Contacts of the helix formed by residues 118 - 142 (chain A) in PDB entry 2F3M
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 GLU 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ASN* 2.8 16.6 + - - +
117A PRO* 1.3 78.6 - - - +
119A PHE* 1.3 65.9 + - - +
120A GLU 2.6 5.9 + - - -
121A LYS* 2.8 50.4 + - + +
122A LEU* 3.4 29.6 + - + -
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Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 3.3 33.9 - - + +
114A CYS* 3.7 18.4 - - - -
116A ASN* 2.7 23.4 + - - +
117A PRO 3.0 2.8 + - - +
118A GLU* 1.3 69.5 - - - +
120A GLU* 1.3 80.7 + - + +
122A LEU* 3.3 6.8 + - - +
123A LYS* 3.1 43.9 + - + +
169A PHE* 3.6 30.7 - + - -
213A VAL* 3.5 29.4 - - + -
214A TRP* 3.7 28.7 - + + -
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO 4.7 1.2 + - - -
118A GLU 2.6 6.1 + - - -
119A PHE* 1.3 94.9 - - + +
121A LYS* 1.3 66.4 + - + +
123A LYS* 3.8 13.7 + - - +
124A PRO* 3.4 17.3 - - - +
213A VAL* 6.0 0.9 - - + -
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU* 2.8 46.8 + - + +
120A GLU* 1.3 78.8 - - + +
122A LEU* 1.3 65.3 + - + +
123A LYS 3.3 0.7 - - - -
124A PRO* 3.1 18.5 - - - +
125A LYS* 4.8 2.8 + - - +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 4.4 24.7 - - + -
116A ASN* 2.8 44.2 - - + +
118A GLU* 3.4 25.3 + - + +
119A PHE 3.3 7.0 + - - +
121A LYS* 1.3 83.1 - - + +
123A LYS* 1.3 63.4 + - - +
124A PRO 3.4 0.2 - - - -
125A LYS* 3.2 10.4 + - - +
126A TYR* 3.1 21.5 + - - +
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 4.5 4.7 - - + -
119A PHE* 3.1 46.1 + - + +
120A GLU* 3.8 14.9 + - - +
122A LEU* 1.3 76.7 - - - +
124A PRO* 1.4 63.5 - - + +
126A TYR* 3.3 7.2 + - - +
127A LEU* 2.9 54.1 + - + +
169A PHE* 4.0 30.6 + - + -
214A TRP* 5.3 5.3 - - - +
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Residues in contact with PRO 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU 3.4 14.1 - - - +
121A LYS* 3.1 19.1 - - - +
122A LEU 3.5 0.4 - - - -
123A LYS* 1.4 92.5 - - + +
125A LYS* 1.3 56.0 + - - +
127A LEU* 3.5 8.7 + - + +
128A GLU* 2.9 30.9 + - - +
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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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121A LYS 4.8 2.0 + - - +
122A LEU* 3.2 11.3 + - - +
124A PRO* 1.3 76.7 - - - +
126A TYR* 1.3 66.3 + - - +
128A GLU* 3.1 39.2 - - - +
129A GLU* 3.3 31.3 + - - +
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASN 4.1 1.4 + - - -
109A GLN* 3.8 23.1 - - + -
110A LEU* 3.2 35.2 + - + +
113A ILE* 3.8 29.6 - - + -
122A LEU 3.1 10.5 + - - +
123A LYS 3.7 6.1 - - - +
125A LYS* 1.3 80.4 - - - +
127A LEU* 1.3 57.0 + - - +
129A GLU* 3.4 10.6 + - - +
130A LEU* 2.8 35.7 + - + -
133A LYS* 3.5 28.5 + - + -
166A HIS* 2.8 34.6 + + - -
169A PHE* 4.8 10.3 - + - -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LYS* 2.9 49.0 + - + +
124A PRO* 3.8 7.2 - - + +
126A TYR* 1.3 74.4 - - + +
128A GLU* 1.3 66.4 + - - +
130A LEU* 2.9 49.4 + - + +
131A PRO* 3.1 7.1 - - - +
169A PHE* 4.0 17.0 - - + -
170A GLU* 3.8 22.7 - - + +
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Residues in contact with GLU 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 PRO 2.9 16.2 + - - +
125A LYS* 3.1 34.0 - - - +
127A LEU* 1.3 77.4 - - - +
129A GLU* 1.3 64.0 + - + +
131A PRO* 3.5 11.1 - - - +
132A GLU* 5.3 0.5 + - - +
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Residues in contact with GLU 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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125A LYS* 3.3 44.1 + - - +
126A TYR* 3.5 8.9 - - - +
127A LEU 3.2 0.2 - - - -
128A GLU* 1.3 80.4 - - + +
130A LEU* 1.3 68.8 + - - +
131A PRO* 3.1 4.5 - - - -
132A GLU* 3.5 19.5 + - + +
133A LYS* 3.5 31.4 + - + +
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Residues in contact with LEU 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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126A TYR* 2.8 17.3 + - + +
127A LEU* 2.9 46.4 - - + +
129A GLU* 1.3 77.0 - - - +
131A PRO* 1.3 77.0 - - + +
133A LYS* 3.7 11.0 - - + +
134A LEU* 2.9 29.2 + - + +
166A HIS* 3.8 28.0 - - + +
169A PHE* 4.5 8.1 - - + -
170A GLU* 3.6 26.5 - - + -
173A CYS* 4.5 2.5 - - + -
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Residues in contact with PRO 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 LEU 3.1 10.5 - - - +
128A GLU 3.5 8.7 - - - +
129A GLU 3.3 3.1 - - - -
130A LEU* 1.3 95.1 - - + +
132A GLU* 1.3 56.4 + - - +
134A LEU* 2.3 47.9 + - + -
135A LYS* 3.1 4.4 + - - -
177A PHE* 4.9 12.6 - - + -
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Residues in contact with GLU 132 (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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128A GLU 5.3 0.6 + - - +
129A GLU* 3.5 17.2 + - + +
131A PRO* 1.3 79.0 - - - +
133A LYS* 1.3 56.3 + - + +
135A LYS* 2.6 56.6 + - - +
136A LEU* 3.1 29.3 + - + +
50B PHE* 4.0 25.5 - - + -
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Residues in contact with LYS 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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106A ASN* 4.0 22.3 + - + +
109A GLN* 2.9 33.6 + - - +
126A TYR* 3.5 38.3 + - + +
129A GLU* 3.5 29.9 + - + +
130A LEU* 3.7 12.6 - - + +
131A PRO 2.6 2.8 + - - -
132A GLU* 1.3 79.3 - - + +
134A LEU* 1.3 65.4 + - + +
136A LEU* 3.3 21.6 + - + +
137A TYR* 3.2 21.7 + - + -
166A HIS* 5.9 3.6 - - + +
56B PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 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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130A LEU* 2.9 47.6 - - + +
131A PRO* 2.3 24.1 + - + +
133A LYS* 1.3 73.6 - - + +
135A LYS* 1.3 64.0 + - - +
137A TYR* 3.2 12.1 + - + +
138A SER* 2.9 21.8 + - - -
162A VAL* 5.7 1.3 - - + -
163A LEU* 3.9 26.7 - - + -
166A HIS* 5.2 12.8 - - + +
173A CYS* 3.7 26.9 - - + +
174A LEU* 4.2 7.0 - - + -
177A PHE* 3.7 19.5 - - + -
180A LEU* 3.7 5.1 - - + +
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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 PRO 3.1 3.4 + - - -
132A GLU* 2.6 47.0 + - - +
134A LEU* 1.3 72.5 - - - +
136A LEU* 1.3 59.1 + - - +
138A SER* 3.1 2.6 + - - -
139A GLU* 2.8 65.5 + - + +
177A PHE* 3.7 27.2 - - + -
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Residues in contact with LEU 136 (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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102A GLN* 5.5 3.1 - - - +
132A GLU* 3.1 29.6 + - + +
133A LYS* 3.5 17.3 - - + +
135A LYS* 1.3 81.0 - - - +
137A TYR* 1.3 56.9 + - - +
139A GLU* 3.6 11.7 + - - +
140A PHE* 2.9 31.2 + - - +
50B PHE* 5.2 6.3 - - + -
55B ASP 3.9 14.3 - - - +
56B PHE* 3.5 31.9 - - + -
57B PRO* 4.3 21.5 - - + +
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Residues in contact with TYR 137 (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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99A LEU* 4.0 19.7 - - + -
102A GLN* 3.8 5.5 + - + +
103A THR* 3.6 27.1 + - + +
106A ASN* 2.5 36.1 + - - +
133A LYS* 3.2 27.5 + - + -
134A LEU* 3.2 17.1 + - + +
136A LEU* 1.3 74.6 - - - +
138A SER* 1.3 66.2 + - - +
140A PHE* 3.0 5.2 + - - +
141A LEU* 2.8 25.1 + - - +
147A PHE* 3.7 10.2 - + + -
159A VAL* 4.0 24.0 - - + -
162A VAL* 4.3 16.0 - - + +
163A LEU* 4.7 5.6 - - + -
180A LEU* 4.2 17.7 - - + -
56B PHE* 4.1 13.7 - + - -
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Residues in contact with SER 138 (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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134A LEU 2.9 12.9 + - - -
135A LYS* 3.4 7.6 - - - -
137A TYR* 1.3 77.8 - - - +
139A GLU* 1.3 65.4 + - - +
141A LEU 3.2 0.2 + - - -
142A GLY* 2.8 21.1 + - - -
177A PHE* 3.7 23.5 - - - +
179A ASN* 2.7 38.3 + - - +
180A LEU* 3.9 12.2 - - - +
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Residues in contact with GLU 139 (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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135A LYS* 2.8 59.1 + - + +
136A LEU* 4.0 10.1 - - - +
138A SER* 1.3 73.9 - - - +
140A PHE* 1.3 63.7 + - - +
142A GLY* 3.4 13.2 + - - +
144A ARG* 5.1 0.5 + - - -
55B ASP* 5.8 0.2 - - - -
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Residues in contact with PHE 140 (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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95A ARG* 2.9 75.4 + - + -
98A ILE* 5.1 9.0 - - + -
99A LEU* 3.5 38.1 - - + -
136A LEU 2.9 19.9 + - - +
137A TYR* 3.0 4.2 + - - +
139A GLU* 1.3 77.7 - - - +
141A LEU* 1.3 60.8 + - - +
144A ARG* 3.0 6.9 + - - -
147A PHE* 4.0 8.7 - + - -
55B ASP* 3.3 47.1 - - + +
56B PHE* 3.5 22.7 - + + -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ARG* 4.6 1.3 - - - +
137A TYR 2.8 14.5 + - - +
138A SER 3.7 2.9 - - - +
140A PHE* 1.3 73.8 - - - +
142A GLY* 1.3 62.1 + - - +
143A LYS 3.2 1.9 + - - -
144A ARG* 2.7 56.3 + - - +
145A PRO 4.5 1.1 - - - +
146A TRP* 3.4 33.2 - - - +
147A PHE* 3.5 34.7 - - + +
179A ASN* 3.7 33.2 - - + +
180A LEU* 4.3 3.6 - - + -
183A PHE* 4.0 18.2 - - + -
186A ARG* 5.0 3.4 - - - +
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A SER 2.8 15.6 + - - -
139A GLU* 3.7 10.1 - - - -
140A PHE 3.3 1.2 - - - -
141A LEU* 1.3 79.1 - - - +
143A LYS* 1.3 63.4 + - - -
144A ARG* 4.4 3.7 - - - +
179A ASN* 3.2 25.4 - - - +
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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
------------------------------------------------------------
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