Contacts of the helix formed by residues 119 - 129 (chain D) in PDB entry 6R7H
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114D TYR* 3.1 32.4 + - + +
115D GLU* 4.4 1.3 + - - -
117D GLU* 3.0 29.5 - - - +
118D GLU* 1.3 77.6 - - - +
120D TRP* 1.3 69.2 + - - +
121D ARG 3.6 0.9 - - - +
122D ASN* 2.9 33.5 + - + +
123D ALA* 3.3 19.4 + - - +
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Residues in contact with TRP 120 (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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115D GLU* 4.3 22.2 - - + -
118D GLU* 4.4 25.3 + - + -
119D ASP* 1.3 80.4 - - - +
121D ARG* 1.3 64.8 + - - +
122D ASN 3.4 0.4 - - - -
123D ALA 4.0 0.2 - - - -
124D ALA* 3.3 24.9 + - - +
153D ARG* 5.5 3.6 - - - -
154D LEU* 3.3 49.0 - - + +
155D TYR* 5.4 0.2 - - - -
157D GLU* 3.3 44.7 + - + +
158D ASP* 3.5 20.6 + - + +
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Residues in contact with ARG 121 (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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119D ASP* 4.6 0.2 - - - +
120D TRP* 1.3 76.8 - - - +
122D ASN* 1.3 70.0 + - - +
124D ALA* 3.6 4.6 + - - +
125D GLN* 3.5 36.6 + - - +
155D TYR* 5.1 11.5 + - + -
158D ASP* 3.4 26.4 + - - +
160D ASP* 3.4 26.4 + - - -
163D GLN* 3.7 24.2 - - - +
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Residues in contact with ASN 122 (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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114D TYR* 3.6 35.6 - - + -
119D ASP* 2.9 31.5 + - + -
120D TRP 3.4 0.2 - - - -
121D ARG* 1.3 83.6 - - - +
123D ALA* 1.3 61.5 + - - +
125D GLN* 3.6 19.2 + - - +
126D VAL* 3.3 21.3 + - - +
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Residues in contact with ALA 123 (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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111D ALA* 3.6 34.5 - - + +
114D TYR* 3.8 11.3 - - + +
115D GLU* 4.2 4.0 - - + +
119D ASP 3.3 20.0 + - - +
120D TRP 3.8 0.2 + - - -
121D ARG 3.4 0.2 - - - -
122D ASN* 1.3 78.1 - - - +
124D ALA* 1.3 62.4 + - - +
125D GLN 3.4 0.2 - - - -
126D VAL* 3.7 10.8 + - - -
127D LEU* 3.8 11.6 + - - +
154D LEU* 3.8 23.2 - - + +
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Residues in contact with ALA 124 (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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120D TRP 3.3 20.3 + - - +
121D ARG 4.1 2.0 - - - +
122D ASN 3.3 0.4 - - - -
123D ALA* 1.3 77.2 - - - +
125D GLN* 1.3 62.8 + - - +
127D LEU* 3.6 6.0 + - - +
128D VAL* 3.3 25.1 + - - +
151D ILE* 4.7 6.2 - - + +
154D LEU* 4.0 19.0 - - + +
155D TYR* 3.6 38.0 - - + -
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Residues in contact with GLN 125 (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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107D ARG* 4.8 2.4 + - - -
121D ARG* 3.5 32.9 + - + +
122D ASN* 3.6 14.3 + - - +
123D ALA 3.4 0.6 - - - -
124D ALA* 1.3 74.6 - - - +
126D VAL* 1.3 65.6 + - + +
128D VAL* 3.5 16.2 + - + +
129D GLY* 3.7 8.7 + - - -
155D TYR* 4.2 13.0 - - - +
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Residues in contact with VAL 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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107D ARG* 3.3 62.3 + - + +
110D LEU* 4.3 17.7 - - + -
111D ALA* 4.0 11.4 - - + +
114D TYR* 4.6 16.8 - - + -
122D ASN 3.3 18.8 - - - +
123D ALA* 3.9 8.3 - - - +
124D ALA 3.2 1.2 - - - -
125D GLN* 1.3 78.7 - - + +
127D LEU* 1.3 62.8 + - - +
128D VAL 3.3 0.7 + - - -
129D GLY 3.5 3.1 + - - -
130D ILE* 3.8 7.6 - - - +
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Residues in contact with LEU 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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107D ARG 4.1 6.5 - - - +
108D GLN* 4.7 12.8 - - + +
111D ALA* 3.9 20.9 - - + -
123D ALA 3.8 14.6 + - - +
124D ALA 3.6 4.1 + - - +
125D GLN 3.5 0.2 - - - -
126D VAL* 1.3 72.8 - - - +
128D VAL* 1.3 64.5 + - - +
130D ILE* 3.6 37.3 + - + +
132D LEU* 4.3 7.8 - - - +
147D THR* 4.3 13.2 - - + +
150D LYS* 4.0 33.0 - - + -
151D ILE* 3.8 33.6 - - + +
154D LEU* 4.7 6.5 - - + -
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Residues in contact with VAL 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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124D ALA 3.3 16.0 + - - +
125D GLN* 3.7 12.6 - - + +
126D VAL 3.2 1.2 - - - -
127D LEU* 1.3 74.8 - - - +
129D GLY* 1.3 59.7 + - - +
130D ILE 3.1 16.6 + - - +
132D LEU* 5.8 0.5 - - - +
151D ILE* 4.5 9.6 - - + -
155D TYR* 4.2 12.1 - - - +
167D TYR* 3.3 45.2 - - + +
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Residues in contact with GLY 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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103D VAL* 5.5 0.2 - - - +
107D ARG* 3.9 27.2 + - - -
125D GLN 3.7 4.7 + - - -
126D VAL 3.5 4.2 + - - -
127D LEU 3.4 0.4 - - - -
128D VAL* 1.3 78.7 - - - +
130D ILE* 1.3 64.0 + - - +
131D PRO* 3.4 8.0 - - - +
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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