Contacts of the helix formed by residues 107 - 128 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J PHE* 3.7 45.3 - - + +
106J MSE 1.3 77.2 - - - +
108J ALA* 1.3 66.0 + - - +
109J GLU* 3.9 15.0 - - + +
110J GLU* 2.9 28.1 + - + +
111J MSE 3.0 9.2 + - - +
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Residues in contact with ALA 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J MSE 3.7 1.6 + - - -
107J ALA* 1.3 72.7 - - - +
109J GLU* 1.3 71.1 + - - +
111J MSE 3.2 9.4 + - - +
112J GLU* 3.0 26.5 + - - +
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Residues in contact with GLU 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I TYR* 3.4 13.5 - - + +
143I ASN* 4.0 19.4 - - + +
144I VAL* 3.1 39.3 - - + -
107J ALA* 3.9 10.9 - - + +
108J ALA* 1.3 94.1 + - - +
110J GLU* 1.3 59.0 + - - +
112J GLU* 3.1 20.3 + - + +
113J TRP 3.1 19.2 + - - -
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Residues in contact with GLU 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I TYR* 3.3 32.6 + - + +
24J PHE* 3.2 11.6 - - - -
83J ARG* 2.8 56.0 + - - +
84J LEU* 4.8 1.2 - - + +
87J ILE* 3.6 25.0 - - + +
106J MSE 3.5 8.6 - - + -
107J ALA* 2.9 31.0 + - + +
109J GLU* 1.3 73.3 - - - +
111J MSE 1.3 66.7 + - - +
112J GLU 3.0 1.6 - - - -
113J TRP* 3.0 6.2 + - - +
114J PHE* 3.0 22.4 + - - +
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Residues in contact with MSE 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J LEU* 4.2 18.4 - - + -
103J ARG* 3.3 50.7 - - - +
106J MSE 4.4 16.0 - - + +
107J ALA 3.0 9.9 + - - +
108J ALA* 3.2 11.6 + - - +
110J GLU* 1.3 77.7 - - - +
112J GLU* 1.3 60.6 + - - +
114J PHE* 3.3 28.0 - - + -
115J ASN* 3.1 43.1 + - - +
118J LYS* 5.9 0.2 - - - +
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Residues in contact with GLU 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J ALA* 3.0 12.2 + - - +
109J GLU* 3.1 29.0 + - - +
111J MSE 1.3 76.1 - - - +
113J TRP* 1.3 66.0 + - - +
115J ASN* 3.3 7.9 + - - +
116J ASN* 3.2 32.2 + - - +
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Residues in contact with TRP 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I PHE* 3.6 36.3 - + - -
136I ASN* 2.9 40.9 + - - +
137I THR* 3.3 26.0 + - - +
140I TYR* 3.4 35.7 - + + -
84J LEU* 3.7 29.0 - - + +
87J ILE* 4.1 18.8 - - + -
88J ARG* 4.2 23.6 - - + -
109J GLU 3.1 9.0 + - - +
110J GLU* 3.0 11.3 + - - +
112J GLU* 1.3 79.5 - - - +
114J PHE* 1.3 62.9 + - - +
116J ASN 3.3 0.7 + - - -
117J TYR* 2.9 49.2 + + + -
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Residues in contact with PHE 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87J ILE* 3.7 30.5 - - + -
90J LEU* 4.2 0.2 - - + -
91J ARG* 3.8 38.4 - - + -
95J GLY 4.0 0.9 - - - -
96J SER 3.9 4.9 - - - -
98J LEU* 3.0 44.0 - - + -
106J MSE 5.3 0.9 - - - -
110J GLU 3.0 12.2 + - - +
111J MSE 3.3 33.4 - - + +
112J GLU 3.2 0.2 - - - -
113J TRP* 1.3 80.1 - - - +
115J ASN* 1.3 59.8 + - - +
117J TYR* 3.2 10.7 + + - +
118J LYS* 2.8 55.5 + - + +
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Residues in contact with ASN 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J ARG* 5.6 0.8 - - - +
111J MSE 3.1 45.2 + - - +
112J GLU* 3.3 7.7 + - - +
114J PHE* 1.3 73.4 - - - +
116J ASN* 1.3 68.1 + - - +
118J LYS* 3.4 24.2 + - - +
119J ARG* 2.9 32.5 + - + +
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Residues in contact with ASN 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I ASN* 3.2 37.5 - - - +
112J GLU* 3.2 18.4 + - - +
113J TRP 3.5 1.6 - - - +
115J ASN* 1.3 77.7 - - - +
117J TYR* 1.3 70.2 + - - +
119J ARG* 3.1 13.4 + - - +
120J SER* 3.1 21.2 + - - -
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Residues in contact with TYR 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I GLU* 2.5 36.0 + - - -
129I PHE* 3.7 17.2 - + - -
133I PHE* 4.2 13.5 - + - -
136I ASN* 3.5 4.9 + - - +
88J ARG* 3.7 18.1 - - + +
91J ARG* 3.7 34.1 - - + -
92J TRP* 3.1 26.2 + - - -
113J TRP* 2.9 43.4 + + + +
114J PHE* 3.3 14.1 - + - +
116J ASN* 1.3 74.0 - - - +
118J LYS* 1.3 66.2 + - - +
120J SER* 2.8 20.2 + - - -
121J LEU* 3.1 18.6 + - + +
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Residues in contact with LYS 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J ARG* 3.6 28.6 + - - +
96J SER* 2.6 41.7 + - - +
97J ILE* 4.0 9.9 - - - +
114J PHE* 2.8 43.2 + - + +
115J ASN* 3.5 22.2 + - - +
117J TYR* 1.3 74.6 - - + +
119J ARG* 1.3 63.3 + - + +
121J LEU* 3.4 7.2 + - - +
122J ALA* 3.0 26.2 + - - +
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Residues in contact with ARG 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I GLU* 5.2 1.3 - - - +
115J ASN* 2.9 24.9 + - - +
116J ASN* 3.1 12.5 + - - +
117J TYR 3.0 0.2 + - - -
118J LYS* 1.3 76.6 - - + +
120J SER* 1.3 58.6 + - - +
122J ALA* 3.5 6.7 - - - +
123J THR* 2.9 34.2 + - - +
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Residues in contact with SER 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I PHE* 3.8 21.4 - - - +
132I GLU* 2.7 48.0 + - - +
133I PHE* 5.6 1.1 - - - -
116J ASN 3.1 9.6 + - - -
117J TYR* 2.8 17.2 + - - -
119J ARG* 1.3 71.8 - - - +
121J LEU* 1.3 51.8 + - - -
123J THR* 3.2 5.8 + - - -
124J TYR* 2.8 34.5 + - - +
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Residues in contact with LEU 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I LEU* 3.9 28.3 - - + -
129I PHE* 3.7 14.7 - - + -
91J ARG* 3.7 35.9 - - + +
92J TRP* 3.6 32.3 - - + -
117J TYR* 3.1 18.5 + - + +
118J LYS* 3.7 8.5 - - - +
120J SER* 1.3 76.1 - - - +
122J ALA* 1.3 57.7 + - - +
124J TYR* 3.1 3.5 + - + +
125J MSE 2.8 61.7 + - + +
136J ILE* 4.2 0.2 - - + -
137J THR* 4.5 1.1 - - + -
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Residues in contact with ALA 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J ARG* 6.3 0.4 - - - +
118J LYS 3.0 18.2 + - - +
119J ARG* 3.5 7.2 - - - +
121J LEU* 1.3 74.7 - - - +
123J THR* 1.3 67.4 + - - +
125J MSE 3.5 17.0 + - + +
126J ARG* 3.2 47.1 + - - +
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Residues in contact with THR 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I ALA* 6.2 3.1 - - + -
132I GLU* 4.8 14.2 + - - +
119J ARG* 2.9 18.7 + - - +
120J SER* 3.4 10.6 - - - -
122J ALA* 1.3 74.9 - - - +
124J TYR* 1.3 69.4 + - - +
126J ARG* 3.1 21.4 + - - +
127J SER* 3.1 21.4 + - - +
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Residues in contact with TYR 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I LEU* 3.7 25.8 - - + +
97I LEU* 3.8 33.6 - - + +
123I SER* 4.7 1.2 + - - -
125I GLU* 3.5 43.3 - - + -
126I GLU* 3.8 29.0 + - + +
129I PHE* 4.1 17.0 - + + -
120J SER 2.8 16.7 + - - +
121J LEU 3.3 8.1 - - - +
123J THR* 1.3 72.6 - - - +
125J MSE 1.3 64.4 + - + +
127J SER* 2.7 34.6 + - - -
128J LEU* 3.4 38.3 + - + +
136J ILE* 5.2 2.7 - - + -
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Residues in contact with MSE 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J ARG* 3.9 20.2 - - - +
118J LYS 5.6 0.2 - - - +
121J LEU* 2.8 46.4 + - + +
122J ALA* 3.8 17.7 - - + +
124J TYR* 1.3 73.9 - - + +
126J ARG* 1.3 58.4 + - + +
127J SER 3.3 0.2 - - - -
128J LEU* 3.5 13.0 - - - +
132J GLU* 4.0 2.9 - - - +
133J GLY* 3.2 3.1 - - - -
134J LEU 3.0 37.6 + - - +
135J ASP* 3.3 25.8 - - - +
136J ILE* 3.3 38.8 - - + -
137J THR* 3.6 6.3 - - + -
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Residues in contact with ARG 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J ALA* 3.2 34.1 + - - +
123J THR* 3.1 13.8 + - - +
124J TYR 2.9 1.2 + - - -
125J MSE 1.3 76.1 - - + +
127J SER* 1.3 64.4 + - - +
128J LEU 3.2 1.1 + - - -
129J GLY 3.4 14.6 - - - +
131J ASP 4.0 5.8 - - - +
132J GLU* 3.4 25.7 + - + +
133J GLY* 3.8 5.6 - - - -
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Residues in contact with SER 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I GLU* 3.8 39.2 - - - +
123J THR* 3.1 20.3 + - - +
124J TYR* 2.7 10.7 + - - -
126J ARG* 1.3 74.3 - - - +
128J LEU* 1.3 64.8 + - - +
129J GLY* 3.0 9.4 + - - +
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Residues in contact with LEU 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I VAL* 5.0 10.1 - - + +
52I GLU* 4.7 15.4 - - - +
55I MSE 3.8 16.9 - - - +
93I LEU* 4.1 17.7 - - + -
125I GLU* 5.5 4.0 - - + -
124J TYR* 3.5 41.5 - - + +
125J MSE 3.5 17.0 - - - +
126J ARG 3.2 0.4 - - - -
127J SER* 1.3 78.5 - - - +
129J GLY* 1.3 57.7 + - - +
134J LEU* 3.1 46.7 - - + +
136J ILE* 3.6 16.6 - - + -
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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