Contacts of the helix formed by residues 159 - 170 (chain M) in PDB entry 3A68
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 159 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40M LYS 3.5 11.0 - - - +
41M TYR* 3.3 15.9 - - - -
42M VAL 4.9 0.2 + - - -
45M SER* 4.1 10.5 + - - +
105M ARG* 2.8 45.0 + - - -
154M ALA* 2.9 23.3 + - - +
155M THR* 5.1 0.4 - - - -
157M ASN* 3.0 6.6 - - + +
158M GLY* 1.3 73.1 - - - +
160M VAL* 1.3 61.9 + - - +
161M GLN* 3.6 2.8 + - - +
162M LEU* 3.1 17.6 + - + -
163M ALA* 3.2 20.0 + - - +
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Residues in contact with VAL 160 (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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155M THR* 5.8 4.9 - - + -
158M GLY* 2.9 20.4 + - - +
159M ASP* 1.3 74.1 + - - +
161M GLN* 1.3 57.6 + - - +
163M ALA* 3.6 8.2 - - - +
164M ASP* 2.9 27.4 + - - +
148T LEU* 3.2 34.5 - - + +
151T HIS* 3.5 38.8 - - + +
167T GLU* 4.5 6.5 - - + +
171T LEU* 3.3 17.9 - - + -
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Residues in contact with GLN 161 (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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101M TYR* 2.5 40.6 + - - -
105M ARG* 3.6 12.4 + - - +
159M ASP* 3.3 2.0 + - - +
160M VAL* 1.3 79.1 - - + +
162M LEU* 1.3 60.0 + - - +
164M ASP* 3.3 9.4 + - + +
165M PHE* 2.9 33.5 + - - +
148T LEU* 5.2 2.9 - - + +
171T LEU* 3.6 42.0 - - + +
172T GLY* 3.6 18.2 - - - -
175T VAL* 3.6 23.1 - - + +
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Residues in contact with LEU 162 (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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41M TYR* 4.4 3.1 - - + -
45M SER* 4.0 27.6 - - - +
49M VAL* 4.1 22.2 - - + -
98M LEU* 5.9 0.4 - - + -
101M TYR* 3.2 37.5 + - + +
105M ARG* 4.0 0.9 - - - +
150M LEU* 4.3 12.3 - - + -
154M ALA* 3.6 22.4 - - + +
159M ASP* 3.1 24.3 + - - +
161M GLN* 1.3 75.9 - - - +
163M ALA* 1.3 63.2 + - - +
165M PHE* 3.2 4.5 + - + +
166M VAL* 2.9 44.9 + - + +
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Residues in contact with ALA 163 (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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151M HIS* 3.2 29.1 + - + +
154M ALA* 3.7 8.0 - - + +
155M THR* 3.6 30.5 - - + -
159M ASP 3.2 13.1 + - - +
160M VAL* 3.6 10.8 - - + +
161M GLN 3.2 0.2 - - - -
162M LEU* 1.3 76.9 - - - +
164M ASP* 1.3 57.5 + - - +
166M VAL* 3.3 1.1 + - - -
167M GLU* 2.9 27.8 + - - +
167T GLU* 5.6 1.8 - - - +
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Residues in contact with ASP 164 (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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160M VAL 2.9 17.3 + - - +
161M GLN* 3.6 14.7 + - + +
162M LEU 3.3 0.2 - - - -
163M ALA* 1.3 76.0 - - - +
165M PHE* 1.3 59.2 + - - +
167M GLU* 3.5 10.2 + - - +
168M THR* 2.8 52.4 + - - +
164T ASP* 5.1 0.3 - - - +
167T GLU* 3.5 43.5 + - + +
168T THR* 3.7 20.6 - - - +
172T GLY* 5.1 3.1 + - - -
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Residues in contact with PHE 165 (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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97M LYS* 3.8 21.5 - - + -
98M LEU* 4.0 13.5 - - + -
101M TYR* 3.7 58.8 - + + -
104M LYS* 6.1 2.7 - - - -
161M GLN* 2.9 21.1 + - - +
162M LEU* 3.2 8.3 + - + +
164M ASP* 1.3 78.4 + - - +
166M VAL* 1.3 68.0 + - + +
168M THR* 4.7 2.7 - - - -
169M GLU* 2.8 60.5 + - + +
170M TYR* 3.7 28.0 - + - -
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Residues in contact with VAL 166 (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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147M LEU* 3.9 34.1 - - + +
150M LEU* 3.7 28.3 - - + -
151M HIS* 4.1 16.4 - - + +
162M LEU* 2.9 34.2 + - + +
163M ALA* 3.8 3.6 - - - +
165M PHE* 1.3 84.7 - - + +
167M GLU* 1.3 63.1 + - - +
170M TYR* 3.0 26.6 + - + +
171M LEU* 3.2 19.6 + - + -
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Residues in contact with GLU 167 (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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160L VAL* 4.3 3.5 - - + +
164L ASP* 3.1 33.0 - - + +
167L GLU* 3.3 0.2 - - - +
381L CA 2.5 26.5 - - - -
382L CA 2.7 24.5 - - - -
151M HIS* 2.8 29.4 + - - +
163M ALA* 2.9 17.6 + - - +
164M ASP* 3.5 12.0 + - - +
166M VAL* 1.3 78.0 - - - +
168M THR* 1.3 68.0 + - - +
171M LEU* 3.6 36.4 + - + +
172M GLY* 3.9 4.9 + - - -
167T GLU* 4.1 5.2 - - - +
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Residues in contact with THR 168 (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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164L ASP* 4.5 5.9 + - - -
164M ASP* 2.8 42.6 + - - +
165M PHE* 4.0 2.5 - - - -
167M GLU* 1.3 82.2 - - - +
169M GLU* 1.3 75.6 + - - +
173M GLU* 3.7 0.7 - - - +
215M CA 2.4 29.7 - - - -
168T THR* 5.0 4.4 - - + +
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Residues in contact with GLU 169 (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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94M HIS* 6.1 0.7 - - - -
97M LYS* 2.9 35.8 + - - +
165M PHE* 2.8 43.9 + - + +
168M THR* 1.3 92.4 - - - +
170M TYR* 1.3 80.4 + - + +
173M GLU* 3.3 22.6 - - - +
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Residues in contact with TYR 170 (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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56M GLU* 4.3 6.5 - - - -
94M HIS* 2.8 52.4 + + + -
97M LYS* 3.3 25.7 - - - +
98M LEU* 3.3 22.7 + - + +
147M LEU* 3.8 34.4 - - + +
165M PHE* 3.7 31.9 - + - -
166M VAL* 3.0 19.3 + - + +
168M THR 3.5 0.4 - - - -
169M GLU* 1.3 93.1 - - + +
171M LEU* 1.3 59.5 + - - +
172M GLY 3.5 1.8 - - - -
173M GLU* 3.4 6.2 + - - +
174M GLN* 2.8 31.3 + - - +
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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