Contacts of the strand formed by residues 107 - 111 (chain M) in PDB entry 3INU
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 THR 107 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6M GLU* 3.5 25.0 + - - +
7M SER* 4.1 6.8 + - - -
8M GLY 3.1 30.1 + - - +
9M GLY* 3.2 20.2 - - - -
20M LEU* 4.1 11.7 - - + -
89M VAL* 3.3 4.8 - - - +
90M TYR* 2.7 37.9 + - - +
106M GLY* 1.3 76.3 + - - -
108M MET* 1.3 65.0 + - - +
109M VAL* 3.5 1.7 + - + -
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Residues in contact with MET 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M GLY* 2.9 24.4 + - - -
41M PRO* 3.8 22.7 - - + -
87M THR* 3.8 23.8 - - + -
88M ALA* 3.5 18.8 - - - +
89M VAL* 4.0 17.6 - - + +
107M THR* 1.3 75.4 - - - +
109M VAL* 1.3 59.9 + - - +
110M THR* 3.7 18.6 - - - +
150M GLU* 3.7 37.4 - - + +
151M PRO* 4.0 22.4 - - + -
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Residues in contact with VAL 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M GLY* 3.8 18.6 - - - -
10M GLY 3.6 2.9 - - - +
12M VAL* 4.0 10.3 - - + -
18M LEU* 3.5 25.8 - - + -
20M LEU* 4.1 12.8 - - + -
82M MET* 4.1 15.5 - - + +
86M ASP 4.8 1.6 - - - +
87M THR* 3.1 7.4 - - - +
88M ALA 2.8 34.9 + - - -
90M TYR* 3.9 28.5 - - + -
107M THR 4.4 2.2 - - - +
108M MET* 1.3 77.6 - - - +
110M THR* 1.3 66.0 + - - +
111M VAL* 4.5 8.1 - - + -
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Residues in contact with THR 110 (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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109L THR* 6.2 0.7 - - + -
10M GLY 3.0 12.6 + - - -
11M LEU* 3.5 5.4 - - + +
12M VAL* 3.1 25.0 + - - -
87M THR* 3.8 12.3 - - + +
108M MET* 3.7 23.4 - - + +
109M VAL* 1.3 73.5 - - - +
111M VAL* 1.3 64.0 + - - +
112M SER* 4.3 6.7 - - - -
148M PHE* 4.0 18.6 - - + -
149M PRO* 3.6 34.7 - - + +
150M GLU 4.3 0.7 + - - -
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Residues in contact with VAL 111 (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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12M VAL* 3.1 15.9 - - + +
13M LYS 4.0 0.2 - - - +
14M PRO* 3.6 30.7 - - + -
82M LEU* 3.8 26.0 - - + +
83M ARG 3.3 37.2 - - - +
84M ALA* 4.0 10.3 - - - +
86M ASP* 4.0 11.0 - - + -
87M THR* 3.0 19.2 + - - +
109M VAL* 4.5 5.4 - - + -
110M THR* 1.3 73.0 - - - +
112M SER* 1.3 61.2 + - - +
229M SO4 4.5 5.4 + - - -
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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