Contacts of the helix formed by residues 107 - 126 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A TYR* 4.8 0.7 - - - +
144A VAL* 5.2 0.7 - - + -
24B PHE* 3.5 38.7 - - + +
26B GLU* 5.7 2.5 - - + +
106B MSE 1.3 76.0 - - - +
108B ALA* 1.3 55.7 + - - +
109B GLU* 2.9 17.3 - - + +
110B GLU* 2.6 41.6 + - + +
111B MSE 3.1 11.0 + - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B MSE 4.0 1.0 + - - -
107B ALA* 1.3 71.1 - - - +
109B GLU* 1.3 73.5 + - - +
111B MSE 3.9 15.9 + - - +
112B GLU* 3.4 22.9 + - - +
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TYR* 3.3 28.9 - - + +
143A ASN* 4.9 10.4 - - + +
144A VAL* 3.8 35.3 - - + +
26B GLU* 5.7 0.7 - - - +
107B ALA* 2.9 6.2 - - + +
108B ALA* 1.3 93.0 + - - +
110B GLU* 1.3 58.0 + - - +
112B GLU* 3.3 18.0 - - - +
113B TRP 3.0 20.4 + - - -
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 2.9 34.6 + - + +
24B PHE* 4.0 5.0 - - - +
80B LEU* 4.9 1.2 - - - +
83B ARG* 2.7 53.2 + - - +
84B LEU* 4.7 1.7 - - + +
87B ILE* 3.5 24.2 - - + +
106B MSE 3.3 10.4 - - + +
107B ALA* 2.6 40.0 + - + +
109B GLU* 1.3 68.5 - - - +
111B MSE 1.3 65.7 + - - +
112B GLU 3.0 1.8 - - - -
113B TRP* 3.1 7.4 + - - +
114B PHE* 2.9 24.1 + - - +
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Residues in contact with MSE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ARG* 3.1 65.1 - - + +
106B MSE 4.1 33.0 - - + +
107B ALA 3.1 7.4 + - - +
108B ALA* 4.2 18.6 - - - +
110B GLU* 1.3 76.9 - - - +
112B GLU* 1.3 56.5 + - - +
114B PHE* 3.5 3.2 - - - +
115B ASN* 2.9 44.8 + - - +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN* 5.7 5.8 + - - -
108B ALA 3.4 14.5 + - - +
109B GLU* 3.3 24.0 - - - +
110B GLU 3.0 0.2 - - - -
111B MSE 1.3 78.5 - - - +
113B TRP* 1.3 66.1 + - - +
115B ASN* 4.0 5.4 - - - +
116B ASN* 3.0 41.5 + - - +
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Residues in contact with TRP 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 3.9 25.6 - + - -
136A ASN* 2.6 67.9 + - - +
137A THR* 3.1 25.5 + - - +
140A TYR* 3.8 18.4 - - + -
84B LEU* 3.7 39.9 - - + +
87B ILE* 4.5 3.8 - - + -
88B ARG* 4.0 30.7 - - + -
109B GLU 3.0 14.2 + - - +
110B GLU 3.1 8.3 + - - +
112B GLU* 1.3 75.8 - - - +
114B PHE* 1.3 72.1 + + + +
116B ASN* 3.4 0.6 + - - +
117B TYR* 2.9 38.7 + + + +
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.4 44.6 - - + -
88B ARG* 4.5 1.3 - - - -
91B ARG* 3.8 37.7 - - + -
95B GLY 4.8 1.3 - - - -
96B SER 4.3 0.4 - - - -
98B LEU* 3.0 51.6 - - + -
103B ARG* 6.1 0.9 - - - -
106B MSE 4.2 3.4 - - + -
110B GLU 2.9 16.2 + - - +
111B MSE 3.5 9.2 - - - +
112B GLU 3.2 0.2 - - - -
113B TRP* 1.3 86.1 - + - +
115B ASN* 1.3 60.8 + - - +
117B TYR* 2.9 7.7 + + - +
118B LYS* 2.7 50.7 + - + +
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Residues in contact with ASN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ARG* 4.6 16.1 + - - +
111B MSE 2.9 33.6 + - - +
112B GLU* 4.1 5.4 - - - +
114B PHE* 1.3 80.9 - - - +
116B ASN* 1.3 59.9 - - - +
118B LYS* 3.1 32.6 + - + +
119B ARG* 2.9 35.0 + - - +
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Residues in contact with ASN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLU* 5.3 0.2 - - - +
136A ASN* 2.9 32.5 + - + +
112B GLU* 3.0 37.0 + - - +
113B TRP* 4.4 0.2 - - - +
114B PHE 3.1 0.6 - - - -
115B ASN* 1.3 77.3 - - - +
117B TYR* 1.3 64.3 + - - +
119B ARG* 3.6 12.4 + - - +
120B SER* 3.2 22.5 + - - -
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLU* 2.6 32.9 + - - -
129A PHE* 4.1 11.7 - + - -
133A PHE* 3.8 28.7 - + - -
136A ASN* 3.9 6.5 - - - +
88B ARG* 3.6 13.3 + - + -
91B ARG* 4.0 31.2 - - + -
92B TRP* 3.1 24.8 + - - -
113B TRP* 2.9 34.6 + + + +
114B PHE* 2.9 14.3 + + - +
116B ASN* 1.3 75.5 - - - +
118B LYS* 1.3 71.0 + - - +
120B SER* 3.0 22.0 + - - -
121B LEU* 3.0 18.9 + - + +
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 4.1 22.4 + - - +
96B SER* 2.4 45.2 + - - +
97B ILE* 4.5 2.2 - - - +
98B LEU* 3.8 6.5 - - - +
103B ARG* 5.2 3.0 - - - +
114B PHE* 2.7 27.0 + - + +
115B ASN* 3.1 38.2 + - + +
117B TYR* 1.3 78.3 - - + +
119B ARG* 1.3 70.6 + - + +
120B SER 2.8 0.7 + - - -
121B LEU* 3.0 6.6 + - - +
122B ALA* 2.8 36.0 + - - +
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 5.1 1.1 - - - +
115B ASN* 2.9 21.7 + - - +
116B ASN* 3.6 15.7 - - - +
118B LYS* 1.3 85.2 - - + +
120B SER* 1.3 58.4 + - - +
122B ALA* 3.7 8.2 - - - +
123B THR* 3.5 19.9 + - - -
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A PHE* 3.2 18.9 - - - -
132A GLU* 3.2 45.4 - - - +
133A PHE* 5.4 1.9 + - - -
116B ASN 3.2 11.2 + - - -
117B TYR* 3.0 14.4 + - - -
118B LYS 2.8 4.8 + - - -
119B ARG* 1.3 72.5 - - - +
121B LEU* 1.3 74.5 + - - +
122B ALA 2.9 1.6 - - - -
123B THR* 2.7 16.6 + - - +
124B TYR* 2.7 13.3 + - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.5 32.1 - - + -
129A PHE* 3.6 21.3 - - + -
91B ARG* 3.8 39.7 - - + +
92B TRP* 3.7 29.2 - - + -
117B TYR* 3.0 15.6 + - + +
118B LYS 3.0 6.5 + - - +
120B SER* 1.3 80.9 + - - +
122B ALA* 1.3 63.6 + - - +
124B TYR* 3.3 3.7 + - + +
125B MSE 3.1 45.3 + - + +
137B THR* 4.7 3.1 - - + -
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ARG* 6.2 1.3 - - - +
118B LYS 2.8 17.4 + - - +
119B ARG* 3.7 11.0 - - - +
121B LEU* 1.3 78.6 - - - +
123B THR* 1.3 62.9 + - - +
125B MSE 4.0 12.8 - - + +
126B ARG* 2.9 51.5 + - - +
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ALA* 6.3 3.1 - - + -
132A GLU* 4.8 10.2 + - - +
119B ARG 3.5 10.9 + - - -
120B SER* 2.7 16.8 + - - -
122B ALA* 1.3 74.4 - - - +
124B TYR* 1.3 70.7 + - - +
126B ARG* 3.0 19.5 + - - +
127B SER* 3.3 12.4 + - - -
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Residues in contact with TYR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 4.4 17.8 - - + +
97A LEU* 3.5 39.3 - - + +
123A SER* 5.1 0.2 - - - -
125A GLU* 3.3 42.0 - - + +
126A GLU* 3.3 38.0 + - + +
129A PHE* 4.1 17.5 - + + -
132A GLU* 5.7 0.2 + - - -
120B SER 2.7 14.4 + - - +
121B LEU* 3.5 8.5 - - + +
123B THR* 1.3 74.1 - - - +
125B MSE 1.3 76.2 + - + +
127B SER* 2.5 26.9 + - - -
128B LEU* 3.0 22.2 - - + +
136B ILE* 4.4 9.2 - - + -
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Residues in contact with MSE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 4.8 8.7 - - - +
121B LEU* 3.1 28.3 + - + +
122B ALA* 4.5 11.9 - - + +
124B TYR* 1.3 77.9 - - + +
126B ARG* 1.3 56.9 + - + +
127B SER 2.6 13.2 + - - -
128B LEU* 2.8 31.6 + - - +
134B LEU 3.4 20.5 + - - +
135B ASP* 3.6 23.3 - - + +
136B ILE* 3.5 35.7 - - + -
137B THR* 3.5 29.4 - - + -
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ALA* 2.9 41.5 + - - +
123B THR* 3.0 9.7 + - - +
125B MSE 1.3 77.8 - - + +
127B SER* 1.3 55.9 + - - +
128B LEU 3.5 0.9 - - - -
129B GLY 4.1 3.3 - - - +
132B GLU* 4.1 36.5 + - + +
133B GLY 3.4 21.3 + - - +
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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