Contacts of the strand formed by residues 46 - 51 (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 GLU 46 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M VAL* 4.0 3.1 - - - -
38M ARG* 2.7 77.5 + - + +
45M LEU* 1.3 75.9 - - - +
47M TRP* 1.3 74.3 + - - +
48M VAL* 3.5 3.4 + - - +
60M ALA* 5.1 1.4 - - + +
62M SER* 2.9 25.0 + - - -
232M GOL 3.7 30.4 - - - +
98N PHE* 4.6 0.4 - - - -
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Residues in contact with TRP 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M ASN* 3.1 26.1 + - + -
36M TRP 3.7 11.2 - - - -
37M VAL* 4.3 6.3 - - + -
46M GLU* 1.3 82.1 - - - +
48M VAL* 1.3 62.0 + - - +
49M SER* 3.3 12.2 + - - -
50M SER* 3.6 28.0 - - - -
56M TYR* 5.4 0.9 - - - -
58M HIS* 3.7 30.1 - + + -
59M TYR 3.9 11.4 - - - -
60M ALA* 3.4 35.5 - - + +
100M PHE* 3.9 17.3 - - - -
94N ALA* 5.1 2.9 - - + -
95N PRO* 3.7 38.8 - - + -
96N LEU* 3.6 31.1 + - + +
98N PHE* 4.1 16.4 - - + -
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Residues in contact with VAL 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36M TRP* 2.9 16.3 + - + +
37M VAL 4.4 0.7 - - - -
38M ARG* 3.7 40.6 - - + +
46M GLU* 3.7 15.0 - - + +
47M TRP* 1.3 76.1 - - - +
49M SER* 1.3 71.5 + - - +
59M TYR* 3.5 0.3 - - - -
60M ALA* 2.9 29.3 + - - -
63M VAL* 3.5 12.5 - - + +
67M PHE* 3.7 29.6 - - + -
80M LEU* 4.3 10.5 - - + -
90M TYR* 4.4 4.0 - - + -
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Residues in contact with SER 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M ASN* 3.1 3.3 - - - -
36M TRP* 2.8 29.6 + - - -
47M TRP* 3.3 11.2 + - - -
48M VAL* 1.3 91.4 - - - +
50M SER* 1.3 63.1 + - - +
58M HIS 3.2 14.2 + - - -
59M TYR* 3.4 15.4 - - - -
69M ILE* 3.1 34.9 - - - +
80M LEU* 4.8 5.2 - - - -
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Residues in contact with SER 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M ARG* 4.7 3.8 - - - -
34M MET 3.3 6.1 - - - -
35M ASN* 2.9 28.3 - - - -
47M TRP* 3.6 7.5 - - - -
49M SER* 1.3 75.7 + - - +
51M ILE* 1.3 62.1 - - - +
56M TYR* 3.6 24.9 + - - -
57M ILE* 3.5 5.0 - - - +
58M HIS* 2.9 34.9 + - - +
69M ILE* 3.7 3.8 - - - -
95M GLU* 4.7 4.3 - - - -
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Residues in contact with ILE 51 (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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33M ARG* 3.3 4.6 - - - +
34M MET* 2.9 27.6 + - + +
50M SER* 1.3 76.2 - - - +
52M SER* 1.3 70.3 + - - +
54M SER* 3.3 33.0 - - - +
56M TYR 3.5 3.1 - - - -
57M ILE* 4.2 12.3 - - + +
69M ILE* 3.4 29.4 - - + +
70M SER* 4.1 16.4 - - - +
71M ARG* 3.0 25.7 + - + +
78M LEU* 3.7 20.2 - - + -
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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
------------------------------------------------------------
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