Contacts of the helix formed by residues 71 - 82 (chain e) in PDB entry 4IL6
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 71 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68e ASP* 2.9 29.3 + - + +
70e PHE* 1.3 88.8 - - + +
72e ALA* 1.3 52.0 + - - +
73e LYS 3.2 3.1 - - - -
74e GLN* 3.3 14.7 + - + +
75e GLN* 2.8 35.8 + - + +
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Residues in contact with ALA 72 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85d MET* 4.4 2.9 - - - -
96d GLU 5.0 0.4 - - - +
107d LEU* 3.8 21.8 - - + -
66e VAL* 3.7 15.7 - - + +
68e ASP 3.1 22.4 + - - +
69e ARG 3.4 12.8 - - - +
70e PHE 3.3 1.4 - - - -
71e GLU* 1.3 79.3 - - - +
73e LYS* 1.3 62.1 + - - +
75e GLN* 3.4 9.5 + - - +
76e VAL* 3.1 30.1 + - - +
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Residues in contact with LYS 73 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96d GLU 3.6 15.4 + - - +
97d ALA 3.4 24.2 - - - +
98d GLN* 3.4 36.3 - - - +
100d ASP* 3.8 23.5 + - - -
103d ARG* 3.8 22.3 + - + +
107d LEU* 4.5 3.3 - - - +
70e PHE 5.0 1.3 + - - +
71e GLU 3.2 1.3 - - - -
72e ALA* 1.3 79.7 - - - +
74e GLN* 1.3 61.0 + - - +
76e VAL* 3.6 0.6 + - - -
77e GLU* 3.2 49.4 + - - +
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Residues in contact with GLN 74 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71e GLU* 3.3 16.2 + - + +
73e LYS* 1.3 75.9 - - - +
75e GLN* 1.3 60.0 + - - +
77e GLU* 3.3 21.7 + - - +
78e THR* 2.9 59.9 + - - +
81e GLU* 5.6 1.4 - - - +
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Residues in contact with GLN 75 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65e LEU 4.6 1.0 - - - +
66e VAL* 3.4 16.4 - - - +
67e THR* 2.7 48.6 + - - +
68e ASP* 3.2 20.8 + - - +
71e GLU* 2.8 15.9 + - + +
72e ALA* 3.5 5.5 - - - +
73e LYS 3.3 0.4 - - - -
74e GLN* 1.3 76.3 - - - +
76e VAL* 1.3 58.1 + - + +
78e THR* 3.4 8.0 + - - -
79e PHE* 3.0 52.4 + - + -
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Residues in contact with VAL 76 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59d TYR* 4.3 22.9 - - + -
103d ARG* 4.0 9.0 - - - +
106d GLN* 3.6 33.2 - - + +
107d LEU* 4.1 11.4 - - + -
66e VAL* 3.8 23.8 - - + -
72e ALA 3.1 17.1 + - - +
73e LYS 3.9 4.3 - - - +
74e GLN 3.3 0.2 - - - -
75e GLN* 1.3 70.8 - - - +
77e GLU* 1.3 61.0 + - - +
79e PHE* 3.1 10.4 + - + +
80e LEU* 2.9 39.5 + - + +
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Residues in contact with GLU 77 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100d ASP* 4.9 0.9 - - - +
103d ARG* 3.1 37.1 + - - +
73e LYS* 3.2 44.0 + - - +
74e GLN* 3.5 31.6 + - - +
76e VAL* 1.3 78.5 - - - +
78e THR* 1.3 56.8 + - - +
80e LEU* 3.3 4.6 + - - +
81e GLU* 3.0 35.9 + - - +
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Residues in contact with THR 78 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74e GLN* 2.9 33.9 + - - +
75e GLN* 3.5 8.1 - - - -
76e VAL 3.3 0.2 - - - -
77e GLU* 1.3 74.8 - - - +
79e PHE* 1.3 67.1 + - + +
81e GLU* 3.3 9.6 + - + +
82e GLN* 3.2 39.7 + - + +
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Residues in contact with PHE 79 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59d TYR* 4.6 8.7 - + + -
63e ILE 5.2 0.7 - - - -
64e PRO* 3.4 51.6 - - + -
65e LEU 3.7 20.2 - - - -
66e VAL* 4.5 2.7 - - + -
75e GLN* 3.0 46.5 + - + -
76e VAL* 3.3 12.6 - - + +
78e THR* 1.3 78.3 - - + +
80e LEU* 1.3 61.8 + - - +
82e GLN* 3.3 35.4 + - - +
83e LEU* 3.7 11.5 + - - +
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Residues in contact with LEU 80 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59d TYR* 3.4 25.4 - - + +
103d ARG* 3.3 37.2 - - - +
106d GLN* 4.4 6.5 - - - +
48e GLY 5.9 0.4 - - - +
54e SER* 6.2 0.7 - - - -
76e VAL* 2.9 25.5 + - + +
77e GLU* 3.7 4.7 - - - +
79e PHE* 1.3 76.7 - - - +
81e GLU* 1.3 58.0 + - - +
83e LEU* 3.2 42.9 + - + +
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Residues in contact with GLU 81 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74e GLN* 5.6 1.6 - - - +
77e GLU* 3.0 21.5 + - - +
78e THR* 3.3 8.8 + - - +
80e LEU* 1.3 77.1 - - - +
82e GLN* 1.3 60.5 + - - +
83e LEU 3.3 2.7 + - - -
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Residues in contact with GLN 82 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57e ALA* 3.9 18.1 - - + +
78e THR* 3.2 28.3 + - + +
79e PHE* 3.4 32.6 - - - +
80e LEU 3.2 0.8 - - - -
81e GLU* 1.3 78.6 - - + +
83e LEU* 1.3 61.4 + - - +
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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