Contacts of the helix formed by residues 81 - 90 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24F HIS* 3.4 27.6 - - + +
26F LEU 5.0 2.2 - - - -
27F PRO* 3.8 11.0 - - + +
29F LEU 3.6 9.6 - - - +
30F ARG* 3.3 34.1 - - - +
80F LYS* 1.3 76.4 - - - +
82F ILE* 1.3 63.8 + - - +
83F GLU* 3.7 5.8 + - - -
84F GLU* 3.0 50.6 + - - +
85F ILE* 3.5 12.9 + - - +
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Residues in contact with ILE 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F LEU* 3.0 34.8 + - + +
30F ARG 3.5 23.1 - - - +
31F TYR* 4.0 12.6 - - + +
33F ALA* 4.3 1.6 - - + -
70F LEU* 3.9 15.7 - - + -
80F LYS 3.8 0.2 + - - -
81F THR* 1.3 71.8 - - - +
83F GLU* 1.3 62.4 + - - +
85F ILE* 3.1 10.3 + - + +
86F ILE* 3.0 19.5 + - + +
102F ALA* 3.3 33.9 - - + +
105F HIS* 3.5 30.5 - - + -
106F PHE* 4.1 14.4 - - + +
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Residues in contact with GLU 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F TYR 5.0 0.2 - - - +
24F HIS* 3.5 18.8 - - + +
25F THR* 2.7 29.2 + - - -
26F LEU* 2.8 36.7 + - - +
29F LEU* 4.8 0.7 + - - +
81F THR* 3.1 8.4 - - - +
82F ILE* 1.3 79.6 - - - +
84F GLU* 1.3 57.0 + - - +
86F ILE* 3.2 7.9 + - - +
87F LEU* 2.9 40.2 + - + +
106F PHE* 3.7 20.8 - - + -
180F LEU* 3.5 28.0 - - + +
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Residues in contact with GLU 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F HIS* 4.0 16.5 + - - +
30F ARG* 4.9 2.3 + - - -
77F TYR* 4.7 4.2 - - + -
80F LYS* 3.7 30.8 + - + +
81F THR* 3.0 45.1 + - - +
83F GLU* 1.3 76.3 - - - +
85F ILE* 1.3 58.1 + - + +
87F LEU* 3.7 8.4 - - + +
88F ALA* 2.9 32.2 + - - +
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Residues in contact with ILE 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F TYR* 3.7 30.1 - - + -
70F LEU* 4.5 8.5 - - + -
74F GLY* 5.1 0.7 - - - -
77F TYR* 3.6 48.9 - - + -
81F THR 3.5 10.1 + - - +
82F ILE* 3.1 15.1 + - + +
84F GLU* 1.3 73.7 - - - +
86F ILE* 1.3 57.6 + - - +
88F ALA* 3.2 1.1 + - - -
89F THR* 2.6 39.2 + - + +
98F MET* 3.9 27.6 - - + -
102F ALA* 3.7 18.6 - - + -
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Residues in contact with ILE 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F ILE* 3.0 18.5 + - + +
83F GLU* 3.2 13.2 + - - +
85F ILE* 1.3 76.0 - - - +
87F LEU* 1.3 59.8 + - + +
89F THR* 3.4 4.5 + - - -
90F THR* 3.0 30.3 + - - -
99F PHE* 3.7 21.7 - - + +
102F ALA* 3.8 6.1 - - + +
103F ALA* 3.7 27.6 - - + +
106F PHE* 3.6 37.2 - - + -
178F CYS* 4.6 8.5 - - + -
180F LEU* 4.2 13.9 - - + -
181F THR* 3.9 16.2 - - + -
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Residues in contact with LEU 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F HIS* 6.2 3.1 - - + -
83F GLU* 2.9 27.6 + - + +
84F GLU* 4.0 7.6 - - + +
86F ILE* 1.3 78.5 - - + +
88F ALA* 1.3 60.8 + - - +
89F THR 3.6 0.2 + - - -
90F THR* 3.7 16.9 - - + +
180F LEU* 3.8 31.6 - - + +
181F THR* 4.2 15.7 - - + +
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Residues in contact with ALA 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F TYR* 3.3 28.6 + - + +
84F GLU 2.9 19.2 + - - +
85F ILE 3.2 2.7 + - - +
87F LEU* 1.3 76.7 - - - +
89F THR* 1.3 60.7 + - - +
90F THR 3.8 0.4 - - - -
92F ILE* 3.4 20.3 - - - +
95F SER* 5.5 0.2 + - - -
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Residues in contact with THR 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F TYR* 4.6 6.7 - - - +
85F ILE* 2.6 27.4 + - + +
86F ILE 3.4 5.0 + - - -
88F ALA* 1.3 79.5 - - - +
90F THR* 1.3 69.5 + - - +
91F GLY 3.4 0.5 + - - -
92F ILE* 3.2 23.0 + - - +
95F SER* 3.7 32.8 - - - +
98F MET* 3.9 28.5 - - + -
99F PHE* 3.5 24.7 - - - +
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Residues in contact with THR 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F ILE 3.0 14.8 + - - +
87F LEU* 3.7 21.6 - - + +
88F ALA 3.8 0.4 - - - -
89F THR* 1.3 80.0 + - - +
91F GLY* 1.3 60.0 + - - +
92F ILE* 3.2 9.9 + - - +
99F PHE* 3.7 16.7 - - - -
181F THR* 3.4 38.0 - - + +
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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