Contacts of the strand formed by residues 41 - 46 (chain M) in PDB entry 1U3E
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 ARG 41 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A T 4.9 2.7 + - - -
13A A 4.6 4.5 - - - +
24C T 3.6 10.5 + - - +
25C T 3.0 43.0 + - - +
26C A 4.2 14.1 - - - +
32M HIS* 3.8 0.2 - - - -
33M GLN* 2.9 39.7 + - + +
35M PRO* 3.7 22.0 - - - +
37M ASP* 2.7 34.3 + - - -
39M TYR* 2.8 28.6 + - - +
40M HIS* 1.3 76.1 - - - +
42M ILE* 1.3 74.3 + - - +
52M THR* 4.2 16.8 - - + +
53M PHE 3.1 15.3 - - - +
54M GLN* 4.2 10.9 + - + -
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Residues in contact with ILE 42 (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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21M VAL* 4.1 12.6 - - + -
30M LEU* 4.0 19.3 - - + -
31M LYS 4.0 16.8 - - - +
32M HIS* 4.0 20.4 - - + -
33M GLN* 3.5 11.7 - - - +
41M ARG* 1.3 84.4 - - - +
43M GLY* 1.3 57.9 + - - +
44M LEU* 3.2 40.6 - - + -
52M THR* 3.5 3.7 - - - +
53M PHE* 2.8 39.2 + - + +
55M VAL* 4.0 12.3 - - + -
58M LEU* 4.0 15.3 - - + -
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Residues in contact with GLY 43 (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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8A A 4.1 11.1 + - - +
9A G 6.1 2.0 + - - -
10A C 6.3 0.2 - - - -
397C EDO 4.6 11.7 - - - -
13M TYR* 4.1 0.2 + - - -
30M LEU* 3.4 18.9 - - - +
33M GLN* 3.9 7.1 - - - +
42M ILE* 1.3 76.5 - - - +
44M LEU* 1.3 63.4 + - - -
45M PHE* 4.1 9.1 + - - -
51M LYS 3.2 10.8 - - - -
52M THR* 4.3 1.8 - - - -
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Residues in contact with LEU 44 (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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6M ILE* 3.9 32.8 - - + -
9M TYR* 3.6 28.2 + - + -
13M TYR* 3.7 31.4 - - + -
21M VAL* 3.9 7.9 - - + -
30M LEU* 3.9 4.9 - - + -
42M ILE* 3.2 28.3 - - + -
43M GLY* 1.3 75.7 - - - +
45M PHE* 1.3 58.6 + - - +
46M LYS 4.0 0.3 + - - -
51M LYS 2.8 36.8 + - - +
53M PHE* 3.6 27.8 - - + -
58M LEU* 4.3 4.5 - - + -
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Residues in contact with PHE 45 (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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7A G 3.3 60.0 + + + +
8A A 3.7 34.1 - + - -
397C EDO 4.5 19.3 - - - -
9M TYR* 3.6 5.6 - - - -
12M HIS* 4.8 8.7 + - - -
13M TYR* 2.8 31.7 + - - +
43M GLY* 4.3 8.1 - - - -
44M LEU* 1.3 73.9 - - - +
46M LYS* 1.3 60.9 + - - +
47M GLY 4.2 0.7 - - - -
48M GLY 3.2 25.4 - - - -
49M LYS 3.6 1.8 - - - -
50M GLY* 3.2 28.9 - - - -
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Residues in contact with LYS 46 (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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8M GLY* 3.0 34.4 + - - +
9M TYR* 3.4 29.3 - - + +
12M HIS* 6.1 4.5 - - + -
44M LEU 4.0 0.2 + - - -
45M PHE* 1.3 74.6 - - - +
47M GLY* 1.3 69.6 + - - +
48M GLY 3.5 0.2 - - - -
49M LYS* 2.7 24.7 + - - +
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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