Contacts of the helix formed by residues 119 - 135 (chain A) in PDB entry 2E34
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 ASP 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A MET* 4.0 1.3 - - - +
117A THR* 3.8 2.8 - - - +
118A THR* 1.3 91.1 + - + +
120A LEU* 1.3 65.7 + - - +
121A GLU* 2.9 18.8 + - + +
122A ALA* 3.0 21.1 + - + +
123A ALA 3.8 3.8 + - - -
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A TRP* 5.8 0.7 - - + -
105A LEU* 3.3 44.6 - - + +
109A LYS* 3.4 50.9 - - + +
112A MET* 4.2 15.9 - - + -
118A THR 3.6 2.6 + - - -
119A ASP* 1.3 74.9 + - - +
121A GLU* 1.3 50.3 + - - +
124A ALA* 2.5 44.9 + - - +
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TRP* 5.2 10.3 - - + -
119A ASP* 2.9 12.1 - - + -
120A LEU* 1.3 81.2 - - - +
122A ALA* 1.3 66.2 + - - +
124A ALA* 3.8 5.8 - - - -
125A ARG* 3.0 31.5 + - + +
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 3.2 23.6 - - + -
118A THR* 5.7 1.8 - - + -
119A ASP* 3.0 12.7 + - + +
121A GLU* 1.3 80.7 - - - +
123A ALA* 1.3 69.0 + - - +
124A ALA 2.8 0.9 + - - -
125A ARG* 3.0 10.9 + - - +
126A MET* 3.0 18.0 + - + +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ALA* 3.3 24.7 - - + +
111A LYS* 5.4 5.2 - - + +
112A MET* 2.9 41.5 - - + -
117A THR* 3.6 7.3 + - + +
119A ASP 3.8 1.0 + - - -
122A ALA* 1.3 78.6 - - - +
124A ALA* 1.3 65.5 + - - +
126A MET* 2.7 31.0 - - - +
127A ILE 2.9 5.2 + - - -
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TRP* 3.7 19.3 - - + -
104A VAL* 4.4 2.2 - - - -
105A LEU* 3.4 27.6 - - + -
108A ALA* 3.8 6.4 - - - +
120A LEU* 2.5 30.1 + - - +
121A GLU* 3.6 4.5 - - - +
122A ALA 2.8 0.6 + - - -
123A ALA* 1.3 73.8 - - - +
125A ARG* 1.3 67.8 + - - +
126A MET 2.6 1.6 + - - -
127A ILE 3.0 0.2 + - - -
128A ALA* 2.7 27.3 + - - +
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TRP* 4.8 4.8 - - + -
121A GLU* 3.0 24.8 + - + +
122A ALA* 3.0 7.4 + - - +
124A ALA* 1.3 76.0 - - - +
126A MET* 1.3 57.5 + - - +
128A ALA* 4.6 1.3 - - - -
129A GLY* 2.3 48.4 + - - +
130A SER 3.0 0.3 + - - -
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Residues in contact with MET 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS* 4.0 26.9 - - + +
117A THR* 5.1 9.2 - - - +
122A ALA* 3.0 17.8 + - + +
123A ALA* 2.7 25.1 + - - +
124A ALA 2.6 4.0 + - - -
125A ARG* 1.3 71.9 - - - +
127A ILE* 1.3 50.6 + - + +
130A SER* 2.2 49.3 + - - +
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ALA* 5.0 9.0 - - + -
76A TYR* 5.1 2.2 - - + +
78A ILE* 3.1 26.6 - - + +
99A ILE* 6.1 0.2 - - + -
104A VAL* 3.4 28.9 - - + +
107A ILE* 3.3 33.0 - - + +
108A ALA* 2.9 36.6 - - + +
111A LYS* 3.6 29.6 - - + -
123A ALA 2.9 4.4 + - - +
124A ALA 3.9 0.9 - - - +
126A MET* 1.3 76.7 - - + +
128A ALA* 1.3 60.7 + - - +
130A SER* 2.1 21.4 + - - +
131A ALA* 2.9 7.1 + - - +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ILE* 3.7 12.3 - - - -
101A TRP* 4.2 11.2 - - + -
104A VAL* 3.6 24.5 - - + -
124A ALA 2.7 17.0 + - - +
125A ARG* 4.6 0.7 - - - -
127A ILE* 1.3 72.4 - - - +
129A GLY* 1.3 60.2 + - - +
131A ALA* 2.4 34.2 + - - +
132A ARG* 3.0 3.5 + - - -
138A VAL* 4.1 21.5 - - + +
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ARG* 2.3 36.1 + - - +
128A ALA* 1.3 73.7 - - - +
130A SER* 1.3 61.7 + - - -
132A ARG* 2.8 28.6 + - - +
133A SER* 3.0 5.2 + - - -
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ALA* 3.8 16.2 - - - +
78A ILE* 3.5 7.0 - - - +
125A ARG 3.0 1.0 + - - -
126A MET* 2.2 40.5 + - - +
127A ILE* 2.1 37.3 + - - -
128A ALA 2.8 1.6 + - - -
129A GLY* 1.3 66.3 - - - -
131A ALA* 1.3 62.1 + - - -
133A SER* 2.7 28.0 + - - -
134A MET* 3.0 5.5 + - - +
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 4.2 11.0 - - + -
99A ILE* 3.5 18.6 - - + -
127A ILE 3.6 4.0 - - - +
128A ALA 2.4 21.5 + - - +
130A SER* 1.3 76.1 + - - +
132A ARG* 1.3 63.9 + - - +
134A MET* 2.8 11.9 + - - -
135A GLY 2.7 16.8 + - - -
136A VAL* 2.8 39.6 + - + -
137A GLU* 5.1 0.7 - - - -
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Residues in contact with ARG 132 (chain A).
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 3.0 5.0 + - - +
129A GLY* 2.8 22.1 + - - +
131A ALA* 1.3 75.0 - - - +
133A SER* 1.3 60.3 + - - +
135A GLY* 2.3 30.6 + - - +
136A VAL 3.1 13.8 + - - +
137A GLU* 5.2 3.1 - - + +
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Residues in contact with SER 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLY 3.0 6.5 + - - -
130A SER* 2.7 24.8 + - - -
132A ARG* 1.3 80.6 - - - +
134A MET* 1.3 52.3 + - - -
135A GLY* 2.3 15.2 + - - -
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Residues in contact with MET 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ALA* 5.2 1.3 - - + -
75A SER* 3.5 21.8 - - - +
78A ILE* 3.5 29.4 - - + -
79A ARG* 2.5 42.8 - - + +
82A ALA* 5.4 0.7 - - - -
130A SER 3.0 3.4 + - - +
131A ALA* 2.8 14.8 + - - +
133A SER* 1.3 74.2 - - - +
135A GLY* 1.3 55.0 + - - +
136A VAL* 2.9 30.8 + - + +
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Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ARG* 2.3 28.7 + - - +
133A SER 2.3 4.8 + - - -
134A MET* 1.3 66.7 - - - +
136A VAL* 1.3 69.3 + - - +
137A GLU* 3.3 15.4 - - - +
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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