Contacts of the helix formed by residues 141 - 153 (chain M) in PDB entry 6D6Q
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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139M ILE* 3.8 5.1 + - - +
140M LEU* 1.3 78.6 - - - +
142M ALA* 1.3 61.4 + - - +
143M PHE* 3.2 18.8 - - + +
144M GLN* 3.3 12.5 + - + +
145M ARG* 2.9 29.0 + - - +
165M ALA* 5.3 4.2 - - - +
311M TYR* 3.8 31.4 + - + -
527M ARG* 5.7 2.8 + - - -
2001M ANP 4.2 16.3 + - - -
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Residues in contact with ALA 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107M VAL* 4.5 20.6 - - + -
108M GLU 5.5 2.5 - - - +
109M GLY* 5.6 4.7 - - - -
110M CYS* 4.4 12.6 - - - -
141M ASP* 1.3 72.9 - - - +
143M PHE* 1.3 63.3 + - - +
145M ARG* 3.2 17.6 - - + +
146M GLU* 2.9 37.7 + - + +
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Residues in contact with PHE 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M GLY 5.3 2.2 + - - +
110M CYS* 4.2 16.2 - - + +
141M ASP* 4.0 11.0 - - + +
142M ALA* 1.3 79.1 - - - +
144M GLN* 1.3 86.5 + - + +
146M GLU* 3.3 3.2 + - - +
147M ALA* 3.0 22.4 + - + +
159M VAL* 3.1 31.0 - - + -
161M ALA* 3.3 30.7 - - + -
165M ALA* 4.1 21.5 - - + -
167M LYS* 4.8 10.3 - - + -
307M ILE* 3.2 41.5 - - + +
309M THR* 3.5 20.2 - - + -
311M TYR* 6.4 3.1 - - + -
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Residues in contact with GLN 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M LEU* 2.9 43.4 - - + +
141M ASP* 3.3 11.6 + - + +
143M PHE* 1.3 96.0 - - + +
145M ARG* 1.3 57.6 + - - +
147M ALA* 3.1 8.3 + - - +
148M ILE* 2.9 34.4 + - + +
165M ALA 3.0 16.6 + - - -
166M GLY* 2.9 35.6 + - - +
169M VAL* 3.9 15.0 - - + +
170M CYS 6.1 0.7 - - - +
2001M ANP 3.9 18.3 + - - -
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Residues in contact with ARG 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M ARG* 6.1 1.3 - - - +
139M ILE* 5.0 11.3 - - - +
140M LEU* 2.4 44.5 + - + +
141M ASP* 2.9 17.7 + - - +
142M ALA* 3.2 16.3 - - - +
144M GLN* 1.3 76.5 - - - +
146M GLU* 1.3 63.8 + - + +
148M ILE* 3.3 8.6 + - - +
149M GLN* 2.9 30.5 + - - +
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Residues in contact with GLU 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M THR* 3.4 34.0 - - + +
107M VAL* 5.2 1.7 + - - +
110M CYS* 3.2 26.7 - - - -
112M HIS* 3.8 16.4 - - + +
125M LEU* 4.7 2.3 - - - +
142M ALA* 2.9 29.8 + - + +
143M PHE 3.6 3.1 - - - +
145M ARG* 1.3 77.7 - - + +
147M ALA* 1.3 64.8 + - - +
149M GLN* 3.3 13.5 + - - +
150M CYS* 3.0 23.9 + - - +
307M ILE* 3.6 25.1 - - + +
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Residues in contact with ALA 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143M PHE* 3.0 16.2 + - + +
144M GLN* 3.4 11.4 - - - +
146M GLU* 1.3 75.6 - - - +
148M ILE* 1.3 58.1 + - - +
150M CYS* 3.3 7.7 + - - +
151M VAL* 2.9 34.3 + - - +
157M VAL* 5.2 3.9 - - + +
159M VAL* 4.7 17.0 - - + -
170M CYS* 4.2 24.2 - - + -
307M ILE* 4.9 9.1 - - + +
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Residues in contact with ILE 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M ARG* 3.2 31.2 - - - +
136M TYR* 4.7 1.6 - - + +
140M LEU* 4.4 14.8 - - + -
144M GLN 2.9 24.3 + - - +
145M ARG* 3.8 6.1 - - - +
147M ALA* 1.3 72.5 - - - +
149M GLN* 1.3 61.7 + - - +
151M VAL* 3.2 3.7 + - - +
152M ASP* 2.9 28.8 + - - +
169M VAL* 4.4 7.6 - - + +
170M CYS* 3.8 23.1 - - + +
173M TYR* 3.3 53.8 - - + -
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Residues in contact with GLN 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125M LEU* 3.7 29.8 + - + +
126M LYS 4.0 24.8 + - - +
127M PRO* 4.3 7.2 - - + +
128M ARG* 5.8 7.6 - - + +
145M ARG 2.9 17.8 + - - +
146M GLU* 3.3 12.7 + - - +
148M ILE* 1.3 77.6 - - - +
150M CYS* 1.3 60.8 + - - +
152M ASP* 3.5 10.6 + - + +
153M ASN* 2.9 25.1 + - - +
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Residues in contact with CYS 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112M HIS* 5.4 2.0 - - - +
125M LEU* 3.4 17.3 - - + +
146M GLU 3.0 13.8 + - - +
147M ALA* 3.5 11.0 - - - +
149M GLN* 1.3 77.7 - - - +
151M VAL* 1.3 62.9 + - - +
152M ASP 3.1 1.0 + - - -
153M ASN* 3.3 12.3 + - - +
154M ASN 3.6 0.2 + - - -
155M GLN* 3.3 33.0 + - - +
156M SER 3.9 2.7 - - - -
157M VAL* 4.0 9.9 - - + -
305M HIS* 3.1 45.3 - - + -
307M ILE* 6.6 0.2 - - + -
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Residues in contact with VAL 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147M ALA 2.9 20.5 + - - +
148M ILE* 3.2 5.1 + - - +
150M CYS* 1.3 75.5 - - - +
152M ASP* 1.3 61.4 + - - +
154M ASN 3.5 6.5 + - - -
155M GLN 4.4 7.0 - - - +
157M VAL* 4.6 7.2 - - + -
170M CYS* 3.3 27.4 - - - -
173M TYR* 3.6 24.2 - - + -
174M ALA* 3.9 22.7 - - + +
177M LEU* 3.4 14.9 - - + +
248M TRP* 3.7 16.7 - - + -
280M VAL* 4.5 12.1 - - + -
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Residues in contact with ASP 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126M LYS 5.8 0.2 - - - +
127M PRO 4.5 0.9 - - - +
128M ARG* 3.6 36.0 + - + +
129M VAL* 4.4 7.8 + - - +
148M ILE 2.9 16.4 + - - +
149M GLN* 3.7 9.6 - - - +
150M CYS 3.1 0.8 - - - -
151M VAL* 1.3 78.3 - - - +
153M ASN* 1.3 67.4 + - - +
154M ASN* 3.0 15.3 + - - +
173M TYR* 2.8 27.3 + - - +
177M LEU* 4.4 8.8 - - - +
180M ARG* 4.5 11.6 + - - -
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Residues in contact with ASN 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125M LEU* 3.4 30.2 - - + +
126M LYS* 3.0 41.7 + - - +
127M PRO 4.6 2.2 + - - -
149M GLN 2.9 18.4 - - - +
150M CYS 3.3 3.4 + - - +
152M ASP* 1.3 81.1 + - - +
154M ASN* 1.3 72.5 + - - +
155M GLN* 3.6 10.3 + - - +
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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