Contacts of the helix formed by residues 85 - 92 (chain C) in PDB entry 4A9J
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 VAL 85 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C TYR* 2.8 59.4 + - + +
84C LYS* 1.3 81.6 - - + +
86C VAL* 1.3 65.6 + - - +
87C MET 3.6 0.4 - - - -
88C LYS* 4.1 1.1 - - - +
89C ALA* 3.3 22.2 + - - +
176C LYS* 4.0 20.6 + - + -
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Residues in contact with VAL 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C TYR* 3.1 27.1 + - + -
82C LEU* 3.3 36.1 - - + +
85C VAL* 1.3 77.5 - - - +
87C MET* 1.3 62.9 + - - +
89C ALA* 3.3 2.1 + - - +
90C LEU* 3.1 37.0 + - + +
145C PHE* 4.4 5.8 - - + -
173C PHE* 3.7 31.9 - - + +
176C LYS* 3.8 24.8 - - + +
177C VAL* 4.7 1.6 - - + +
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Residues in contact with MET 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU 2.8 20.3 + - - +
83C HIS* 3.5 11.9 - - + +
86C VAL* 1.3 74.4 - - - +
88C LYS* 1.3 58.7 + - - +
90C LEU* 4.5 2.2 - - - +
91C TRP* 2.8 57.1 + - + +
123C MET* 3.5 31.9 - - + +
126C ILE* 3.4 35.2 - - + -
127C LYS* 3.6 23.1 - - + +
130C LEU* 4.0 10.8 - - + -
145C PHE* 3.4 22.0 - - + -
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C HIS* 3.4 13.4 + - + +
84C LYS* 3.3 47.0 + - - +
85C VAL 3.8 2.2 + - - +
86C VAL 3.3 0.4 - - - -
87C MET* 1.3 79.5 - - - +
89C ALA* 1.3 60.8 + - - +
91C TRP* 4.2 3.5 - - - +
92C LYS* 3.3 34.5 + - - +
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Residues in contact with ALA 89 (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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85C VAL 3.3 13.3 + - - +
86C VAL 3.8 3.1 - - - +
87C MET 3.3 0.4 - - - -
88C LYS* 1.3 78.4 - - - +
90C LEU* 1.3 65.5 + - - +
92C LYS* 4.1 11.5 - - - +
93C HIS* 3.5 23.7 + - - +
172C ILE* 4.9 5.8 - - + +
176C LYS* 3.4 29.2 - - + +
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Residues in contact with LEU 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 VAL* 3.1 21.7 + - + +
87C MET* 4.1 3.6 - - - +
89C ALA* 1.3 77.5 - - - +
91C TRP* 1.3 66.4 + - - +
93C HIS* 3.1 15.4 + - - +
96C ALA* 3.2 14.6 - - - +
123C MET* 3.8 17.7 - - - +
145C PHE* 3.4 33.9 - - + -
149C PHE* 4.8 4.7 - - + -
169C LEU* 3.7 29.1 - - + +
172C ILE* 3.7 32.1 - - + -
173C PHE* 3.9 21.8 - - + +
176C LYS* 6.2 0.2 - - + -
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Residues in contact with TRP 91 (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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87C MET* 2.8 30.4 + - + +
88C LYS* 4.2 4.7 - - - +
90C LEU* 1.3 72.9 - - - +
92C LYS* 1.3 62.8 + - + +
96C ALA* 3.3 2.3 - - - +
100C ARG* 3.0 80.3 + - + +
123C MET* 3.8 19.9 - - + -
124C GLY* 3.7 29.6 - - - -
127C LYS* 3.7 39.6 - - + +
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Residues in contact with LYS 92 (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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88C LYS* 3.3 28.1 + - + +
89C ALA* 4.1 9.6 - - - +
91C TRP* 1.3 81.0 - - + +
93C HIS* 1.3 68.0 + - - +
94C GLN* 3.6 1.6 + - - -
100C ARG* 4.3 5.8 + - - +
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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
------------------------------------------------------------
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