Contacts of the helix formed by residues 71 - 81 (chain N) in PDB entry 3L73
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 PRO 71 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66N GLY* 4.1 3.6 - - - -
67N THR 3.4 10.0 - - - +
68N LYS 4.3 7.0 - - - +
69N LYS 4.5 0.7 - - - +
70N ARG* 1.3 90.7 - - + +
72N CYS* 1.3 67.7 + - - +
73N ALA* 3.7 2.0 - - + +
74N ALA* 3.3 13.3 + - + +
75N PHE* 2.9 14.7 + - - +
121N ALA* 5.9 1.3 - - + -
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Residues in contact with CYS 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N LYS* 3.9 36.9 + - - +
66N GLY* 3.9 8.6 - - - +
71N PRO* 1.3 71.6 - - + +
73N ALA* 1.3 67.2 + - - +
75N PHE* 2.9 13.5 + - - +
76N GLU* 3.0 38.6 + - - +
126N GLN* 4.4 12.6 - - - +
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Residues in contact with ALA 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71N PRO* 3.7 1.9 - - + +
72N CYS* 1.3 78.2 - - - +
74N ALA* 1.3 63.5 + - - +
76N GLU* 3.5 8.4 + - - +
77N LYS* 3.0 29.7 + - - +
291O VAL* 4.7 11.6 - - + +
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Residues in contact with ALA 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N ARG* 4.2 18.6 - - + -
71N PRO* 3.3 18.4 + - + +
72N CYS 3.2 0.6 - - - -
73N ALA* 1.3 78.7 - - - +
75N PHE* 1.3 54.5 + - - +
77N LYS* 3.4 5.7 + - - +
78N GLU* 2.8 38.0 + - - +
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Residues in contact with PHE 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63N ALA 4.7 1.3 - - - -
64N PHE* 3.3 40.2 - + + -
66N GLY* 4.2 9.6 - - - -
67N THR* 4.9 9.0 - - + -
70N ARG* 3.9 24.8 + - + +
71N PRO 2.9 12.5 + - - +
72N CYS 2.9 7.8 + - - +
74N ALA* 1.3 78.6 - - - +
76N GLU* 1.3 70.7 + - + +
78N GLU* 3.1 10.1 + - - +
79N VAL* 3.1 26.9 + - + +
86N PHE* 3.5 36.3 - + - -
112N LEU* 3.9 28.7 - - + -
115N ASP* 5.3 0.7 - - - -
116N VAL* 4.1 17.9 - - + -
285O ILE* 5.2 4.9 - - + -
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Residues in contact with GLU 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64N PHE 4.5 14.5 - - - +
65N LYS* 5.1 3.0 + - - +
72N CYS* 3.0 34.9 + - - +
73N ALA* 3.9 3.9 + - - +
75N PHE* 1.3 77.8 - - - +
77N LYS* 1.3 59.5 + - - +
79N VAL* 2.9 5.0 + - - +
80N GLU* 2.8 45.3 + - - +
285O ILE* 3.5 20.1 - - + +
288O GLY* 3.7 7.4 - - - -
289O SER* 2.8 47.3 + - - +
291O VAL* 4.2 11.2 - - + +
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Residues in contact with LYS 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73N ALA* 3.0 18.8 + - + +
74N ALA* 3.7 4.7 - - - +
76N GLU* 1.3 78.0 - - - +
78N GLU* 1.3 51.9 + - - +
80N GLU* 4.2 9.4 + - - -
81N SER* 2.4 40.3 + - - +
291O VAL* 4.6 19.4 - - + +
292O THR* 4.5 6.0 + - - +
355O GLU* 5.6 2.9 + - - -
359O LYS* 3.3 30.1 - - - +
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Residues in contact with GLU 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N ARG* 3.2 40.9 + - - -
74N ALA 2.8 21.4 + - - +
75N PHE* 3.1 4.9 + - - +
77N LYS* 1.3 75.3 - - - +
79N VAL* 1.3 61.4 + - + +
81N SER* 3.0 14.9 + - - -
82N MET* 3.2 21.5 - - - +
108N LYS* 3.6 26.7 + - - +
112N LEU* 4.2 12.6 - - + +
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Residues in contact with VAL 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75N PHE* 3.1 44.2 - - + +
76N GLU 2.9 4.4 + - - +
78N GLU* 1.3 75.0 - - + +
80N GLU* 1.3 69.6 + - - +
82N MET* 2.9 24.9 + - + +
84N ALA* 3.5 34.2 + - + +
86N PHE* 4.4 21.8 - - + -
99N ILE* 5.1 4.7 - - + -
112N LEU* 4.3 15.3 - - + -
285O ILE* 4.1 11.2 - - + -
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Residues in contact with GLU 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N GLU* 2.8 35.3 + - - +
77N LYS 4.1 2.0 - - - +
79N VAL* 1.3 71.9 - - - +
81N SER* 1.3 52.7 + - - +
82N MET 2.7 0.7 + - - -
83N GLY* 2.6 32.7 + - - -
84N ALA 4.7 0.2 - - - -
284O LEU* 4.1 22.2 - - + +
285O ILE* 4.0 13.6 - - + +
289O SER 3.2 20.5 - - - +
290O SER* 3.7 10.2 - - - -
291O VAL* 3.1 10.9 + - - +
292O THR* 2.7 50.3 + - - +
363O GLN* 3.5 13.8 + - - +
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Residues in contact with SER 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77N LYS* 2.4 25.7 + - - +
78N GLU* 3.0 16.8 + - - -
80N GLU* 1.3 76.0 - - - +
82N MET* 1.3 55.7 + - - +
83N GLY 3.3 1.5 + - - -
292O THR* 3.9 3.2 + - - -
359O LYS* 3.8 42.7 - - - +
362O ASN* 3.8 21.5 + - - +
363O GLN* 4.8 4.5 - - - +
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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