Contacts of the helix formed by residues 107 - 127 (chain F) in PDB entry 2EHO
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F PHE* 3.5 39.8 - - + +
26F GLU* 6.0 1.6 - - - +
106F MSE 1.3 77.8 - - - +
108F ALA* 1.3 67.8 + - - +
109F GLU* 4.3 11.7 - - + +
110F GLU* 2.7 37.3 + - + +
111F MSE 3.1 11.4 + - - +
1014F SO4 5.3 1.3 - - - +
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Residues in contact with ALA 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ALA* 6.2 4.5 - - + -
106F MSE 3.8 0.6 + - - -
107F ALA* 1.3 72.3 - - - +
109F GLU* 1.3 75.0 + - - +
111F MSE 3.1 11.3 + - - +
112F GLU* 3.1 20.8 + - - +
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Residues in contact with GLU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E TYR* 3.5 21.7 - - + -
143E ASN* 4.6 14.3 - - + +
144E VAL* 3.2 31.4 - - + +
107F ALA* 4.5 6.4 - - + +
108F ALA* 1.3 90.4 + - - +
110F GLU* 1.3 58.2 + - - +
112F GLU* 3.3 17.9 - - + +
113F TRP* 2.9 21.8 + - - +
1014F SO4 2.7 33.1 + - - +
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Residues in contact with GLU 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E TYR* 3.0 33.8 + - + +
24F PHE* 3.8 5.8 - - - -
83F ARG* 2.6 57.1 + - - +
84F LEU* 4.5 4.3 + - + +
87F ILE* 3.6 21.0 - - + +
106F MSE 3.6 8.2 - - + +
107F ALA* 2.7 34.7 + - + +
109F GLU* 1.3 75.2 - - - +
111F MSE 1.3 67.3 + - - +
113F TRP* 3.0 8.6 + - - +
114F PHE* 2.8 23.9 + - - +
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Residues in contact with MSE 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D TYR* 5.4 4.9 - - + +
162D SER* 4.4 17.0 - - - +
98F LEU* 4.4 10.3 - - + -
103F ARG* 4.4 27.1 - - + +
106F MSE 3.7 21.4 - - + +
107F ALA 3.1 8.0 + - - +
108F ALA* 3.1 12.0 + - - +
110F GLU* 1.3 77.9 - - - +
112F GLU* 1.3 63.2 + - - +
114F PHE* 3.2 25.5 + - + -
115F ASN* 3.1 58.0 + - - +
118F LYS* 5.1 1.6 - - - +
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Residues in contact with GLU 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F ALA 3.1 10.7 + - - +
109F GLU* 3.3 21.1 + - - +
110F GLU 3.1 0.2 - - - -
111F MSE 1.3 78.2 - - - +
113F TRP* 1.3 62.0 + - - +
115F ASN* 3.3 9.9 + - - +
116F ASN* 3.1 39.4 + - - +
119F ARG* 5.1 1.1 + - - +
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Residues in contact with TRP 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E PHE* 3.9 26.7 - + - -
136E ASN* 2.8 65.2 + - - +
137E THR* 2.8 42.4 - - + +
140E TYR* 3.7 17.3 - - + -
84F LEU* 3.8 34.7 - - + +
87F ILE* 4.6 5.8 - - + -
88F ARG* 4.0 31.9 - - + -
109F GLU 2.9 13.8 + - - +
110F GLU* 3.0 12.8 + - - +
112F GLU* 1.3 75.8 - - - +
114F PHE* 1.3 66.3 + + + +
116F ASN* 3.4 1.7 + - - +
117F TYR* 3.0 29.0 + + + -
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Residues in contact with PHE 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F ILE* 3.8 29.8 - - + -
88F ARG* 5.2 1.1 - - - -
90F LEU* 4.7 0.4 - - + -
91F ARG* 3.8 46.4 - - + -
95F GLY 4.6 1.1 - - - -
96F SER 4.3 1.8 - - - -
98F LEU* 3.2 42.6 - - + -
106F MSE 4.3 2.5 - - + -
110F GLU 2.8 11.1 + - - +
111F MSE 3.2 31.9 - - + +
113F TRP* 1.3 81.6 - + - +
115F ASN* 1.3 54.3 + - - +
117F TYR* 2.9 11.0 + + + +
118F LYS* 2.7 58.6 + - - +
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Residues in contact with ASN 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D TYR* 4.7 10.9 + - - -
159D GLU* 5.9 4.2 + - - -
111F MSE 3.1 46.4 + - - +
112F GLU* 3.7 10.3 - - + +
114F PHE* 1.3 73.3 - - - +
116F ASN* 1.3 65.6 + - - +
118F LYS* 2.9 28.1 + - + +
119F ARG* 2.9 48.5 + - - +
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Residues in contact with ASN 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E ASN* 2.8 33.2 + - + +
112F GLU* 3.1 30.7 + - - +
113F TRP* 3.8 1.0 - - - +
115F ASN* 1.3 76.0 - - - +
117F TYR* 1.3 55.9 + - - +
119F ARG* 2.5 39.6 + - - +
120F SER* 2.9 34.2 + - - +
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Residues in contact with TYR 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E GLU* 2.7 42.7 + - - -
129E PHE* 4.1 12.7 - + - -
133E PHE* 3.5 27.6 - + - -
136E ASN* 3.9 5.1 - - - +
88F ARG* 3.3 10.8 + - + -
91F ARG* 4.0 31.9 - - + -
92F TRP* 3.1 21.7 + - - -
113F TRP* 3.0 28.9 + + + +
114F PHE* 2.9 18.3 + + - +
116F ASN* 1.3 75.3 - - - +
118F LYS* 1.3 65.5 + - - +
120F SER* 3.3 6.4 + - - -
121F LEU* 2.9 35.6 + - + +
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Residues in contact with LYS 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ARG* 3.9 27.3 + - - +
96F SER* 2.6 38.2 + - - +
97F ILE* 4.8 6.7 - - - +
111F MSE 5.1 1.2 - - - +
114F PHE* 2.7 35.9 + - + +
115F ASN* 2.9 47.5 + - + +
117F TYR* 1.3 75.1 - - - +
119F ARG* 1.3 68.1 + - + +
121F LEU* 3.2 4.2 + - - +
122F ALA* 3.0 23.2 + - - +
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Residues in contact with ARG 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F GLU* 6.1 0.8 - - - +
115F ASN* 2.9 37.5 + - - +
116F ASN* 2.5 35.8 + - - +
118F LYS* 1.3 83.3 - - + +
120F SER* 1.3 63.3 + - - +
122F ALA* 3.1 8.6 + - - +
123F THR* 3.0 26.2 + - - -
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Residues in contact with SER 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E PHE* 4.0 16.1 - - - -
132E GLU* 2.8 47.9 + - - +
133E PHE* 5.7 1.3 - - - -
116F ASN* 2.9 20.6 + - - +
117F TYR* 3.7 7.2 - - - -
119F ARG* 1.3 76.2 - - - +
121F LEU* 1.3 62.3 + - - +
123F THR* 3.6 5.6 + - - +
124F TYR* 3.1 22.9 + - - +
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Residues in contact with LEU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E LEU* 3.5 31.4 - - + -
129E PHE* 4.0 17.2 - - + -
91F ARG* 3.9 39.0 - - + +
92F TRP* 3.8 26.7 - - + -
117F TYR* 2.9 23.3 + - + +
118F LYS 3.5 5.2 - - - +
120F SER* 1.3 74.4 - - - +
122F ALA* 1.3 66.0 + - - +
124F TYR* 3.0 5.7 + - + +
125F MSE 2.9 40.6 + - + +
137F THR* 4.4 5.4 - - + -
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Residues in contact with ALA 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ARG* 5.7 1.8 - - - +
118F LYS 3.0 12.9 + - - +
119F ARG* 3.4 9.6 - - - +
121F LEU* 1.3 75.3 - - - +
123F THR* 1.3 65.1 + - - +
125F MSE 2.9 18.1 + - + +
126F ARG* 2.8 52.6 + - - +
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Residues in contact with THR 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E ALA* 6.1 3.4 - - + -
132E GLU* 4.4 13.1 + - - +
119F ARG 3.0 14.5 + - - -
120F SER* 3.7 10.7 - - - +
122F ALA* 1.3 76.2 - - - +
124F TYR* 1.3 66.0 + - - +
126F ARG* 3.4 12.5 + - - +
127F SER* 3.3 22.7 + - - +
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Residues in contact with TYR 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E LEU* 4.2 14.3 + - + +
97E LEU* 4.1 28.2 - - + +
123E SER* 4.8 1.6 + - - -
125E GLU* 3.4 39.0 - - + +
126E GLU* 3.5 41.8 + - + +
129E PHE* 4.2 16.6 - + + -
120F SER 3.1 10.7 + - - +
121F LEU* 3.0 10.0 + - - +
123F THR* 1.3 82.3 - - - +
125F MSE 1.3 73.4 + - + +
127F SER* 3.2 17.4 + - - -
128F LEU* 3.5 36.7 - - + +
136F ILE* 4.4 7.2 - - + -
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Residues in contact with MSE 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ARG* 4.3 16.4 - - - +
121F LEU* 3.1 26.0 - - + +
122F ALA* 2.9 24.1 + - + +
124F TYR* 1.3 75.3 - - + +
126F ARG* 1.3 62.2 + - + +
127F SER 2.9 10.8 + - - -
128F LEU* 3.0 18.2 + - - +
132F GLU 5.2 0.2 - - - -
134F LEU 3.1 33.7 + - - +
135F ASP* 3.4 32.5 - - + +
136F ILE* 3.5 30.1 - - + -
137F THR* 4.0 9.0 - - + -
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Residues in contact with ARG 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F ALA* 2.8 41.5 + - - +
123F THR* 3.8 9.5 + - - +
125F MSE 1.3 72.4 - - + +
127F SER* 1.3 57.6 + - - +
128F LEU 3.4 0.4 - - - -
131F ASP 3.6 13.3 + - - +
132F GLU* 4.1 20.6 + - - +
133F GLY 3.5 17.3 + - - +
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Residues in contact with SER 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E GLU* 3.9 34.9 + - - +
123F THR* 3.3 13.6 + - - +
124F TYR* 3.2 14.5 + - - -
125F MSE 2.9 2.0 + - - -
126F ARG* 1.3 79.2 - - - +
128F LEU* 1.3 58.6 + - - +
129F GLY 3.4 4.1 + - - -
130F GLY 5.3 1.7 + - - +
131F ASP 6.3 0.2 - - - +
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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