Contacts of the helix formed by residues 114 - 130 (chain D) in PDB entry 3E2A
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 GLY 114 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C SER* 3.4 19.7 - - - -
112D ASP* 3.4 5.5 + - - +
113D LEU* 1.3 76.4 - - - +
115D LEU* 1.3 66.6 + - - +
116D ILE 3.2 2.9 - - - -
117D ASN* 3.0 20.7 + - - +
82F GLN* 3.7 4.3 - - - -
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PHE* 5.3 1.8 - - + -
78C LEU* 4.3 1.8 - - + -
162C SER* 4.2 2.7 + - - +
163C ILE* 6.3 0.4 - - + -
114D GLY* 1.3 72.1 - - - -
116D ILE* 1.3 61.8 + - - +
118D ASN* 3.0 33.0 + - - +
119D TRP 3.8 1.9 + - - -
115E LEU* 3.7 39.5 - - + -
75F PHE* 3.8 29.6 - - + -
78F LEU* 4.2 17.9 - - + +
79F SER* 4.2 24.2 - - - +
82F GLN* 3.5 18.7 - - + +
163F ILE* 4.4 11.4 - - + -
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Residues in contact with ILE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D VAL* 4.3 15.0 - - + -
113D LEU* 3.6 32.5 - - + +
115D LEU* 1.3 75.0 - - - +
117D ASN* 1.3 66.6 + - - +
119D TRP* 3.0 23.8 + - + +
120D LEU* 3.0 30.7 + - + +
79F SER* 3.8 33.8 + - - +
82F GLN* 2.9 22.0 + - - +
83F TYR* 3.8 34.3 - - + -
87F VAL* 4.5 0.4 - - + -
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Residues in contact with ASN 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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160C ARG 6.0 1.6 - - - +
162C SER* 4.7 4.3 - - - +
165C LYS* 4.7 2.0 - - - +
106D ALA 4.9 2.8 - - - +
111D LYS 3.4 6.6 + - - +
112D ASP* 2.7 51.3 + - - +
113D LEU* 3.6 31.4 + - - +
114D GLY 3.0 12.8 + - - +
116D ILE* 1.3 80.7 - - - +
118D ASN* 1.3 58.2 + - - +
120D LEU* 3.1 12.4 + - - +
121D LEU* 2.9 33.1 + - + +
124D ARG* 5.9 0.5 - - - -
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Residues in contact with ASN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C HIS* 3.5 37.3 - - - +
73C THR* 3.6 4.0 - - - +
78C LEU* 4.0 16.8 - - - +
161C THR* 3.3 18.0 - - - +
162C SER* 2.6 49.4 + - - -
115D LEU* 3.0 26.3 + - - +
117D ASN* 1.3 76.3 - - - +
119D TRP* 1.3 63.0 + - - +
121D LEU* 3.3 18.7 + - + +
75F PHE* 3.7 8.7 - - + -
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Residues in contact with TRP 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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73C THR* 3.7 24.1 - - + +
65D ASN* 3.9 26.0 - - + -
66D VAL* 2.9 38.0 + - + +
69D GLN* 3.2 33.3 + - + +
71D ILE* 3.6 27.6 - - + -
74D ASP* 3.7 15.5 - - + -
115D LEU 3.8 1.0 + - - -
116D ILE* 3.0 18.0 + - + +
118D ASN* 1.3 79.2 - - - +
120D LEU* 1.3 74.2 + - + +
121D LEU 3.4 0.7 + - - -
122D HIS* 3.6 15.1 + - - -
75F PHE* 4.1 10.9 - + + -
76F ASN* 3.5 48.9 - - + -
79F SER* 3.7 18.2 - - - +
80F VAL* 6.6 0.2 - - + -
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Residues in contact with LEU 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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66D VAL* 4.1 15.7 - - + -
67D ALA* 5.0 1.6 - - + -
69D GLN* 4.9 0.4 - - - +
103D GLY* 4.0 14.4 - - - +
106D ALA* 3.7 20.2 - - + +
107D ALA* 3.6 34.3 - - + +
113D LEU* 4.7 2.5 - - + -
116D ILE* 3.0 25.9 + - + +
117D ASN* 3.1 20.1 + - - +
119D TRP* 1.3 90.6 - - + +
121D LEU* 1.3 64.8 + - - +
122D HIS 3.1 3.1 - - - -
123D ILE* 3.0 25.7 + - + +
124D ARG* 3.2 16.4 + - + +
83F TYR* 5.7 0.2 - - + -
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C HIS* 3.5 34.3 - - + +
157C ASN 4.9 1.1 - - - +
160C ARG* 3.6 45.5 + - + +
161C THR* 4.4 2.2 - - + +
165C LYS* 6.1 0.4 - - - -
231C SO4 3.6 32.5 - - - +
117D ASN* 2.9 18.0 + - + +
118D ASN* 3.6 25.8 - - + +
119D TRP 3.3 1.2 - - - -
120D LEU* 1.3 76.7 - - - +
122D HIS* 1.3 55.9 + - - +
124D ARG* 3.3 11.6 + - - +
125D ASP* 2.9 31.9 + - - +
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Residues in contact with HIS 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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72C HIS* 3.4 32.7 - + + +
73C THR* 3.2 26.4 + - + -
122C HIS* 4.0 21.9 + + - -
69D GLN* 3.3 21.5 - - - +
71D ILE* 3.3 39.4 - - + +
72D HIS* 6.1 0.8 - - - -
119D TRP 3.6 11.4 - - - +
120D LEU 3.1 0.6 - - - -
121D LEU* 1.3 78.2 - - - +
123D ILE* 1.3 55.0 - - - +
125D ASP* 3.4 11.7 + - - +
126D ILE* 3.2 30.4 + - + +
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ALA* 4.2 14.1 - - + -
69D GLN* 3.8 30.5 - - + +
104D ILE* 4.3 9.0 - - + -
107D ALA* 3.7 24.2 - - + -
120D LEU* 3.0 14.8 + - + +
122D HIS* 1.3 73.4 - - - +
124D ARG* 1.3 57.1 + - - +
126D ILE* 3.1 7.0 + - + +
127D TRP* 2.8 31.4 + - - +
146D LEU* 3.8 27.5 - - + +
150D ASN* 3.0 36.8 - - + +
154D GLN* 4.6 0.4 - - - +
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Residues in contact with ARG 124 (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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160C ARG* 4.3 2.7 - - - +
231C SO4 2.7 52.2 + - - +
107D ALA* 3.0 36.6 + - + +
108D MET 4.0 1.2 + - - -
109D ALA 3.1 19.6 + - - -
110D ASP* 3.7 18.9 + - - +
117D ASN 5.9 0.4 - - - -
120D LEU* 3.2 13.1 + - - +
121D LEU* 3.3 18.4 + - - +
123D ILE* 1.3 75.8 - - - +
125D ASP* 1.3 59.5 + - - +
127D TRP* 3.2 38.9 + - + +
128D PHE* 2.9 28.4 + - - +
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Residues in contact with ASP 125 (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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72C HIS* 2.7 28.4 + - - -
157C ASN* 5.2 0.2 - - - +
160C ARG* 2.9 32.9 + - - +
121D LEU 2.9 13.4 + - - -
122D HIS* 3.4 12.8 + - - +
123D ILE 3.2 0.2 - - - -
124D ARG* 1.3 72.6 - - - +
126D ILE* 1.3 62.0 + - + +
128D PHE* 3.3 8.7 + - - +
129D LYS* 2.9 27.5 + - - +
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Residues in contact with ILE 126 (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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69D GLN* 5.3 0.2 - - - +
122D HIS* 3.2 15.9 + - + +
123D ILE* 3.1 12.6 + - - +
125D ASP* 1.3 74.0 - - + +
127D TRP* 1.3 67.1 + - - +
129D LYS* 3.1 19.0 + - + +
130D HIS* 3.1 15.5 + - + +
146D LEU* 4.1 11.7 - - + -
149D ILE* 3.7 17.9 - - + -
150D ASN* 3.6 13.7 - - - +
153D GLU* 3.7 37.5 - - + +
154D GLN* 3.4 28.5 - - - +
157D ASN* 5.4 3.4 - - - +
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Residues in contact with TRP 127 (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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107D ALA 5.3 0.2 - - - -
108D MET* 3.9 45.5 - - + -
123D ILE 2.8 14.0 + - - +
124D ARG* 3.3 42.4 - - + +
126D ILE* 1.3 77.1 - - - +
128D PHE* 1.3 62.2 + - - +
130D HIS 3.2 2.9 - - - -
131D GLY* 3.1 20.6 + - - -
134D LEU* 3.6 30.8 - - + +
135D GLY* 6.0 0.2 - - - -
142D ARG* 3.6 39.3 - - - +
146D LEU* 4.2 12.7 - - + +
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Residues in contact with PHE 128 (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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129C LYS* 3.8 38.4 - - + -
205C TYR* 5.8 4.3 - + - -
124D ARG 2.9 13.9 + - - +
125D ASP* 3.6 10.3 - - - +
127D TRP* 1.3 74.5 - - - +
129D LYS* 1.3 68.7 + - - +
131D GLY* 2.9 17.5 + - - +
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Residues in contact with LYS 129 (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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125C ASP* 5.9 1.2 + - - -
128C PHE* 3.7 40.2 - - + -
125D ASP 2.9 14.6 + - - +
126D ILE* 3.3 14.4 - - + +
128D PHE* 1.3 80.7 - - - +
130D HIS* 1.3 67.3 + - + +
131D GLY 3.4 1.1 + - - -
153D GLU* 3.0 31.2 + - - +
156D TYR* 4.7 10.5 - - - -
160D ARG* 5.7 2.0 - - - +
205D TYR* 3.0 24.5 + - - -
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Residues in contact with HIS 130 (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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126D ILE* 3.1 19.5 + - + -
127D TRP 3.2 3.8 - - - -
128D PHE 3.1 0.4 - - - -
129D LYS* 1.3 87.3 + - + +
131D GLY* 1.3 63.2 + - - +
132D HIS 3.3 2.4 + - - -
133D LEU* 3.6 9.0 + - + +
134D LEU* 3.1 37.1 + - + +
149D ILE* 3.3 34.0 - - + +
153D GLU* 2.6 29.8 + - - -
205D TYR* 4.3 2.9 - - - -
209D ILE* 3.7 39.9 - - + +
213D SER* 5.2 3.0 + - - -
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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