Contacts of the helix formed by residues 128 - 137 (chain D) in PDB entry 2QMR
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 128 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D LEU* 5.1 4.9 - - + -
126D TRP* 3.2 14.3 - - + +
127D PRO* 1.3 84.1 - - + +
129D LEU* 1.3 66.3 + - - +
130D LEU 3.8 0.2 - - - -
131D PRO* 3.8 7.9 - - - +
132D LYS* 3.2 26.4 + - - +
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Residues in contact with LEU 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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96D LEU* 4.0 18.6 - - + -
114D ILE* 4.1 12.8 - - + -
118D ALA* 3.9 14.1 - - + -
126D TRP* 3.5 56.3 + - + +
127D PRO 3.3 1.8 - - - -
128D ASP* 1.3 74.9 - - - +
130D LEU* 1.3 65.5 + - + +
132D LYS* 2.8 9.3 + - - +
133D LEU* 2.8 47.5 + - + -
155D ILE* 3.7 26.2 - - + -
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Residues in contact with LEU 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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126D TRP 5.0 1.5 + - - +
127D PRO 5.2 0.2 - - - -
129D LEU* 1.3 82.2 - - + +
131D PRO* 1.4 73.5 - - + +
133D LEU* 3.2 11.7 + - + +
134D CYS* 2.8 34.4 + - - -
152D LEU* 4.3 13.2 - - + -
155D ILE* 3.8 44.0 - - + -
156D CYS* 6.6 0.4 - - - -
164D ASP* 3.9 22.9 - - - +
167D VAL* 4.1 14.8 - - + +
168D LEU* 3.9 19.5 - - + -
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Residues in contact with PRO 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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127D PRO 3.5 23.3 - - - +
128D ASP* 3.8 8.3 - - - +
129D LEU 3.6 2.0 - - - -
130D LEU* 1.4 92.9 - - + +
132D LYS* 1.3 57.0 + - - +
135D SER* 2.7 30.8 + - - -
167D VAL 3.9 4.7 - - - +
168D LEU* 3.5 22.4 - - - +
169D ASP* 3.7 30.1 - - + +
170D ARG* 2.7 8.9 + - - +
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Residues in contact with LYS 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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96D LEU* 4.2 28.9 - - + -
128D ASP* 3.2 22.3 + - - +
129D LEU 2.8 10.7 + - - +
131D PRO* 1.3 75.8 - - - +
133D LEU* 1.3 55.4 + - - +
135D SER* 3.4 14.8 + - - +
136D LEU* 3.0 69.9 + - + +
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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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96D LEU* 4.3 4.0 - - + -
99D ILE* 3.3 34.3 - - + -
114D ILE* 5.4 0.2 - - + -
129D LEU* 2.8 40.3 + - + +
130D LEU* 3.7 14.8 - - + +
132D LYS* 1.3 73.0 - - - +
134D CYS* 1.3 62.9 + - - +
136D LEU* 3.2 14.6 + - + +
137D LEU* 3.3 19.3 + - - +
148D ALA* 3.7 16.6 - - + +
151D ALA* 4.1 5.4 - - + -
152D LEU* 3.8 29.6 - - + +
155D ILE* 3.7 23.6 - - + -
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Residues in contact with CYS 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 LEU* 2.8 28.4 + - - +
133D LEU* 1.3 73.0 - - - +
135D SER* 1.3 62.1 + - - +
137D LEU* 3.5 17.4 - - - +
152D LEU* 4.4 17.9 - - - -
168D LEU* 4.0 25.8 - - - -
170D ARG* 3.4 20.0 - - - +
175D MET* 3.0 32.5 - - + +
178D LYS* 3.4 19.4 + - - -
179D PHE* 5.8 0.4 - - - -
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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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131D PRO 2.7 11.4 + - - -
132D LYS* 3.6 19.4 - - - +
133D LEU 3.2 0.2 - - - -
134D CYS* 1.3 76.5 - - - +
136D LEU* 1.3 62.8 + - - +
137D LEU 3.2 1.4 + - - -
138D ASP* 3.4 21.4 + - - +
139D SER* 4.1 2.1 + - - -
170D ARG* 2.5 34.3 + - - +
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Residues in contact with LEU 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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96D LEU* 4.6 12.3 - - + +
99D ILE* 4.1 28.9 - - + -
132D LYS* 3.0 60.6 + - + +
133D LEU* 3.2 7.1 + - - +
135D SER* 1.3 72.1 - - - +
137D LEU* 1.3 65.0 + - - +
138D ASP 3.0 2.9 - - - -
139D SER* 2.9 32.3 + - - +
144D THR* 3.8 18.6 - - + -
145D CYS* 4.0 10.6 + - - -
148D ALA* 3.8 14.4 - - + -
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Residues in contact with LEU 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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133D LEU 3.3 13.9 + - - +
134D CYS* 3.5 18.2 - - - +
135D SER 3.1 1.2 - - - -
136D LEU* 1.3 76.8 - - - +
138D ASP* 1.3 61.0 + - - +
145D CYS* 3.4 26.5 - - - +
148D ALA* 4.0 1.6 - - + -
149D PHE* 3.7 52.5 - - + +
152D LEU* 3.8 23.6 - - + -
175D MET* 4.1 10.8 - - + -
178D LYS* 4.7 8.1 - - + +
179D PHE* 4.0 17.9 - - + -
182D PHE* 3.5 22.8 - - + -
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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