Contacts of the helix formed by residues 81 - 90 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C HIS* 3.5 24.8 + - + +
26C LEU 4.8 2.2 - - - -
27C PRO* 3.8 13.0 - - + +
29C LEU 3.3 10.5 - - - +
30C ARG* 3.5 31.0 - - - +
80C LYS* 1.3 75.3 - - - +
82C ILE* 1.3 64.4 + - - +
83C GLU* 3.6 7.6 + - - +
84C GLU* 2.9 53.6 + - - +
85C ILE* 3.3 12.8 + - - +
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Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LEU* 2.9 37.1 + - + +
30C ARG 3.4 23.3 - - - +
31C TYR* 3.8 11.7 - - + +
33C ALA* 4.5 1.8 - - + -
70C LEU* 4.0 13.7 - - + -
81C THR* 1.3 71.1 - - - +
83C GLU* 1.3 55.5 + - - +
85C ILE* 3.1 10.0 + - + +
86C ILE* 3.0 25.1 + - + +
102C ALA* 3.3 35.9 - - + +
105C HIS* 3.6 30.1 - - + -
106C PHE* 4.2 12.1 - - + -
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Residues in contact with GLU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TYR* 4.4 2.3 - - - +
24C HIS* 3.5 27.9 - - + +
25C THR* 2.8 29.4 + - - -
26C LEU* 2.8 32.7 + - - +
29C LEU 4.8 0.2 + - - -
81C THR* 3.1 3.0 - - - +
82C ILE* 1.3 75.1 - - - +
84C GLU* 1.3 60.0 + - - +
86C ILE* 3.4 9.0 + - + +
87C LEU* 2.9 35.3 + - + +
106C PHE* 3.5 25.5 - - + -
180C LEU* 3.4 30.6 - - + +
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Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C CYS* 6.4 0.2 - - - -
24C HIS* 3.7 19.3 - - + +
30C ARG* 4.5 2.4 + - - -
77C TYR* 5.0 4.6 - - + -
80C LYS* 3.3 33.5 + - + +
81C THR* 2.9 50.9 + - - +
83C GLU* 1.3 72.4 - - - +
85C ILE* 1.3 66.8 + - - +
87C LEU* 3.4 9.7 + - + +
88C ALA* 3.0 24.8 + - - +
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TYR* 3.8 40.2 - - + -
70C LEU* 4.6 6.7 - - + -
74C GLY* 5.4 1.1 - - - -
77C TYR* 3.7 35.0 - - + -
80C LYS* 5.4 0.2 - - + -
81C THR 3.3 8.7 + - - +
82C ILE* 3.1 20.0 + - + +
84C GLU* 1.3 76.1 - - - +
86C ILE* 1.3 64.3 + - - +
88C ALA* 3.1 6.2 + - - +
89C THR* 3.0 28.9 + - + +
98C MET* 4.0 28.0 - - + -
102C ALA* 3.8 18.6 - - + -
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ILE 3.0 17.8 + - - +
83C GLU* 3.6 12.8 - - - +
85C ILE* 1.3 74.7 - - - +
87C LEU* 1.3 64.2 + - - +
89C THR* 3.2 6.6 + - - -
90C THR* 3.0 24.8 + - - -
99C PHE* 3.7 22.6 - - + +
102C ALA* 3.7 6.3 - - + +
103C ALA* 3.6 35.2 - - + +
106C PHE* 3.6 26.0 - - + -
178C CYS* 4.1 15.7 - - + -
180C LEU* 4.0 20.6 - - + -
181C THR* 4.1 6.5 - - + -
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C CYS* 4.3 24.0 - - - -
23C TYR 5.9 0.7 - - - +
24C HIS* 5.3 4.9 - - + +
83C GLU* 2.9 21.8 + - + +
84C GLU* 3.8 9.2 - - + +
86C ILE* 1.3 76.9 - - - +
88C ALA* 1.3 61.3 + - - +
90C THR* 3.4 25.8 - - + +
180C LEU* 3.5 33.0 - - + +
181C THR* 5.2 2.9 - - - -
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Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C TYR* 3.8 28.7 + - + +
84C GLU 3.0 17.7 + - - +
85C ILE 3.1 4.4 + - - +
87C LEU* 1.3 76.0 - - - +
89C THR* 1.3 61.5 + - + +
90C THR 3.8 0.2 - - - -
92C ILE* 3.4 20.5 - - - +
95C SER* 5.5 0.3 + - - -
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Residues in contact with THR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C TYR* 5.2 3.4 - - - +
85C ILE* 3.0 20.0 + - + +
86C ILE* 3.3 6.8 + - - -
88C ALA* 1.3 84.6 - - + +
90C THR* 1.3 66.8 + - - +
91C GLY 3.4 0.2 + - - -
92C ILE* 3.2 23.4 + - - +
95C SER* 3.9 19.9 - - - +
96C LYS* 5.6 0.2 - - - -
98C MET* 3.7 37.2 - - + -
99C PHE* 3.3 32.8 - - - +
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Residues in contact with THR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ILE 3.0 14.4 + - - +
87C LEU* 3.4 27.1 - - + +
88C ALA 5.2 0.2 - - - +
89C THR* 1.3 77.5 + - - +
91C GLY* 1.3 64.3 + - - +
92C ILE* 3.3 7.8 + - - +
99C PHE* 3.7 23.2 - - - -
181C THR* 3.5 30.3 + - + +
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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