Contacts of the helix formed by residues 81 - 90 (chain E) in PDB entry 4F2N
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 THR 81 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E HIS* 3.6 25.9 - - + -
26E LEU 4.9 2.9 - - - -
27E PRO 3.6 25.4 - - - +
29E LEU 3.4 9.6 - - - -
30E ARG* 3.7 19.3 - - - +
80E LYS* 1.3 75.7 - - - +
82E ILE* 1.3 65.5 + - - +
83E GLU* 3.6 5.8 + - - -
84E GLU* 2.9 48.6 + - - +
85E ILE* 3.4 13.0 + - - +
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Residues in contact with ILE 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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29E LEU* 2.9 37.4 + - + +
30E ARG 3.6 21.8 - - - +
31E TYR* 3.8 7.0 - - + +
33E ALA* 4.4 2.0 - - + -
70E LEU* 4.0 14.1 - - + -
81E THR* 1.3 72.1 - - - +
83E GLU* 1.3 62.5 - - + +
85E ILE* 3.0 30.7 + - + +
86E ILE* 3.0 17.8 + - + +
102E ALA* 3.3 35.0 - - + +
105E HIS* 3.7 19.5 - - + -
106E PHE* 4.1 11.9 - - + +
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Residues in contact with GLU 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E TYR 4.6 1.2 - - - +
24E HIS* 3.6 24.9 + - + +
25E THR* 2.9 27.5 + - - -
26E LEU* 2.8 37.6 + - - +
29E LEU* 4.8 0.5 + - - +
81E THR* 3.1 2.9 - - - +
82E ILE* 1.3 77.4 - - - +
84E GLU* 1.3 57.2 + - - +
86E ILE* 3.6 7.9 - - + +
87E LEU* 2.9 36.4 + - + +
106E PHE* 3.5 30.7 - - + -
180E LEU* 3.7 23.0 - - + +
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Residues in contact with GLU 84 (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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22E CYS* 6.1 0.4 - - - -
24E HIS* 4.0 17.5 + - + -
30E ARG* 4.7 2.6 + - - -
77E TYR* 4.8 4.0 - - + -
80E LYS* 3.3 34.2 + - + +
81E THR* 2.9 49.6 + - - +
82E ILE 3.2 0.2 - - - -
83E GLU* 1.3 75.9 - - - +
85E ILE* 1.3 57.9 + - - +
87E LEU* 3.4 7.2 + - + +
88E ALA* 2.9 30.9 + - - +
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Residues in contact with ILE 85 (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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31E TYR* 3.8 42.0 - - + -
70E LEU* 4.7 7.6 - - + -
74E GLY* 5.6 0.2 - - - -
77E TYR* 3.6 35.0 - - + -
80E LYS* 5.2 0.4 - - + -
81E THR 3.4 7.8 + - - +
82E ILE* 3.0 21.6 + - + +
84E GLU* 1.3 77.6 - - - +
86E ILE* 1.3 54.7 + - - +
88E ALA* 3.2 0.5 + - - -
89E THR* 2.7 39.8 + - + +
98E MET* 4.0 27.6 - - + -
102E ALA* 3.7 19.5 - - + -
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Residues in contact with ILE 86 (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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82E ILE* 3.0 15.1 + - + +
83E GLU* 3.6 12.6 - - - +
84E GLU 3.3 0.2 - - - -
85E ILE* 1.3 75.7 - - - +
87E LEU* 1.3 62.1 + - - +
89E THR* 3.5 5.0 + - - -
90E THR* 3.0 25.1 + - - -
99E PHE* 3.6 24.2 - - + -
102E ALA* 3.7 7.6 - - + +
103E ALA* 3.7 26.9 - - + +
106E PHE* 3.6 35.2 - - + -
178E CYS* 4.3 12.8 - - + -
180E LEU* 3.9 17.5 - - + -
181E THR* 3.9 9.6 - - + -
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Residues in contact with LEU 87 (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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22E CYS* 5.2 9.2 - - - -
23E TYR 6.0 0.7 - - - +
24E HIS* 5.0 11.7 - - + +
83E GLU* 2.9 24.5 + - + +
84E GLU* 4.0 7.2 - - + +
86E ILE* 1.3 76.8 - - - +
88E ALA* 1.3 62.6 + - - +
90E THR* 3.4 19.7 - - + +
180E LEU* 3.7 40.6 - - + +
181E THR* 4.6 7.2 - - + -
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Residues in contact with ALA 88 (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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77E TYR* 3.5 28.5 - - + +
84E GLU 2.9 18.4 + - - +
85E ILE 3.8 2.5 - - - +
86E ILE 3.2 0.2 - - - -
87E LEU* 1.3 79.8 - - - +
89E THR* 1.3 59.4 + - - +
90E THR 4.7 0.3 - - - +
92E ILE* 3.9 12.1 - - - +
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Residues in contact with THR 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E TYR* 4.3 10.1 - - - +
85E ILE* 2.7 32.7 + - + +
86E ILE* 3.5 3.5 + - - -
88E ALA* 1.3 77.6 - - - +
90E THR* 1.3 68.9 + - - +
91E GLY 3.4 0.2 + - - -
92E ILE* 3.2 24.6 + - - +
95E SER* 3.9 24.0 - - - +
96E LYS* 5.7 0.2 - - - -
98E MET* 4.1 22.4 - - + -
99E PHE* 3.4 32.5 - - - +
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Residues in contact with THR 90 (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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86E ILE 3.0 14.7 + - - +
87E LEU* 3.4 23.5 - - + +
88E ALA 3.6 1.1 - - - +
89E THR* 1.3 77.6 - - - +
91E GLY* 1.3 64.3 + - - +
92E ILE* 3.2 10.0 + - - +
99E PHE* 3.7 21.7 - - - -
181E THR* 3.4 31.4 + - + +
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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