Contacts of the helix formed by residues 76 - 82 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G GLY* 5.6 0.9 - - - -
46G VAL* 3.5 32.1 - - + -
67G THR* 5.0 2.5 - - - +
71G GLU* 6.1 0.7 - - - +
74G ARG 2.6 16.3 + - - +
75G ALA* 1.3 90.1 - - + +
77G THR* 1.3 64.5 + - + +
78G SER* 3.4 2.9 - - - +
79G ALA* 3.9 10.6 + - + +
80G TYR* 3.4 21.2 + - + +
739I ASP* 3.7 22.9 - - + +
742I ILE* 4.0 14.4 - - + -
743I VAL* 3.1 26.7 - - + +
746I MET* 5.3 3.4 - - - +
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Residues in contact with THR 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G GLU* 3.9 28.5 - - + +
72G ARG 6.2 0.2 - - - +
73G TYR* 5.2 4.9 - - + -
74G ARG 3.7 24.4 - - - +
76G ILE* 1.3 80.2 - - + +
78G SER* 1.3 69.0 + - - +
80G TYR* 3.3 5.5 + - - -
81G TYR* 3.1 46.0 + - - -
108G GLU* 4.7 6.5 - - - +
112G HIS* 3.3 23.2 + - - -
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Residues in contact with SER 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G ILE* 5.8 0.9 - - - -
77G THR* 1.3 81.9 + - - +
79G ALA* 1.3 60.7 + - - +
81G TYR* 3.6 1.7 + - - +
82G ARG* 3.2 38.8 + - - +
112G HIS* 4.5 21.7 - - - +
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Residues in contact with ALA 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LYS* 3.5 4.0 + - - -
76G ILE* 3.9 11.0 + - + +
77G THR 3.2 0.2 - - - -
78G SER* 1.3 78.2 - - - +
80G TYR* 1.3 66.3 + - - +
82G ARG* 3.2 37.8 + - - +
743I VAL* 5.4 11.7 - - + +
746I MET* 3.4 39.9 - - + +
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Residues in contact with TYR 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LYS* 2.9 25.3 + - - -
15G VAL* 3.5 29.9 - - + +
16G LEU 2.9 24.1 + - - -
17G ILE* 4.2 9.0 - - + -
46G VAL* 3.8 26.7 - - + -
65G TRP* 3.2 29.2 + + + -
66G ASP* 3.4 11.0 - - - -
67G THR* 3.4 34.4 + - + -
71G GLU* 4.8 7.4 - - - +
76G ILE* 3.4 19.0 + - + +
77G THR* 3.3 7.4 + - - +
79G ALA* 1.3 79.3 - - - +
81G TYR* 1.3 71.2 + + - +
746I MET* 3.8 8.4 - - + +
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Residues in contact with TYR 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G VAL* 4.4 11.2 - - + -
17G ILE* 3.9 27.5 - - + +
71G GLU* 4.0 8.6 + - - -
77G THR* 3.1 37.7 + - - +
78G SER 4.3 0.2 - - - +
80G TYR* 1.3 86.1 - + - +
82G ARG* 1.3 65.5 + - - +
83G GLY 3.3 0.5 + - - -
84G ALA* 3.0 24.3 + - + +
105G TRP* 4.2 4.3 - - - -
108G GLU* 3.2 40.0 + - - +
109G LEU* 3.3 34.3 - - + -
112G HIS* 3.7 37.0 - - + +
113G ALA* 3.8 16.4 - - + +
114G ASP 5.3 1.7 + - - -
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Residues in contact with ARG 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LYS* 2.8 29.3 + - - +
78G SER* 3.2 35.6 + - - +
79G ALA* 3.2 33.4 + - - +
81G TYR* 1.3 75.7 - - - +
83G GLY* 1.3 62.2 + - - +
84G ALA 3.2 0.9 + - - -
112G HIS 5.3 0.9 + - - -
746I MET 5.6 2.0 + - - -
747I GLU* 5.5 10.1 - - - +
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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