Contacts of the helix formed by residues 155 - 171 (chain M) in PDB entry 5IY8
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 ALA 155 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153M GLY 3.9 0.4 + - - -
154M ARG* 1.3 72.2 - - - +
156M ASN* 1.3 60.2 + - - +
157M ASP* 3.2 2.2 - - + +
158M ALA* 2.8 38.7 + - + +
159M ILE* 2.9 12.2 + - - +
185M ARG* 6.1 1.6 - - - +
186M ILE* 5.0 7.9 - - + -
190M GLU* 4.8 8.1 + - + +
23X T 5.0 15.5 - - - -
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Residues in contact with ASN 156 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M ALA* 3.2 29.9 + - - +
116M ASN* 5.9 0.4 - - - +
117M ALA* 3.9 11.6 - - - +
142M PHE* 3.3 23.0 - - - -
146M TYR* 5.1 8.4 - - - -
154M ARG 3.1 6.8 + - - +
155M ALA* 1.3 71.8 - - - +
157M ASP* 1.3 64.5 + - - +
159M ILE* 3.2 9.2 + - - +
160M ALA* 2.9 27.0 + - - +
23X T 5.6 3.0 - - - -
24X G 3.8 23.9 + - - +
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Residues in contact with ASP 157 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ARG* 5.8 0.3 + - - -
116M ASN* 5.5 1.2 - - - +
117M ALA* 5.9 1.4 - - - -
120M GLU* 4.4 20.7 - - + +
124M MET* 5.0 1.4 - - + +
155M ALA* 3.2 1.7 - - + +
156M ASN* 1.3 81.1 + - - +
158M ALA* 1.3 63.8 + - - +
160M ALA* 3.9 6.9 - - - +
161M SER* 3.0 30.9 + - - +
184M SER* 5.7 0.7 - - - +
185M ARG* 2.5 35.7 + - + +
186M ILE* 3.9 20.9 - - + -
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Residues in contact with ALA 158 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155M ALA* 2.8 22.8 + - + +
157M ASP* 1.3 77.8 - - - +
159M ILE* 1.3 64.1 + - - +
161M SER* 3.4 3.0 + - - -
162M ALA* 3.0 24.9 + - - +
186M ILE* 3.8 30.8 - - + +
190M GLU* 3.9 8.7 - - + +
191M ILE* 5.2 2.0 - - - -
194M CYS* 3.6 24.2 - - - +
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Residues in contact with ILE 159 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142M PHE* 3.8 21.8 - - + -
145M VAL* 4.1 21.5 - - + -
151M LEU* 4.6 19.3 - - + +
154M ARG* 4.1 19.5 - - + +
155M ALA 2.9 18.3 + - - +
156M ASN* 3.2 11.6 + - - +
158M ALA* 1.3 77.5 - - - +
160M ALA* 1.3 62.8 + - - +
162M ALA* 3.3 5.2 + - - +
163M CYS* 3.0 26.6 + - - -
194M CYS* 4.0 23.1 - - + -
198M ILE* 4.6 13.0 - - + -
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Residues in contact with ALA 160 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M ALA* 4.8 9.2 - - + +
120M GLU* 5.3 3.6 - - + -
121M ILE* 3.9 24.0 - - + +
124M MET* 4.2 10.3 - - + -
138M THR* 4.3 2.9 - - - +
142M PHE* 4.0 17.2 - - + -
156M ASN 2.9 15.6 + - - +
157M ASP* 3.9 7.9 - - - +
158M ALA 3.4 0.2 - - - -
159M ILE* 1.3 74.1 - - - +
161M SER* 1.3 63.6 + - - +
163M CYS* 3.2 6.2 + - - +
164M LEU* 3.0 21.8 + - - +
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Residues in contact with SER 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M MET* 3.5 18.9 - - - +
157M ASP 3.0 18.5 + - - -
158M ALA* 3.8 4.9 - - - -
160M ALA* 1.3 75.7 - - - +
162M ALA* 1.3 61.1 + - - +
164M LEU* 3.4 6.0 + - - +
165M TYR* 3.1 18.5 + - - +
180M ILE* 3.7 22.5 - - - +
184M SER* 3.5 19.6 + - - -
186M ILE* 4.3 1.0 - - - +
191M ILE* 4.4 19.5 - - - +
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Residues in contact with ALA 162 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158M ALA 3.0 17.4 + - - +
161M SER* 1.3 73.6 - - - +
163M CYS* 1.3 67.1 + - - +
165M TYR* 3.0 7.3 + - - +
166M ILE* 3.0 25.4 + - - +
191M ILE* 4.1 13.0 - - + +
194M CYS* 3.9 16.6 - - + -
195M PHE* 3.9 13.2 - - + +
198M ILE* 3.5 24.2 - - + -
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Residues in contact with CYS 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138M THR* 3.8 19.5 + - + +
141M LEU* 3.9 12.1 - - + +
142M PHE* 3.5 40.4 - - + -
145M VAL* 4.7 3.8 - - - -
159M ILE* 3.0 20.7 + - - -
160M ALA* 3.4 9.4 - - - +
162M ALA* 1.3 75.8 - - - +
164M LEU* 1.3 57.0 + - - +
166M ILE* 3.3 10.1 + - - +
167M ALA* 3.0 31.2 + - - +
198M ILE* 4.1 12.3 - - - +
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Residues in contact with LEU 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M ILE* 4.8 8.3 - - + +
124M MET* 4.1 32.8 - - + +
125M ALA* 4.6 7.2 - - + +
128M ILE* 5.0 1.1 - - + -
130M LEU* 3.8 29.2 - - + -
134M ILE* 4.3 5.2 - - + -
135M VAL* 5.6 0.7 - - - -
138M THR* 3.3 28.0 - - + +
160M ALA 3.0 11.9 + - - +
161M SER* 3.5 10.5 - - - +
163M CYS* 1.3 76.1 - - - +
165M TYR* 1.3 64.6 + - - +
167M ALA* 3.6 0.5 + - - +
168M CYS* 3.1 24.5 + - - -
180M ILE* 4.1 27.6 - - + -
183M VAL* 5.2 1.1 - - + -
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Residues in contact with TYR 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161M SER 3.1 12.1 + - - +
162M ALA* 3.0 12.5 + - - +
164M LEU* 1.3 77.4 - - - +
166M ILE* 1.3 64.4 + - - +
168M CYS* 3.2 7.2 + - - +
169M ARG* 2.6 66.4 + - + +
174M PRO* 5.4 1.5 - - + +
175M ARG 3.0 29.7 + - - -
176M THR* 5.4 0.3 - - - -
177M PHE* 3.3 51.0 - + + -
180M ILE* 4.3 23.3 - - + +
191M ILE* 5.1 2.7 - - + -
195M PHE* 3.7 21.1 - + + -
209M ILE* 4.9 4.9 - - - +
284P GLU* 4.4 2.3 + - - -
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Residues in contact with ILE 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141M LEU* 3.9 19.3 - - + -
162M ALA 3.0 16.3 + - - +
163M CYS* 3.3 8.0 + - - +
165M TYR* 1.3 73.9 - - - +
167M ALA* 1.3 61.9 + - - +
169M ARG* 3.1 5.6 + - - +
170M GLN* 2.8 49.3 + - + +
195M PHE* 4.0 29.4 - - + +
198M ILE* 3.6 39.7 - - + -
199M LEU* 5.1 8.5 - - + -
204M THR* 6.1 2.9 - - + -
206M VAL* 4.5 10.1 - - + -
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Residues in contact with ALA 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M ILE* 4.0 7.4 - - + +
137M ARG* 3.8 14.8 - - + -
138M THR* 3.3 41.1 - - - +
141M LEU* 3.8 8.4 - - + +
163M CYS 3.0 12.2 + - - +
164M LEU 3.9 1.1 - - - +
166M ILE* 1.3 75.4 - - - +
168M CYS* 1.3 63.6 + - - +
170M GLN* 3.4 5.6 + - - +
171M GLU* 3.1 30.0 + - - +
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Residues in contact with CYS 168 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M LEU* 3.8 28.5 - - - -
134M ILE* 3.5 27.4 - - - -
164M LEU* 3.1 19.2 + - - +
165M TYR* 3.4 11.7 - - - +
167M ALA* 1.3 77.8 - - - +
169M ARG* 1.3 58.3 + - - +
171M GLU 3.8 2.6 + - - -
173M VAL* 3.3 33.4 + - - +
174M PRO* 4.0 1.8 - - - -
175M ARG* 4.1 28.9 - - + +
180M ILE* 5.2 1.8 - - - -
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Residues in contact with ARG 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M TYR* 2.6 54.0 + - + +
166M ILE* 3.1 8.9 + - - +
168M CYS* 1.3 74.5 - - - +
170M GLN* 1.3 66.8 + - - +
171M GLU 3.2 0.4 - - - -
172M GLY* 3.2 13.7 + - - -
174M PRO* 3.5 30.4 - - + +
177M PHE* 4.2 0.4 - - - -
195M PHE* 3.6 10.6 - - - -
206M VAL* 3.6 29.0 - - + +
207M ASP* 3.2 35.9 + - + +
208M LEU* 4.7 3.0 - - - +
209M ILE* 4.2 20.6 - - - +
283P TYR 5.3 2.8 + - - -
284P GLU* 3.0 28.3 + - - -
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Residues in contact with GLN 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137M ARG* 3.1 32.5 + - - +
141M LEU* 4.6 16.0 - - - +
166M ILE* 2.8 34.4 + - + +
167M ALA* 3.9 4.6 - - - +
169M ARG* 1.3 76.4 - - - +
171M GLU* 1.3 63.6 + - - +
172M GLY* 3.1 4.4 + - - -
204M THR* 4.7 16.6 + - - +
205M SER 4.8 2.8 + - - -
206M VAL* 4.0 23.5 - - + +
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Residues in contact with GLU 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 2.8 34.3 + - - +
133M ASN* 3.5 22.4 + - - +
134M ILE* 3.5 28.5 - - + -
137M ARG* 3.2 43.4 + - + +
167M ALA 3.1 17.4 + - - +
168M CYS 4.3 3.1 - - - +
169M ARG 3.2 0.8 - - - -
170M GLN* 1.3 78.5 - - - +
172M GLY* 1.3 59.6 + - - +
173M VAL* 3.3 2.7 - - + -
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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