - - + +
30A GLU* 3.6 18.8 + - - +
36A THR* 4.5 4.7 + - - +
125A LYS* 2.7 24.3 + - - +
126A VAL* 3.2 14.2 + - - +
128A ASP* 1.3 74.2 - - - +
130A VAL* 1.3 59.9 + - - +
132A GLN* 3.6 7.5 + - - +
133A ASP* 3.5 17.7 + - - +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 4.0 19.7 - - + -
16A LEU* 3.7 32.3 - - + -
18A VAL* 3.4 29.2 - - + -
27A VAL* 4.1 12.1 - - + -
126A VAL 2.9 16.1 + - - +
127A LYS* 3.7 4.7 - - - +
129A THR* 1.3 72.5 - - - +
131A LYS* 1.3 57.8 + - - +
132A GLN 3.1 2.2 - - - -
133A ASP* 3.9 0.2 - - - +
134A THR* 2.6 43.7 + - + -
138A ILE* 4.3 13.7 - - + -
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Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LYS* 2.8 53.5 + - + +
128A ASP* 2.8 23.8 + - - +
130A VAL* 1.3 71.1 - - - +
132A GLN* 1.3 57.8 + - + +
134A THR* 3.1 6.7 + - - -
135A LYS* 2.8 27.9 + - - -
136A ALA 3.7 11.4 + - - +
137A ASN* 5.6 2.9 - - - +
138A ILE* 3.7 27.3 - - + +
562A LYS* 5.4 6.8 - - - +
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Residues in contact with GLN 132 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A LYS* 6.1 1.2 - - - +
128A ASP* 2.6 42.2 + - - +
129A THR* 3.9 6.0 - - - +
131A LYS* 1.3 77.1 - - + +
133A ASP* 1.3 62.3 + - - +
135A LYS* 3.0 33.5 + - - +
562A LYS* 5.8 2.6 - - - +
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Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG* 3.7 22.1 + - - -
27A VAL* 3.5 38.2 - - + +
28A VAL* 3.5 24.0 + - - +
129A THR 3.5 6.8 + - - +
130A VAL 3.2 2.2 + - - +
132A GLN* 1.3 79.6 - - - +
134A THR* 1.3 61.9 + - - +
135A LYS* 3.7 5.4 + - - +
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Residues in contact with THR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 4.6 9.2 - - - +
18A VAL* 4.3 11.2 - - + -
20A ARG* 3.5 24.2 - - - +
27A VAL* 5.3 0.2 - - + -
130A VAL* 2.6 40.1 + - + +
131A LYS* 3.1 12.6 + - - -
133A ASP* 1.3 78.3 - - + +
135A LYS* 1.3 60.8 + - - +
136A ALA* 2.7 33.7 + - - +
138A ILE* 3.8 10.6 - - + +
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Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LYS 2.8 14.1 + - - -
132A GLN* 3.0 31.6 + - - +
133A ASP 3.4 5.7 - - - +
134A THR* 1.3 77.8 - - - +
136A ALA* 1.3 58.5 + - - +
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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