Contacts of the helix formed by residues 76 - 82 (chain M) in PDB entry 4UJ3
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 ILE 76 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45M GLY* 6.0 0.9 - - - -
46M VAL* 4.5 13.2 - - + -
75M ALA* 1.3 87.3 - - + +
77M THR* 1.3 60.8 + - - +
78M SER* 3.4 7.9 - - - +
79M ALA* 4.0 9.6 + - + +
80M TYR* 4.0 13.2 + - - +
739O ASP* 3.9 32.8 - - + +
742O ILE* 4.0 28.3 - - + -
743O VAL* 3.1 33.9 - - + -
746O MET* 6.0 1.1 - - + +
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Residues in contact with THR 77 (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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71M GLU* 3.5 32.5 - - + +
72M ARG 5.8 0.7 - - - +
75M ALA* 3.2 21.9 - - - +
76M ILE* 1.3 77.3 - - - +
78M SER* 1.3 68.9 + - - +
79M ALA 3.2 0.4 - - - -
80M TYR* 3.0 18.5 + - - +
81M TYR* 3.1 32.7 + - - -
108M GLU* 4.6 5.6 - - - +
112M HIS* 3.3 25.0 + - - -
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Residues in contact with SER 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76M ILE* 4.6 4.3 - - - -
77M THR* 1.3 84.7 + - - +
79M ALA* 1.3 62.7 + - - +
81M TYR* 3.6 1.6 + - - +
82M ARG* 3.2 36.4 + - - +
112M HIS* 4.9 17.2 - - - +
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Residues in contact with ALA 79 (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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13M LYS* 3.5 8.7 + - - -
76M ILE* 4.0 12.5 + - + +
77M THR 3.2 0.6 - - - -
78M SER* 1.3 83.0 + - - +
80M TYR* 1.3 62.1 + - - +
82M ARG* 3.4 33.9 + - - +
743O VAL* 5.6 7.6 - - + +
746O MET* 3.9 38.9 - - + +
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Residues in contact with TYR 80 (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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13M LYS* 2.9 27.8 + - - +
15M VAL* 3.5 32.5 - - + +
16M LEU 2.8 25.9 + - - -
17M ILE* 4.0 10.1 - - + -
46M VAL* 4.2 20.6 - - + -
65M TRP* 3.2 31.8 + + + -
66M ASP* 3.5 13.8 - - - -
67M THR* 3.5 33.2 + - + -
71M GLU* 5.0 6.1 - - - +
76M ILE 4.0 7.7 + - - +
77M THR* 3.0 16.0 + - - +
79M ALA* 1.3 79.9 - - - +
81M TYR* 1.3 71.8 + + - +
746O MET* 5.1 6.6 - - + +
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Residues in contact with TYR 81 (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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15M VAL* 4.2 12.3 - - + -
17M ILE* 3.6 31.3 - - + +
71M GLU* 4.6 2.0 + - - -
77M THR* 3.1 30.6 + - - +
78M SER 4.4 0.9 - - - +
80M TYR* 1.3 88.3 - + - +
82M ARG* 1.3 65.9 + - - +
83M GLY 3.2 0.7 + - - -
84M ALA* 3.0 24.2 + - + +
105M TRP* 4.6 2.1 - - - -
108M GLU* 2.5 44.7 + - + +
109M LEU* 3.1 29.4 - - + +
112M HIS* 3.7 28.0 - - + +
113M ALA* 3.6 31.9 - - + +
114M ASP 5.3 1.4 + - - -
117M ILE* 5.5 0.4 - - + -
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Residues in contact with ARG 82 (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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13M LYS* 2.9 28.6 + - - +
78M SER* 3.2 25.8 + - - +
79M ALA* 3.5 32.2 - - - +
80M TYR 3.3 0.8 - - - -
81M TYR* 1.3 75.5 - - - +
83M GLY* 1.3 61.8 + - - +
84M ALA 3.1 2.3 + - - -
112M HIS 5.3 0.4 + - - -
746O MET* 5.0 10.1 + - - +
747O GLU* 5.4 6.5 - - - +
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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