Contacts of the helix formed by residues 141 - 158 (chain C) 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 141 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLY 4.5 4.9 - - - +
139C SER* 2.9 11.3 + - - +
140C GLU* 1.3 76.9 - - - +
142C TYR* 1.3 68.5 + - - +
143C ASN* 4.5 12.1 + - - +
144C THR* 3.0 30.2 + - - +
145C CYS 3.1 9.5 + - - -
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Residues in contact with TYR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ARG* 4.3 3.8 - - - -
139C SER 5.0 0.4 - - - -
140C GLU 3.5 6.1 + - - -
141C ASP* 1.3 71.8 + - - +
143C ASN* 1.3 83.3 + - - +
145C CYS* 2.9 19.5 + - - +
146C GLU* 2.9 42.5 + - + +
185C HIS* 3.7 13.5 - + + -
187C SER* 3.0 40.6 + - - -
189C LYS* 4.1 5.4 - - - +
190C ILE* 3.2 24.2 - - + -
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Residues in contact with ASN 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ILE 3.8 0.5 - - - +
100C GLY* 3.4 26.0 + - - +
101C ASP 3.2 21.3 + - - +
102C SER* 3.6 18.6 + - - +
107C ARG* 3.2 29.9 + - - +
141C ASP* 3.3 8.5 + - - +
142C TYR* 1.3 93.0 - - - +
144C THR* 1.3 57.0 + - - +
146C GLU* 4.0 0.6 - - - +
147C GLY* 3.0 23.2 + - - -
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Residues in contact with THR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LEU 5.8 1.3 - - - +
97C ASN 6.1 0.9 - - - +
99C ILE* 3.6 16.0 - - + +
100C GLY* 3.5 15.9 + - - +
136C LEU* 3.7 30.7 - - + -
139C SER* 3.5 12.7 + - - +
141C ASP* 3.0 30.8 + - - +
143C ASN* 1.3 72.9 - - - +
145C CYS* 1.3 68.7 + - - +
147C GLY 3.3 0.5 + - - -
148C ALA* 3.1 23.6 + - - +
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Residues in contact with CYS 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LEU 3.6 12.9 + - - -
137C LEU* 3.3 25.8 - - - +
139C SER* 4.2 8.7 - - - +
141C ASP 3.1 7.3 + - - +
142C TYR* 2.9 13.5 + - + +
144C THR* 1.3 79.9 - - - +
146C GLU* 1.3 58.9 + - - +
148C ALA* 3.3 2.8 + - - +
149C PHE* 2.9 32.4 + - - +
182C PHE* 3.6 23.3 - - - -
185C HIS* 5.1 3.8 - - + -
190C ILE* 3.7 19.5 - - + -
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Residues in contact with GLU 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ARG* 3.4 34.4 + - - +
142C TYR* 2.9 37.6 + - + +
143C ASN* 4.0 2.9 - - - +
145C CYS* 1.3 74.8 - - - +
147C GLY* 1.3 58.6 + - - +
149C PHE* 3.1 4.4 + - - +
150C GLY* 2.8 28.6 + - - -
189C LYS* 3.6 23.4 - - + +
190C ILE* 3.9 30.1 - - + -
193C HIS* 4.3 14.0 + - + -
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Residues in contact with GLY 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ILE* 3.7 32.3 - - - +
107C ARG* 4.7 9.7 - - - +
111C GLY* 5.4 2.8 - - - -
143C ASN 3.0 12.6 + - - -
144C THR 3.3 0.6 + - - -
146C GLU* 1.3 81.1 + - - +
148C ALA* 1.3 60.4 + - - +
150C GLY* 3.3 1.8 + - - -
151C ALA* 3.1 21.7 + - - +
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Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ILE* 3.5 13.4 - - + +
133C LEU* 3.6 35.0 - - + +
136C LEU* 3.8 16.4 - - + -
137C LEU* 4.1 5.6 - - + -
144C THR 3.1 16.5 + - - +
145C CYS 3.6 3.8 - - - +
147C GLY* 1.3 73.4 - - - +
149C PHE* 1.3 60.5 + - - +
151C ALA* 3.3 2.6 + - - +
152C LEU* 2.8 31.6 + - - +
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Residues in contact with PHE 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU* 3.6 19.4 - - + +
145C CYS* 2.9 14.6 + - - +
146C GLU* 3.5 10.5 - - - +
148C ALA* 1.3 75.0 - - - +
150C GLY* 1.3 55.8 + - - +
152C LEU* 3.4 3.2 + - + +
153C GLN* 2.9 27.7 + - - +
179C PHE* 3.5 37.2 - + - -
182C PHE* 3.5 38.8 - + + -
190C ILE* 3.9 22.9 - - + -
193C HIS* 3.8 18.0 + - + -
194C ALA* 3.6 32.5 - - + -
197C CYS* 4.0 10.1 - - - -
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Residues in contact with GLY 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C GLU 2.8 12.9 + - - -
147C GLY* 3.7 3.8 - - - -
149C PHE* 1.3 73.4 - - - +
151C ALA* 1.3 65.6 + - - +
153C GLN* 3.0 13.3 + - - +
154C LYS* 3.1 27.6 + - - +
193C HIS* 3.4 24.6 + - - -
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Residues in contact with ALA 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ILE* 4.3 7.4 - - + -
111C GLY* 4.5 17.7 - - - +
114C ILE* 4.5 11.0 - - + -
115C THR* 4.3 8.8 + - - +
133C LEU* 4.1 22.0 - - + -
147C GLY 3.1 12.6 + - - +
148C ALA 3.7 6.3 - - - +
150C GLY* 1.3 74.4 - - - +
152C LEU* 1.3 61.9 + - - +
154C LYS* 3.4 6.1 + - - +
155C ILE* 3.1 30.6 + - + +
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Residues in contact with LEU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LEU* 5.0 4.0 - - + +
133C LEU* 3.8 31.9 - - + +
134C CYS* 4.4 17.9 - - - -
137C LEU* 3.8 35.9 - - + -
148C ALA 2.8 17.2 + - - +
149C PHE* 3.4 9.6 - - + +
150C GLY 3.1 0.2 - - - -
151C ALA* 1.3 76.7 - - - +
153C GLN* 1.3 56.9 + - - +
155C ILE* 3.4 7.3 + - + +
156C CYS* 2.8 32.6 + - - +
172C LEU* 4.5 19.2 - - + +
179C PHE* 3.8 23.6 - - + -
197C CYS* 4.1 2.9 - - - -
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Residues in contact with GLN 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C PHE 2.9 14.4 + - - +
150C GLY 3.0 7.8 + - - +
152C LEU* 1.3 73.2 - - - +
154C LYS* 1.3 59.0 + - - +
156C CYS* 3.1 2.7 + - + +
157C GLU* 2.8 63.2 + - - +
192C SER* 5.3 2.2 + - - -
193C HIS* 2.6 37.5 + - - +
196C ALA* 3.2 31.6 - - + +
197C CYS* 3.5 17.0 - - - +
230C GLU* 5.7 3.2 + - - -
234C ASN* 5.0 3.6 + - - +
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Residues in contact with LYS 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ALA* 3.8 14.8 + - - +
111C GLY* 3.8 7.8 - - - +
112C ILE* 3.4 35.7 - - + +
115C THR* 3.6 36.2 - - + +
150C GLY* 3.1 21.5 + - - +
151C ALA 3.8 2.0 - - - +
153C GLN* 1.3 79.3 - - + +
155C ILE* 1.3 61.7 + - - +
157C GLU* 4.0 9.7 - - - +
158C ASP* 3.2 29.1 + - - +
193C HIS* 6.1 2.0 - - - -
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Residues in contact with ILE 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ILE* 5.0 4.7 - - + -
115C THR* 4.8 12.1 - - + +
118C ALA* 4.9 11.0 - - + -
129C LEU* 4.2 18.4 - - + -
130C LEU* 4.4 20.9 - - + -
133C LEU* 3.8 26.7 - - + -
151C ALA* 3.1 19.8 + - + +
152C LEU* 3.6 8.1 - - + +
154C LYS* 1.3 76.1 - - - +
156C CYS* 1.3 66.8 + - - +
157C GLU 3.2 0.9 + - - -
158C ASP* 3.2 22.9 - - - -
172C LEU* 4.7 7.9 - - + -
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Residues in contact with CYS 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C LEU* 2.8 22.3 + - - +
153C GLN* 3.4 7.6 - - - +
155C ILE* 1.3 74.4 - - - +
157C GLU* 1.3 64.4 + - - +
158C ASP 4.3 2.3 - - - -
168C LEU* 4.3 16.0 - - - +
172C LEU* 3.9 17.3 - - - -
179C PHE* 4.4 6.1 - - - -
197C CYS* 4.2 17.9 - - - -
200C GLN* 3.7 26.7 - - + +
201C PHE* 3.7 34.1 - - - -
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Residues in contact with GLU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLN* 2.8 53.6 + - - +
154C LYS* 4.0 9.1 - - - +
156C CYS* 1.3 75.0 - - - +
158C ASP* 1.3 64.7 - - - +
196C ALA* 4.2 5.2 - - - +
200C GLN* 3.4 37.8 + - + +
234C ASN* 5.2 2.8 + - - -
237C ARG* 4.6 11.9 + - - +
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Residues in contact with ASP 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C THR* 4.9 9.2 - - + +
119C SER* 4.6 14.7 + - - +
154C LYS 3.2 16.7 + - - +
155C ILE* 3.2 15.7 - - - +
156C CYS 4.3 2.2 - - - -
157C GLU* 1.3 85.7 - - - +
164C ASP 5.9 0.9 + - - -
165C SER 5.4 3.6 - - - +
166C ASP 5.6 1.9 - - - +
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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
------------------------------------------------------------
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