Contacts of the helix formed by residues 130 - 139 (chain D) 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 GLU 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88D LEU* 2.8 34.4 - - + +
93D GLN* 5.4 1.6 - - - +
94D GLU* 3.7 14.8 - - - +
97D ARG* 3.0 25.5 + - - +
128D SER* 3.2 14.8 - - - +
129D PRO* 1.3 82.6 - - + +
131D ASN* 1.3 66.0 + - - +
132D ALA* 3.3 3.5 + - - -
133D ASP* 3.5 9.9 + - + +
134D ILE* 3.4 19.0 + - - +
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Residues in contact with ASN 131 (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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123D LEU 4.6 1.0 + - - -
124D LEU* 3.0 45.7 + - + +
127D ASP* 4.0 4.5 - - - +
128D SER* 3.0 46.5 + - - +
129D PRO 2.9 5.6 + - - +
130D GLU* 1.3 76.1 - - - +
132D ALA* 1.3 68.2 + - - +
134D ILE* 3.0 27.2 + - - +
135D SER* 3.2 9.9 + - - -
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Residues in contact with ALA 132 (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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129D PRO 4.4 3.9 + - - +
130D GLU* 5.0 1.1 - - - -
131D ASN* 1.3 79.4 - - - +
133D ASP* 1.3 65.7 + - - +
134D ILE 2.9 1.2 + - - -
135D SER* 3.0 7.3 + - - -
136D GLN* 2.9 24.6 + - - +
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Residues in contact with ASP 133 (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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94D GLU* 4.7 4.9 - - - +
97D ARG* 3.3 43.1 + - - +
130D GLU* 3.5 11.5 + - + +
131D ASN 3.4 0.6 - - - -
132D ALA* 1.3 79.7 - - - +
134D ILE* 1.3 63.6 + - - +
136D GLN* 3.6 20.0 + - - +
137D SER* 3.5 10.6 + - - -
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Residues in contact with ILE 134 (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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88D LEU* 3.6 28.9 - - + -
92D TYR* 3.9 25.4 - - + +
97D ARG* 2.9 27.6 - - - +
120D GLY 4.6 2.9 - - - +
123D LEU* 5.5 8.5 - - + +
124D LEU* 4.5 15.7 - - + -
128D SER* 5.3 0.4 - - - -
130D GLU 3.4 8.5 + - - +
131D ASN* 3.0 21.4 + - - +
132D ALA 2.9 0.2 + - - -
133D ASP* 1.3 75.4 - - - +
135D SER* 1.3 55.6 + - - +
137D SER* 2.6 31.2 + - - -
138D LEU* 2.9 31.1 + - + +
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Residues in contact with SER 135 (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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173C ASN* 3.0 39.7 + - - +
124D LEU* 3.7 15.1 - - - +
131D ASN 3.2 9.7 + - - -
132D ALA* 3.0 9.7 + - - -
134D ILE* 1.3 72.6 - - - +
136D GLN* 1.3 54.5 + - - +
137D SER 2.7 15.9 + - - -
138D LEU* 3.0 19.7 + - - +
139D LEU* 3.1 20.4 - - - +
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Residues in contact with GLN 136 (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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132D ALA 2.9 16.1 + - - +
133D ASP* 3.7 20.2 - - - +
134D ILE 3.1 0.4 + - - -
135D SER* 1.3 73.0 - - - +
137D SER* 1.3 57.7 + - - +
139D LEU* 4.7 4.7 - - - -
140D GLN* 3.9 14.0 - - - +
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Residues in contact with SER 137 (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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97D ARG* 3.5 30.2 + - - +
100D PHE* 4.7 1.9 - - - +
101D SER* 5.0 0.2 + - - -
116D PHE* 6.0 0.7 - - - -
133D ASP* 3.5 10.1 - - - -
134D ILE* 2.6 15.8 + - - -
136D GLN* 1.3 74.4 - - - +
138D LEU* 1.3 53.6 + - - +
139D LEU 2.9 5.4 - - - -
140D GLN* 3.2 22.4 + - - -
141D THR* 2.6 48.0 + - - +
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Residues in contact with LEU 138 (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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170C LEU* 3.5 24.4 - - + +
173C ASN* 5.6 2.7 - - + +
92D TYR* 4.7 3.6 - - + -
116D PHE* 3.7 41.7 - - + +
117D TYR* 3.3 34.2 - - + +
120D GLY* 3.9 10.3 - - - +
121D SER* 3.9 28.9 - - - +
124D LEU* 5.1 0.9 - - + -
134D ILE* 2.9 26.3 + - + +
135D SER* 3.0 16.1 + - - +
137D SER* 1.3 76.9 - - - +
139D LEU* 1.3 63.9 + - + +
141D THR* 3.7 3.8 - - - -
142D PHE* 3.5 2.6 - - - +
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Residues in contact with LEU 139 (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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139C GLN* 4.1 9.2 - - - +
167C MSE 4.1 5.4 - - - +
170C LEU* 3.0 39.3 - - + +
171C ARG* 3.5 32.3 - - + +
173C ASN* 4.7 0.2 - - - +
135D SER 3.1 19.3 - - - +
136D GLN* 5.2 2.5 - - - -
137D SER 2.9 0.8 - - - +
138D LEU* 1.3 86.2 - - + +
140D GLN* 1.3 55.9 + - - +
141D THR 2.9 4.0 - - - -
142D PHE* 2.8 5.9 + - - -
143D ILE* 2.6 58.4 + - + +
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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