Contacts of the helix formed by residues 125 - 135 (chain D) in PDB entry 2V5Q
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 HIS 125 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88D ALA 3.4 14.1 - - - +
89D MET 2.9 29.8 + - - -
90D THR* 3.5 6.2 - - - -
91D GLY* 3.5 23.0 + - - -
120D ALA* 2.9 12.4 + - + +
123D GLU* 3.6 23.7 - - + +
124D GLY* 1.3 74.8 + - - +
126D LEU* 1.3 64.1 + - - +
127D GLU 3.5 2.5 - - - -
128D ILE* 3.3 21.1 + - + +
129D VAL* 3.2 21.5 + - - +
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Residues in contact with LEU 126 (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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117C LEU* 3.7 30.7 - - + -
118C HIS* 3.5 38.1 - - + +
121C ALA* 3.6 28.5 - - + -
129C VAL* 5.8 0.7 - - + -
133C LEU* 5.3 0.3 - - - +
139C VAL* 3.5 28.1 - - + +
121D ALA 4.9 1.3 - - - +
124D GLY* 3.1 21.0 + - - +
125D HIS* 1.3 72.2 - - - +
127D GLU* 1.3 61.3 + - - +
129D VAL* 3.2 19.5 + - + +
130D GLU* 2.9 28.4 + - - +
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Residues in contact with GLU 127 (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 VAL* 3.9 18.3 - - + +
140C ASN* 3.7 27.3 + - - +
93D LEU* 3.7 34.2 - - + +
125D HIS 3.5 0.4 - - - -
126D LEU* 1.3 76.6 - - - +
128D ILE* 1.3 59.2 + - + +
130D GLU* 3.3 18.3 + - - +
131D VAL* 2.9 29.8 + - + +
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Residues in contact with ILE 128 (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 ALA* 3.8 15.3 - - + +
91D GLY* 4.1 15.3 - - - +
93D LEU* 3.4 44.9 - - + +
96D VAL* 3.9 17.5 - - + -
120D ALA* 3.8 12.6 - - + -
125D HIS* 3.3 25.5 + - + +
126D LEU 3.2 0.4 - - - -
127D GLU* 1.3 75.1 - - + +
129D VAL* 1.3 56.4 + - - +
131D VAL* 3.0 4.8 + - - +
132D LEU* 2.8 60.9 + - + +
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Residues in contact with VAL 129 (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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121C ALA* 6.1 0.2 - - + -
126C LEU* 6.0 1.6 - - + -
129C VAL* 3.7 29.8 - - + -
133C LEU* 4.6 2.5 - - + -
117D LEU* 3.7 29.1 - - + +
120D ALA* 4.1 2.2 - - + -
121D ALA* 3.7 35.4 - - + +
125D HIS 3.2 13.1 + - - +
126D LEU* 3.4 17.9 - - + +
128D ILE* 1.3 75.9 - - - +
130D GLU* 1.3 59.0 + - - +
132D LEU* 3.3 5.2 + - - +
133D LEU* 2.9 40.2 + - + +
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Residues in contact with GLU 130 (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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133C LEU* 4.1 29.1 - - + +
137C ALA 5.1 2.8 - - - +
139C VAL* 3.5 32.3 + - + +
126D LEU 2.9 12.6 + - - +
127D GLU* 3.3 15.8 - - - +
128D ILE 3.1 0.2 - - - -
129D VAL* 1.3 77.9 - - - +
131D VAL* 1.3 63.1 + - + +
133D LEU* 3.5 4.7 + - - +
134D LYS* 3.1 21.5 + - - +
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Residues in contact with VAL 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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93D LEU* 3.6 26.7 - - + -
96D VAL* 4.1 11.4 - - + -
97D GLU* 4.6 17.9 - - + +
100D LEU* 3.9 22.7 - - + -
127D GLU* 2.9 15.0 + - + +
128D ILE* 3.8 5.6 - - - +
130D GLU* 1.3 73.9 - - + +
132D LEU* 1.3 67.9 + - - +
134D LYS* 3.1 13.6 + - + +
135D TYR* 2.9 32.5 + - + -
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Residues in contact with LEU 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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84D LEU* 4.1 16.6 - - + -
88D ALA* 4.4 0.4 - - + -
96D VAL* 3.8 22.4 - - + -
100D LEU* 4.1 6.3 - - + -
106D VAL* 3.6 18.5 - - + +
116D PRO* 3.7 10.8 - - + +
117D LEU* 3.4 37.5 - - + +
120D ALA* 4.6 0.9 - - + -
128D ILE* 2.8 42.1 + - + +
129D VAL* 3.7 4.7 - - - +
131D VAL* 1.3 72.2 - - - +
133D LEU* 1.3 61.3 + - - +
135D TYR* 3.2 12.3 + - - +
136D GLY 3.2 0.5 + - - -
137D ALA* 2.9 34.4 + - + +
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Residues in contact with LEU 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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129C VAL* 4.7 1.8 - - + -
130C GLU* 3.5 41.7 - - + +
133C LEU* 3.7 30.5 - - + -
117D LEU* 3.9 10.8 - - + -
129D VAL* 2.9 28.3 + - + +
130D GLU 3.6 4.7 - - - +
132D LEU* 1.3 76.7 - - - +
134D LYS* 1.3 55.8 + - - +
136D GLY* 3.0 18.5 + - - -
137D ALA* 3.7 19.7 + - - +
139D VAL* 3.8 15.5 - - + -
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Residues in contact with LYS 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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130D GLU 3.1 13.5 + - - +
131D VAL* 3.1 16.7 + - + +
133D LEU* 1.3 76.3 - - - +
135D TYR* 1.3 84.1 + - + +
136D GLY* 3.1 3.7 + - - -
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Residues in contact with TYR 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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97D GLU* 4.5 14.4 + - - +
100D LEU* 3.5 63.0 - - + +
101D LYS* 3.8 22.2 - - - +
106D VAL* 3.7 13.3 - - + +
131D VAL* 2.9 29.8 + - + +
132D LEU 3.2 6.5 + - - +
134D LYS* 1.3 99.1 + - + +
136D GLY* 1.3 59.5 + - - +
137D ALA 3.6 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
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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