Contacts of the strand formed by residues 149 - 154 (chain A) in PDB entry 3MOS
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 VAL 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ARG* 3.4 19.3 - - + -
72A VAL* 4.8 1.1 - - + -
132A ALA* 3.7 39.0 - - + +
135A MET* 4.1 13.2 - - + -
136A ALA* 3.7 29.2 - - + +
147A TYR* 4.3 10.1 - - + -
148A ARG* 1.3 81.3 - - - +
150A TYR* 1.4 66.8 + - - +
177A ASN* 3.0 9.3 + - - +
178A LEU* 3.4 11.2 - - + +
179A VAL* 2.9 27.0 + - - +
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Residues in contact with TYR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.6 17.9 - - + -
55A THR* 3.5 31.1 + - + +
56A MET* 3.6 23.3 - - + -
69A ASP* 3.8 12.8 + - + -
70A ARG 2.8 19.3 + - - +
71A PHE* 3.3 16.2 - - + -
72A VAL* 2.7 33.4 + - - +
148A ARG* 3.2 43.6 + - + +
149A VAL* 1.4 74.5 - - - +
151A CYS* 1.3 57.0 + - - +
179A VAL* 3.4 39.7 - - + -
181A ILE* 4.1 9.4 - - + -
228A PHE* 4.9 7.0 + + + -
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Residues in contact with CYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PHE* 4.9 0.2 - - - -
72A VAL* 3.3 9.4 - - + +
74A SER* 3.8 15.7 - - - -
128A GLY 3.7 7.9 - - - -
129A LEU* 3.6 42.2 - - + -
132A ALA* 3.8 17.7 - - + -
150A TYR* 1.3 75.8 - - - +
152A LEU* 1.3 60.0 + - - +
153A LEU* 3.9 10.0 + - - +
178A LEU* 4.9 0.7 - - + -
179A VAL 2.9 13.3 + - - +
180A ALA* 3.4 2.8 - - - -
181A ILE* 2.8 30.3 + - - +
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA* 3.8 25.1 - - + -
47A ILE* 3.9 17.9 - - + -
48A MET* 4.1 16.2 - - - -
71A PHE* 3.8 19.4 - - + -
72A VAL 2.9 7.8 + - - +
73A LEU* 3.8 20.6 - - + -
74A SER* 2.8 31.5 + - - -
75A LYS* 3.3 16.6 + - + +
150A TYR 4.3 0.4 - - - -
151A CYS* 1.3 71.0 - - - +
153A LEU* 1.4 65.2 + - - +
181A ILE* 3.5 30.3 - - + +
183A ASP* 4.2 13.0 - - + -
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A SER* 3.7 22.4 - - - +
75A LYS* 3.7 4.7 - - - +
129A LEU* 4.2 19.1 - - + -
151A CYS* 3.9 21.5 - - - +
152A LEU* 1.4 74.8 - - - +
154A GLY* 1.3 66.3 + - - +
157A GLU* 3.3 15.9 - - - +
158A LEU* 4.0 13.0 - - + -
163A VAL* 4.0 24.2 - - + -
167A MET* 6.3 0.2 - - - -
180A ALA* 4.0 11.9 - - + -
181A ILE 3.0 5.7 + - - -
182A LEU* 3.7 24.2 - - + -
183A ASP* 2.8 31.2 + - - +
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Residues in contact with GLY 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 3.5 17.9 - - - +
153A LEU* 1.3 77.0 - - - +
155A ASP* 1.3 63.4 + - - -
157A GLU* 2.9 18.6 + - - +
158A LEU* 3.4 18.7 - - - +
182A LEU 5.6 0.2 - - - -
183A ASP 4.0 5.4 - - - -
700A TPP 3.4 23.6 - - - -
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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