Contacts of the helix formed by residues 81 - 90 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D HIS* 3.4 37.9 + - + +
26D LEU 4.7 1.8 - - - +
27D PRO* 3.8 11.4 - - + +
29D LEU 3.4 10.1 - - - +
30D ARG* 3.6 34.4 - - - +
80D LYS* 1.3 76.9 - - - +
82D ILE* 1.3 65.2 + - - +
83D GLU* 3.7 6.1 - - - -
84D GLU* 3.0 31.6 + - - +
85D ILE* 3.5 13.1 + - - +
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Residues in contact with ILE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU* 3.0 32.5 + - + +
30D ARG 3.5 21.8 - - - +
31D TYR* 3.9 11.0 - - + +
33D ALA* 4.4 2.0 - - + -
70D LEU* 3.9 15.7 - - + -
81D THR* 1.3 72.7 - - - +
83D GLU* 1.3 63.2 + - + +
85D ILE* 2.9 18.3 + - + +
86D ILE* 3.1 12.1 + - + +
102D ALA* 3.3 36.1 - - + +
105D HIS* 3.6 28.9 - - + -
106D PHE* 4.2 12.1 - - + -
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Residues in contact with GLU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D TYR 4.8 0.9 - - - +
24D HIS* 3.4 19.1 - - + +
25D THR* 2.8 26.4 + - - -
26D LEU* 2.7 39.2 + - - +
29D LEU* 4.8 0.6 + - - +
81D THR* 3.1 8.5 - - - +
82D ILE* 1.3 79.7 - - + +
84D GLU* 1.3 60.6 - - - +
86D ILE* 3.2 9.2 + - - +
87D LEU* 3.0 33.2 + - + +
106D PHE* 3.6 21.3 - - + -
180D LEU* 3.6 27.0 - - + +
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Residues in contact with GLU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D HIS* 4.9 6.9 + - - +
77D TYR* 4.8 8.1 - - + -
80D LYS* 3.6 44.3 + - + +
81D THR* 3.0 25.6 + - - +
83D GLU* 1.3 74.9 - - - +
85D ILE* 1.3 62.6 + - - +
87D LEU* 3.5 9.0 + - + +
88D ALA* 3.0 25.0 + - + +
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Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D TYR* 3.8 35.2 - - + -
70D LEU* 4.4 10.8 - - + -
74D GLY* 5.2 0.4 - - - -
77D TYR* 3.6 41.1 - - + -
81D THR 3.5 9.1 + - - +
82D ILE* 2.9 17.7 + - + +
84D GLU* 1.3 77.0 - - - +
86D ILE* 1.3 59.4 + - - +
88D ALA* 3.2 1.7 + - - +
89D THR* 2.9 34.2 + - + +
98D MET* 4.0 26.5 - - + -
102D ALA* 3.6 18.2 - - + -
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Residues in contact with ILE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ILE 3.1 14.0 + - - +
83D GLU* 3.2 14.1 + - - +
85D ILE* 1.3 75.7 - - - +
87D LEU* 1.3 59.4 + - + +
89D THR* 3.5 5.6 + - - -
90D THR* 3.0 30.1 + - - -
99D PHE* 3.7 22.7 - - + +
102D ALA* 3.8 7.0 - - + +
103D ALA* 3.7 28.7 - - + +
106D PHE* 3.6 36.6 - - + -
178D CYS* 4.7 7.4 - - + -
180D LEU* 4.4 10.3 - - + -
181D THR* 3.8 16.8 - - + -
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D CYS* 5.8 8.7 - - - -
24D HIS* 6.0 3.6 - - + +
83D GLU* 3.0 26.7 + - + +
84D GLU* 3.9 7.9 - - + +
86D ILE* 1.3 76.2 - - + +
88D ALA* 1.3 61.3 + - - +
90D THR* 3.4 19.4 - - + +
180D LEU* 3.9 31.0 - - + +
181D THR* 4.2 15.0 - - + +
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D TYR* 3.4 28.0 - - + +
84D GLU* 3.0 21.1 + - + +
85D ILE 3.2 2.4 + - - +
87D LEU* 1.3 77.7 - - - +
89D THR* 1.3 58.2 + - - +
90D THR 5.1 0.2 - - - -
92D ILE* 2.9 24.7 - - - +
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Residues in contact with THR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D TYR* 4.5 7.0 - - - +
85D ILE* 2.9 26.2 + - + +
86D ILE 3.5 2.9 + - - -
88D ALA* 1.3 78.9 - - - +
90D THR* 1.3 68.3 + - - +
91D GLY 3.3 0.7 + - - -
92D ILE* 3.2 25.0 + - + +
95D SER* 3.9 18.1 - - - +
96D LYS* 5.7 0.5 - - - +
98D MET* 3.8 35.2 - - + -
99D PHE* 3.4 34.1 + - - +
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Residues in contact with THR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ILE 3.0 15.9 + - - +
87D LEU* 3.4 25.0 - - + +
88D ALA 5.0 0.2 - - - +
89D THR* 1.3 76.6 - - - +
91D GLY* 1.3 64.4 + - - +
92D ILE* 3.2 7.8 + - - +
99D PHE* 3.8 21.1 - - - -
181D THR* 3.6 29.0 + - + +
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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