Contacts of the strand formed by residues 145 - 155 (chain M) in PDB entry 6MUO
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 ASN 145 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLY 4.0 12.9 + - - -
83A ASP* 2.7 41.0 + - - +
-22I A 5.4 1.6 + - - -
136M ALA* 3.8 15.1 - - - +
137M TRP 3.0 16.2 + - - +
143M LYS 3.9 1.1 + - - +
144M PRO* 1.3 71.0 - - - +
146M GLN* 1.3 64.0 + - - +
147M TYR* 3.3 16.8 + - - +
148M LYS* 4.2 25.4 + - + +
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Residues in contact with GLN 146 (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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81A GLY 5.3 0.8 + - - -
8M PHE* 3.7 16.3 - - + -
63M ILE* 4.5 26.4 - - + +
67M ALA* 4.7 8.1 - - - +
119M VAL 5.0 3.5 - - - +
134M ARG* 2.6 51.1 + - - +
136M ALA* 3.5 23.0 - - - +
144M PRO* 3.9 23.8 + - + +
145M ASN* 1.3 74.9 - - - +
147M TYR* 1.3 79.6 + - + +
148M LYS 3.8 0.2 - - - -
149M PRO* 4.6 0.2 - - - +
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Residues in contact with TYR 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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80A ARG 4.8 0.2 + - - -
81A GLY* 3.5 38.8 - - - -
82A VAL* 3.5 32.2 + - + +
83A ASP* 5.3 3.6 - - - +
27J C 6.2 0.4 - - - +
4M THR 4.9 0.7 + - - -
7M GLU* 4.1 3.5 + - - +
8M PHE* 3.3 52.0 + + - +
11M ARG* 4.5 17.0 - - + -
12M THR* 5.5 0.7 - - - -
145M ASN* 3.3 7.7 - - - +
146M GLN* 1.3 94.1 - - + +
148M LYS* 1.3 66.7 + - + +
149M PRO* 3.5 11.2 - - - +
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Residues in contact with LYS 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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83A ASP* 5.4 7.9 - - - +
-23I C 4.5 9.3 + - - -
-22I A 3.7 25.4 - - - +
26J G 4.1 32.3 + - - -
27J C 4.7 4.6 + - - -
135M ILE 4.7 0.3 - - - +
136M ALA* 5.0 1.6 - - - -
137M TRP* 5.0 9.5 + - - +
145M ASN* 4.2 26.8 + - + +
147M TYR* 1.3 84.0 - - + +
149M PRO* 1.3 67.5 - - - +
150M THR* 4.8 1.0 + - - -
167M MET* 4.6 27.1 - - + +
168M LEU* 5.2 13.9 + - + +
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Residues in contact with PRO 149 (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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70M ASP* 4.4 2.2 - - - +
81M LYS* 5.3 12.3 + - - +
134M ARG* 3.6 37.2 - - + +
135M ILE 3.3 11.0 - - - +
136M ALA* 4.7 3.6 - - - -
145M ASN 5.5 0.2 - - - +
146M GLN 4.6 0.2 - - - +
147M TYR* 3.5 8.3 - - - +
148M LYS* 1.3 91.5 - - - +
150M THR* 1.3 69.5 + - - +
151M TYR* 3.8 35.4 - - + +
165M SER 4.6 7.1 - - - +
167M MET* 4.9 9.9 + - - +
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Residues in contact with THR 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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133M ILE 3.7 0.2 - - - +
134M ARG* 3.8 1.7 - - - -
135M ILE* 2.6 57.1 + - + +
137M TRP* 3.8 14.6 + - - +
148M LYS 4.8 0.2 + - - -
149M PRO* 1.3 78.2 + - - +
151M TYR* 1.3 66.7 + - - +
152M VAL* 4.7 5.6 - - + -
163M THR* 4.5 11.4 - - + -
164M SER* 3.4 19.1 - - - +
165M SER 5.1 0.2 - - - -
166M SER* 3.3 31.2 + - - +
168M LEU* 6.0 0.9 - - - +
175M LEU* 5.1 8.5 - - + -
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Residues in contact with TYR 151 (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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70M ASP* 2.1 35.7 + - - -
71M ILE* 4.6 10.5 - - + -
74M MET* 3.6 49.2 - - + +
81M LYS* 4.9 9.2 - - + -
83M TRP* 3.8 14.8 - + + -
132M TRP* 4.8 15.3 - + + -
133M ILE 3.9 4.9 - - - +
134M ARG* 4.1 24.7 - - + -
149M PRO* 3.8 26.9 - - + +
150M THR* 1.3 70.7 - - - +
152M VAL* 1.3 61.4 + - - +
153M VAL 4.2 0.2 - - - -
162M PHE 3.8 1.3 - - - +
163M THR* 3.4 1.4 - - - +
164M SER* 2.4 67.2 + - - +
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Residues in contact with VAL 152 (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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131M VAL* 3.4 12.7 - - + +
132M TRP* 5.5 0.4 - - - -
133M ILE* 3.6 25.1 + - + +
135M ILE* 3.7 21.8 - - + -
150M THR* 4.7 2.9 - - + -
151M TYR* 1.3 79.4 - - - +
153M VAL* 1.3 69.9 + - - +
154M TYR* 4.0 5.5 + - + +
161M ALA* 4.6 5.2 - - + -
162M PHE 3.3 3.1 - - - +
163M THR* 3.8 29.2 - - + +
175M LEU* 3.8 17.7 - - + -
179M LEU* 3.7 26.9 - - + -
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Residues in contact with VAL 153 (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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83M TRP* 4.6 7.9 - - + -
130M ALA* 4.2 10.1 - - + -
131M VAL 3.4 10.1 - - - +
132M TRP* 3.7 49.4 - - + -
152M VAL* 1.3 75.0 - - - +
154M TYR* 1.3 59.1 + - - +
155M TYR* 3.7 31.2 + - + +
160M TYR 4.4 0.5 - - - +
161M ALA* 3.5 0.3 - - - -
162M PHE* 2.5 57.9 + - + +
198M LEU* 5.9 5.8 - - + -
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Residues in contact with TYR 154 (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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88M MET* 3.3 29.9 - - + +
101M MET* 4.2 25.4 - - + +
104M PHE* 4.9 17.5 - + + -
129M ASN 3.1 12.5 - - - +
131M VAL* 3.2 35.2 + - + +
152M VAL* 3.9 8.7 - - + -
153M VAL* 1.3 74.9 - - - +
155M TYR* 1.3 87.6 + - - +
156M SER* 4.7 1.5 - - - -
158M THR 4.9 0.3 - - - -
159M PRO* 3.5 32.1 - - - +
160M TYR 3.2 13.5 - - - -
161M ALA* 3.8 16.2 - - + -
179M LEU* 4.9 8.3 - - + -
183M SER* 5.7 1.8 - - - -
185M HIS* 3.8 13.0 + - - -
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Residues in contact with TYR 155 (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 GLU* 3.4 35.0 + - + +
129M ASN* 3.3 6.5 - - + +
130M ALA* 3.6 22.6 - - + +
153M VAL* 3.7 13.3 - - + +
154M TYR* 1.3 102.9 - - - +
156M SER* 1.3 59.9 + - - +
157M GLN* 3.2 3.6 - - + +
158M THR* 2.9 48.7 - - + +
160M TYR* 3.7 5.6 + - + -
162M PHE* 3.5 32.2 - + - -
198M LEU* 4.9 10.0 - - - +
206M PHE* 3.2 35.7 - + - -
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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
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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