Contacts of the helix formed by residues 168 - 184 (chain M) in PDB entry 2DFS
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 GLY 168 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111M ASN* 4.6 7.6 - - - -
166M GLY* 3.3 5.5 - - - +
167M ALA* 1.3 79.2 - - - +
169M LYS* 1.3 65.6 + - - +
170M THR* 3.4 4.7 - - - -
171M VAL* 3.1 20.3 + - - +
172M SER* 3.0 23.7 + - - -
661M CYS* 4.0 5.2 - - - -
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Residues in contact with LYS 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161M VAL* 3.7 29.4 - - + +
162M SER 3.8 1.6 - - - -
163M GLY 2.8 31.1 + - - +
164M GLU 3.4 17.6 + - - +
165M SER* 4.0 11.7 + - - +
167M ALA 3.8 0.4 - - - +
168M GLY* 1.3 76.1 - - - +
170M THR* 1.3 57.7 + - - +
172M SER* 3.3 5.0 + - - -
173M ALA* 3.1 27.7 + - - +
218M SER* 5.9 6.8 - - - -
437M ASP* 3.1 31.5 - - - +
438M ILE 3.2 28.5 + - - +
439M TYR* 4.3 5.9 - - - +
661M CYS* 3.8 18.1 - - + -
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Residues in contact with THR 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168M GLY* 4.6 1.0 - - - -
169M LYS* 1.3 77.4 + - + +
171M VAL* 1.3 65.9 + - - +
173M ALA* 3.6 6.4 + - - +
174M LYS* 3.1 22.2 + - - +
197M LEU* 5.9 0.2 - - - +
200M ASN* 4.8 6.3 - - - +
204M GLU* 4.2 20.0 + - - +
218M SER* 6.1 1.8 - - - +
222M LYS* 4.7 11.4 - - - +
437M ASP* 3.3 21.3 - - - +
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Residues in contact with VAL 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M TYR* 6.3 0.2 - - + -
168M GLY* 3.1 20.5 + - - +
170M THR* 1.3 76.5 - - - +
172M SER* 1.3 64.0 + - - +
174M LYS* 3.3 10.8 + - + +
175M TYR* 3.2 47.1 + - + +
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Residues in contact with SER 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M TYR* 4.9 7.7 + - - -
109M ALA* 4.7 6.4 - - - +
139M ILE* 3.6 30.7 - - - +
161M VAL* 4.1 16.8 - - - -
168M GLY 3.0 12.9 + - - -
169M LYS 3.4 8.7 - - - -
171M VAL* 1.3 74.7 - - - +
173M ALA* 1.3 61.3 + - - +
175M TYR* 3.5 4.3 + - - -
176M ALA* 3.1 19.5 + - - +
659M VAL* 4.5 5.0 - - - +
661M CYS* 3.5 14.1 - - - -
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Residues in contact with ALA 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161M VAL* 5.1 2.4 - - + +
169M LYS 3.1 12.9 + - - +
170M THR* 3.7 10.8 - - - +
172M SER* 1.3 72.5 - - - +
174M LYS* 1.4 65.1 + - - +
176M ALA* 3.3 5.0 + - - +
177M MET* 3.1 36.3 + - + +
435M VAL* 3.9 30.6 - - + +
437M ASP* 5.5 7.2 - - + +
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Residues in contact with LYS 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170M THR 3.1 14.9 + - - +
171M VAL* 3.3 13.7 + - + +
173M ALA* 1.4 75.0 - - - +
175M TYR* 1.3 107.3 + - + +
177M MET* 3.6 15.3 + - - +
178M ARG* 3.2 26.8 + - - +
193M GLU* 4.4 16.2 - - - +
197M LEU* 3.8 33.2 - - + -
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Residues in contact with TYR 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M TYR* 5.7 0.9 - - - -
119M TYR* 3.6 57.2 - + + +
139M ILE* 4.1 20.6 - - + -
140M PHE* 3.7 18.1 - + + -
171M VAL* 3.2 44.0 + - + +
172M SER* 3.5 2.0 + - - +
174M LYS* 1.3 111.7 + - + +
176M ALA* 1.4 62.8 + - - +
178M ARG* 3.5 15.3 + - + +
179M TYR* 3.2 22.2 + - - +
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Residues in contact with ALA 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M ILE* 4.3 16.0 - - + +
140M PHE* 5.6 0.2 - - - -
143M ALA* 4.5 11.7 - - + -
159M ILE* 4.5 14.8 - - + -
172M SER 3.1 17.8 + - - +
173M ALA* 3.3 7.8 + - - +
175M TYR* 1.4 73.5 - - - +
177M MET* 1.4 61.0 + - - +
179M TYR* 3.4 5.6 + - - +
180M PHE* 3.0 41.6 + - + -
435M VAL* 4.9 7.9 - - + -
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Residues in contact with MET 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173M ALA* 3.1 27.3 + - + +
174M LYS* 3.7 17.3 - - - +
175M TYR 3.4 0.2 - - - -
176M ALA* 1.4 73.9 - - - +
178M ARG* 1.4 58.8 + - - +
180M PHE* 3.3 9.7 + - + +
181M ALA* 2.9 30.5 + - - +
193M GLU* 4.5 16.7 - - + +
196M VAL* 3.8 32.5 - - + -
197M LEU* 4.0 22.9 - - + -
200M ASN* 5.8 0.7 - - - +
224M ILE* 4.9 5.4 - - - -
226M ILE* 4.3 27.6 - - + -
435M VAL* 5.2 9.2 - - + -
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Residues in contact with ARG 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119M TYR 5.3 6.3 - - - -
121M GLU* 4.9 15.4 + - - -
124M ILE* 4.5 13.2 - - + -
140M PHE* 5.7 0.9 - - + -
174M LYS* 3.2 19.7 + - - +
175M TYR* 3.9 20.2 - - + +
176M ALA 3.4 0.2 - - - -
177M MET* 1.4 76.5 - - - +
179M TYR* 1.3 57.0 + - - +
181M ALA* 3.4 3.3 + - + +
182M THR* 3.0 45.1 + - - +
193M GLU* 2.7 47.4 + - - +
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Residues in contact with TYR 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M ILE* 3.8 36.9 - - + +
127M TYR* 3.3 8.8 + - + +
128M SER* 3.2 20.6 + - - -
140M PHE* 3.6 40.6 - + + -
143M ALA* 3.5 23.3 - - + -
144M GLU* 2.6 44.3 + - - +
147M TYR* 5.7 0.9 - - + -
175M TYR 3.2 12.4 + - - +
176M ALA 3.4 10.1 - - - +
178M ARG* 1.3 76.4 - - - +
180M PHE* 1.4 64.1 + + - +
182M THR* 3.9 1.0 - - - -
183M VAL* 3.0 47.1 + - + +
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Residues in contact with PHE 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M ALA* 3.2 40.4 - - + -
146M ALA* 4.0 1.8 - - + -
147M TYR* 4.1 18.6 - + + -
159M ILE* 3.9 16.6 - - + -
176M ALA* 3.0 28.3 + - + -
177M MET* 3.3 10.1 + - + +
179M TYR* 1.4 78.8 - + - +
181M ALA* 1.3 59.1 + - - +
183M VAL* 3.7 6.1 - - + +
184M SER* 2.8 28.1 + - - -
226M ILE* 5.1 14.4 - - + -
228M PHE* 4.3 15.6 - + + -
234M ILE* 3.8 5.9 - - + +
433M ILE* 3.4 48.9 - - + -
435M VAL* 5.1 5.2 - - + -
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Residues in contact with ALA 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177M MET 2.9 17.3 + - - +
178M ARG* 3.6 9.0 - - + +
179M TYR 3.3 0.2 - - - -
180M PHE* 1.3 76.6 - - - +
182M THR* 1.3 61.5 + - - +
184M SER* 3.2 13.5 + - - -
186M SER* 3.7 18.9 + - - -
191M ASN 6.3 0.7 - - - -
192M VAL 6.0 0.2 - - - +
193M GLU* 4.9 15.3 - - + +
234M ILE* 3.9 25.6 - - + +
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Residues in contact with THR 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M GLU* 5.2 10.7 + - + +
124M ILE* 4.1 27.4 - - + +
125M ASN* 5.4 7.6 - - - +
178M ARG* 3.0 28.8 + - - +
179M TYR 3.9 2.2 - - - -
181M ALA* 1.3 76.8 - - - +
183M VAL* 1.3 62.3 + - + +
184M SER 3.3 1.0 + - - -
185M GLY 4.4 4.0 + - - -
186M SER* 4.6 7.6 + - - -
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Residues in contact with VAL 183 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M ILE* 4.3 12.8 - - + -
128M SER* 4.3 17.7 - - - +
144M GLU* 4.9 1.6 - - - +
147M TYR* 3.8 35.9 + - + -
179M TYR* 3.0 52.1 + - + +
180M PHE* 3.7 14.4 - - + +
182M THR* 1.3 75.3 - - + +
184M SER* 1.4 59.2 + - - +
185M GLY 3.7 1.5 + - - -
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Residues in contact with SER 184 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147M TYR* 3.3 24.2 - - - -
180M PHE 2.8 23.5 + - - -
181M ALA 3.2 9.0 + - - -
182M THR 3.3 1.6 - - - -
183M VAL* 1.4 77.6 - - - +
185M GLY* 1.3 60.2 + - - +
186M SER 4.4 0.2 + - - -
228M PHE* 4.5 3.6 - - - -
232M TYR 3.4 6.5 - - - +
233M ARG* 3.4 19.6 - - - +
234M ILE* 3.4 28.3 + - - +
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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
------------------------------------------------------------
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