Contacts of the helix formed by residues 108 - 123 (chain D) in PDB entry 1EN6
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 SER 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D ILE* 4.2 0.6 - - - +
103D GLU* 3.8 16.7 + - - +
106D PHE* 3.1 7.3 + - - +
107D GLY* 1.3 79.3 - - - +
109D VAL* 1.3 65.1 + - - +
110D ASP* 3.5 10.7 + - - +
111D ASN* 2.6 32.8 + - - +
112D PHE* 3.1 20.6 + - - +
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Residues in contact with VAL 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D LEU* 3.8 31.2 - - + -
99D LYS* 4.3 13.2 - - + -
102D ILE* 4.2 10.5 - - + -
103D GLU* 4.2 23.3 + - + +
108D SER* 1.3 72.9 - - - +
110D ASP* 1.3 62.7 + - - +
112D PHE* 3.2 7.1 + - + +
113D LYS* 2.9 49.3 + - + +
194D TRP* 6.3 0.9 - - + -
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Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D SER* 3.2 9.2 + - - +
109D VAL* 1.3 78.0 - - - +
111D ASN* 1.3 66.4 + - - +
113D LYS* 3.4 14.4 + - - +
114D ALA* 3.0 23.7 + - - +
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Residues in contact with ASN 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PHE* 3.1 22.5 + - + +
107D GLY* 3.6 5.1 - - - -
108D SER* 2.6 35.6 + - - +
110D ASP* 1.3 78.6 - - - +
112D PHE* 1.3 61.5 + - - +
114D ALA* 3.3 7.0 + - - +
115D GLU* 3.0 30.2 + - + +
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Residues in contact with PHE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D LEU* 6.0 0.4 - - + -
102D ILE* 3.5 34.1 - - + -
106D PHE* 3.7 34.2 - + + +
108D SER 3.1 7.3 + - - +
109D VAL* 3.4 12.6 - - + +
111D ASN* 1.3 76.7 - - - +
113D LYS* 1.3 64.4 + - + +
115D GLU* 3.0 3.7 + - - +
116D PHE* 2.9 43.6 + + + +
131D LEU* 3.8 40.6 - - + -
140D VAL* 3.9 14.6 - - + -
164D MET* 4.7 5.2 - - + -
189D TRP* 3.9 24.2 - + - -
194D TRP* 4.1 14.6 - + - -
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D VAL* 2.9 36.4 + - + +
110D ASP* 3.7 14.1 + - - +
112D PHE* 1.3 79.4 - - + +
114D ALA* 1.3 56.6 + - - +
116D PHE* 3.3 1.2 + - - +
117D GLU* 2.9 43.8 + - - +
189D TRP* 3.8 64.2 - - + +
194D TRP* 5.5 5.8 - - - -
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Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ASP 3.0 17.2 + - - +
111D ASN* 3.5 8.7 - - - +
113D LYS* 1.3 77.1 - - - +
115D GLU* 1.3 62.7 + - + +
117D GLU* 3.5 7.2 + - - +
118D LYS* 3.0 35.9 + - + +
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Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PHE* 4.6 14.5 - - + -
111D ASN* 3.0 18.6 + - + +
112D PHE* 3.0 9.4 + - - +
114D ALA* 1.3 73.7 - - + +
116D PHE* 1.3 66.9 + - - +
118D LYS* 3.4 30.5 + - - +
119D ALA* 3.1 23.0 + - - +
140D VAL* 3.9 18.2 - - + +
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Residues in contact with PHE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D PHE* 2.9 32.3 + + + +
113D LYS 3.7 3.6 - - - +
115D GLU* 1.3 77.4 - - - +
117D GLU* 1.3 60.8 + - + +
119D ALA* 3.2 3.1 + - - +
120D ALA* 2.9 29.3 + - + +
129D ALA* 3.8 24.2 - - + -
130D TRP 3.8 32.1 - - - -
140D VAL* 3.9 12.5 - - + +
164D MET* 3.9 21.5 - - - -
166D LEU* 3.8 27.8 - - + -
185D ILE* 5.3 1.1 - - + -
188D PHE* 3.7 19.7 - + - -
189D TRP* 3.7 26.2 - + + -
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Residues in contact with GLU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LYS* 2.9 29.0 + - - +
114D ALA* 3.9 6.5 - - - +
116D PHE* 1.3 75.2 - - - +
118D LYS* 1.3 58.5 + - + +
120D ALA* 3.8 0.7 - - - +
121D ALA* 2.8 34.0 + - - +
185D ILE* 3.6 30.3 - - + +
186D LYS* 4.0 28.2 + - - +
189D TRP* 2.9 32.8 + - + +
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Residues in contact with LYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ALA* 3.0 26.7 + - + +
115D GLU* 3.6 31.0 - - - +
116D PHE 3.2 0.2 - - - -
117D GLU* 1.3 78.1 - - + +
119D ALA* 1.3 50.9 + - - +
121D ALA* 3.9 3.2 - - - +
122D SER* 2.7 40.5 + - - -
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Residues in contact with ALA 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D GLU 3.1 7.6 + - - +
116D PHE 3.6 2.9 - - - +
118D LYS* 1.3 78.0 - - - +
120D ALA* 1.3 61.6 + - - +
122D SER* 3.2 15.8 + - - -
123D ARG* 3.4 13.9 + - - +
129D ALA* 4.5 4.7 - - + -
140D VAL* 3.5 31.9 - - + -
141D VAL* 4.8 4.3 - - - +
142D SER* 4.2 20.4 + - - -
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D PHE* 2.9 18.4 + - + +
117D GLU* 3.8 3.1 - - - +
119D ALA* 1.3 78.7 - - - +
121D ALA* 1.3 58.6 + - - +
123D ARG* 3.7 4.7 + - - +
129D ALA* 3.8 22.1 - - + +
166D LEU* 4.2 17.0 - - + -
168D VAL* 3.8 12.6 - - + +
181D ARG* 3.0 22.0 + - - -
185D ILE* 3.6 21.1 - - + -
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Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D GLU 2.8 18.8 + - - +
118D LYS* 4.2 2.9 - - - +
120D ALA* 1.3 78.2 - - - +
122D SER* 1.3 61.7 + - - +
123D ARG 3.5 1.2 + - - +
181D ARG* 3.7 15.9 + - - +
182D PRO* 5.4 10.3 - - + -
185D ILE* 4.0 13.9 - - + -
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Residues in contact with SER 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LYS 2.7 23.1 + - - -
119D ALA* 3.2 13.7 + - - -
121D ALA* 1.3 75.3 - - - +
123D ARG* 1.3 64.7 + - - +
124D PHE* 3.0 8.9 + - - +
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Residues in contact with ARG 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ALA 3.4 15.2 + - - +
120D ALA* 3.9 9.4 - - - +
121D ALA 3.3 2.6 - - - +
122D SER* 1.3 73.7 - - - +
124D PHE* 1.3 72.6 + - - +
125D GLY 4.2 2.5 - - - +
126D SER 4.0 9.9 - - - -
127D GLY* 3.8 11.7 - - - +
128D TRP 4.5 1.6 - - - +
142D SER* 2.9 42.5 + - - +
143D THR* 3.5 15.4 + - - +
144D ALA* 3.6 22.6 - - - +
168D VAL* 3.8 21.8 - - + -
181D ARG* 2.7 32.8 + - - +
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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