Contacts of the helix formed by residues 154 - 170 (chain M) in PDB entry 1MVW
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 HIS 154 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M LEU* 5.0 4.5 - - + +
116M TYR* 2.9 38.8 + + - +
118M TYR* 3.9 6.2 + - - -
123M CYS* 4.4 6.7 - - - -
134M VAL* 3.0 33.4 - - + +
135M TYR* 4.9 0.8 - - - -
139M VAL* 4.0 4.7 - - + -
143M TYR* 2.9 41.3 - - + +
152M PRO 3.1 2.2 + - - -
153M PRO* 1.3 75.7 - - - +
155M ILE* 1.3 75.6 + - + +
156M PHE* 2.9 38.1 - + - +
157M SER* 2.6 35.2 + - - -
158M ILE* 3.5 3.8 + - - +
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Residues in contact with ILE 155 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116M TYR* 4.2 12.7 - - + +
123M CYS* 4.3 11.2 - - - -
125M THR* 4.1 11.4 - - - +
135M TYR* 5.5 1.1 - - + +
154M HIS* 1.3 80.1 - - + +
156M PHE* 1.3 84.0 + - + +
157M SER 2.8 1.8 - - - -
158M ILE* 3.2 8.0 + - + +
159M SER* 2.9 21.8 + - - -
177M ILE* 6.2 0.2 - - + -
188M ASN* 3.3 40.2 - - + +
191M ARG* 5.8 3.8 - - + -
192M VAL* 4.4 23.3 - - + +
672M VAL* 4.5 23.6 - - + -
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Residues in contact with PHE 156 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M VAL 3.6 11.7 - - - -
135M TYR* 4.3 22.2 - + + -
139M VAL* 4.2 10.3 - - + -
140M VAL* 3.9 19.1 - - + -
143M TYR* 3.7 21.3 - - + +
154M HIS* 2.9 43.2 - + - -
155M ILE* 1.3 89.3 - - + +
157M SER* 1.3 60.8 + - - +
159M SER* 3.7 4.5 - - - -
160M ASP* 2.7 32.4 + - - +
191M ARG* 4.4 13.9 - - + -
192M VAL* 6.0 0.2 - - - -
195M TYR* 2.9 49.6 - + + -
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Residues in contact with SER 157 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118M TYR* 3.2 23.0 + - - -
143M TYR* 4.0 25.3 - - - -
146M LYS 4.3 3.5 + - - -
147M LYS 4.6 0.5 + - - -
148M ARG* 3.4 22.3 - - - +
151M ALA* 4.9 0.7 + - - +
152M PRO 4.7 0.5 + - - -
154M HIS 2.6 20.0 + - - -
156M PHE* 1.3 80.3 - - - +
158M ILE* 1.3 60.2 - - - -
160M ASP* 4.0 1.3 - - - +
161M ASN* 2.7 35.8 + - - +
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Residues in contact with ILE 158 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118M TYR* 3.8 17.9 - - + -
121M LEU 5.0 5.4 - - - +
123M CYS* 3.0 44.0 - - + -
148M ARG* 5.6 1.8 - - - +
154M HIS 3.5 3.3 + - - +
155M ILE* 3.2 9.8 + - + +
157M SER* 1.3 80.4 - - - +
159M SER* 1.3 59.9 + - - +
160M ASP 3.1 0.3 + - - -
161M ASN* 3.2 6.3 + - - +
162M ALA* 2.9 28.4 + - - +
175M ILE* 4.0 26.2 - - + -
192M VAL* 6.5 0.9 - - + -
670M HIS* 4.5 18.3 + - + +
671M PHE 4.4 10.1 - - - +
672M VAL* 4.2 13.2 - - + -
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Residues in contact with SER 159 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155M ILE* 2.9 18.8 + - - -
156M PHE* 3.5 6.0 + - - -
158M ILE* 1.3 82.2 - - - +
160M ASP* 1.3 61.5 + - - +
162M ALA* 4.0 2.5 - - - -
163M TYR 3.8 1.9 + - - -
175M ILE* 4.8 2.0 - - - -
192M VAL* 4.0 24.9 - - - -
195M TYR* 2.8 35.3 - - - -
196M PHE* 3.1 32.3 - - - -
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Residues in contact with ASP 160 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M TYR 3.4 19.3 - - - +
144M ARG* 2.3 46.3 + - - -
145M GLY* 3.3 6.9 + - - -
146M LYS 4.6 0.6 + - - +
156M PHE 2.7 18.3 + - - +
157M SER* 4.0 1.6 - - - +
159M SER* 1.3 78.2 - - - +
161M ASN* 1.3 71.9 + - - +
162M ALA 3.0 1.8 - - - -
163M TYR* 3.0 8.4 + - - +
164M GLN* 2.8 26.0 + - - +
195M TYR* 2.4 33.1 + - - +
199M ILE* 4.1 2.0 - - - +
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Residues in contact with ASN 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146M LYS 3.2 22.2 + - - -
147M LYS* 3.6 16.7 - - - +
148M ARG* 4.0 14.3 + - - +
157M SER* 2.7 31.1 + - - +
158M ILE* 3.7 5.2 - - - +
160M ASP* 1.3 79.9 - - - +
162M ALA* 1.3 52.8 + - - +
164M GLN* 2.7 22.5 + - - +
165M PHE* 2.8 61.5 + - + +
670M HIS* 5.2 3.1 - - + -
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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 ILE 2.9 15.9 + - - +
159M SER* 3.8 10.8 - - - +
161M ASN* 1.3 76.7 - - - +
163M TYR* 1.3 52.2 + - - +
165M PHE* 3.0 4.6 - - - +
166M MET* 2.6 37.3 + - - +
173M GLN* 3.6 27.4 - - + +
175M ILE* 4.5 9.9 - - + -
196M PHE* 4.3 9.9 - - + -
459M ILE* 4.6 2.5 - - + -
670M HIS* 4.1 11.8 + - + -
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Residues in contact with TYR 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M ARG* 4.1 28.3 - - - -
159M SER 3.8 6.9 + - - +
160M ASP* 3.0 13.6 + - - +
162M ALA* 1.3 77.4 - - - +
164M GLN* 1.3 70.8 + - - +
166M MET* 2.9 30.9 + - - +
167M LEU* 3.0 28.4 + - + +
196M PHE* 4.0 18.8 - + + -
199M ILE* 4.3 16.4 + - + -
200M ALA* 3.1 24.1 - - + +
254M PHE* 4.1 14.8 - + - -
258M GLY* 2.4 37.6 + - - -
259M LYS* 4.4 6.1 + - - -
459M ILE* 4.3 5.1 - - + +
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Residues in contact with GLN 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M ARG* 4.3 8.1 - - - +
145M GLY* 4.2 17.7 - - - +
146M LYS 4.1 4.4 + - - -
147M LYS* 3.0 32.2 - - - +
160M ASP* 2.8 26.6 + - - +
161M ASN* 2.7 46.1 + - - +
163M TYR* 1.3 71.3 - - - +
165M PHE* 1.3 57.8 + - + +
166M MET 2.7 0.7 + - - -
167M LEU* 2.6 36.0 + - - +
168M THR* 2.8 19.9 + - - +
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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
----------------------------------------------------------
147M LYS* 6.2 4.0 - - + -
161M ASN* 2.8 42.3 + - + +
162M ALA 3.0 5.2 - - - +
164M GLN* 1.3 78.0 - - + +
166M MET* 1.3 65.9 + - - +
168M THR* 3.7 8.3 - - + -
169M ASP* 2.9 52.3 + - - +
171M GLU 4.6 0.3 + - - -
173M GLN* 3.6 17.0 + - - +
668M HIS* 4.5 12.6 - + - -
670M HIS* 3.9 24.2 - + - -
763M THR* 6.4 1.6 - - + -
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Residues in contact with MET 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162M ALA 2.6 17.3 + - - +
163M TYR* 3.0 24.7 - - - +
164M GLN 2.7 1.4 + - - -
165M PHE* 1.3 79.6 - - - +
167M LEU* 1.3 60.5 + - - -
170M ARG* 3.0 24.4 + - - -
171M GLU 3.7 12.2 + - - +
173M GLN* 3.6 12.1 - - - +
254M PHE* 3.0 52.0 - - + -
457M TYR* 3.6 42.0 - - + -
458M PHE 3.6 12.8 - - - +
459M ILE* 3.7 13.2 - - + -
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Residues in contact with LEU 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144M ARG* 5.5 3.8 - - - +
163M TYR* 3.0 42.3 + - + +
164M GLN* 2.6 14.1 + - - +
166M MET* 1.3 79.3 - - + +
168M THR* 1.3 62.9 + - - +
170M ARG* 4.0 11.8 + - - +
256M ALA 5.0 1.6 - - - +
257M THR 3.7 9.9 - - - +
258M GLY* 3.6 30.7 - - - -
457M TYR* 4.9 18.2 + - + +
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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
----------------------------------------------------------
164M GLN* 2.8 26.3 + - - +
165M PHE* 4.1 8.3 - - + -
167M LEU* 1.3 75.4 - - - +
169M ASP* 1.3 74.7 + - - +
170M ARG* 4.5 3.6 - - - +
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Residues in contact with ASP 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M PHE* 2.9 40.9 + - - +
168M THR* 1.3 95.2 - - - +
170M ARG* 1.3 72.7 + - - +
171M GLU* 3.3 30.2 + - + +
173M GLN* 5.2 0.5 - - - +
668M HIS* 4.7 6.1 + - - -
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Residues in contact with ARG 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166M MET 3.0 13.5 + - - -
167M LEU 4.1 12.6 - - - +
168M THR 3.5 3.8 - - - +
169M ASP* 1.3 83.4 - - - +
171M GLU* 1.3 59.7 + - - +
456M GLN* 5.2 8.7 + - - +
457M TYR* 3.9 39.3 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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