Contacts of the helix formed by residues 129 - 133 (chain E) in PDB entry 6F0X
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 ALA 129 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103E ASN* 3.1 38.3 - - + +
105E ASP 3.9 15.7 - - - +
125E TRP* 5.8 3.6 - - + -
126E VAL* 3.9 16.1 + - + +
127E LEU 2.0 27.5 + - - +
128E PRO 1.3 71.7 - - - +
130E ALA* 1.3 65.9 + - - +
131E GLU* 2.9 7.1 + - + +
132E PHE* 3.7 9.5 + - - +
194E GLN* 4.2 2.4 - - - +
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Residues in contact with ALA 130 (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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102E LEU* 3.4 30.6 - - + +
103E ASN 2.3 31.6 + - - +
104E GLU* 3.5 18.2 - - - +
129E ALA* 1.3 66.2 - - - +
131E GLU* 1.3 54.9 + - + +
132E PHE 2.5 16.8 + - - -
133E HIS* 2.9 19.6 + - - +
289F ARG* 3.4 22.2 - - - +
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Residues in contact with GLU 131 (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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103E ASN 5.6 0.9 - - - +
104E GLU 5.6 3.1 - - - +
105E ASP 5.4 1.6 - - - +
106E GLY* 3.0 27.9 - - - -
125E TRP* 2.6 36.5 + - + -
129E ALA* 2.9 7.8 + - + +
130E ALA* 1.3 72.8 - - + +
132E PHE* 1.3 71.1 + - + +
133E HIS 3.5 0.4 + - - -
166F SER* 5.6 0.2 + - - -
167F ASN* 2.7 30.0 + - - +
285F ASP* 5.8 4.5 - - - +
289F ARG* 4.2 15.9 - - - +
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Residues in contact with PHE 132 (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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102E LEU* 5.6 0.2 - - - -
125E TRP* 4.2 13.0 - + + -
129E ALA 3.7 5.3 + - - +
130E ALA 2.5 11.3 + - - -
131E GLU* 1.3 106.8 - - + +
133E HIS* 1.3 63.4 + - - -
134E GLY 3.6 0.5 + - - -
135E LEU* 3.2 37.2 + - + +
136E TRP 4.6 1.0 + - - -
190E LYS* 3.4 58.3 - - + +
193E ALA* 6.4 0.4 - - + -
194E GLN* 4.2 32.2 - - + +
209E LEU* 4.3 11.4 - - + -
167F ASN* 3.6 4.9 - - - +
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Residues in contact with HIS 133 (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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26E HIS* 3.1 41.4 + + + -
71E GLN* 5.5 2.8 + - - -
72E SER* 4.2 7.6 + - - -
100E PHE* 4.0 13.4 - + - -
102E LEU* 3.7 29.9 - - + +
130E ALA 2.9 5.8 + - - +
131E GLU 3.5 2.6 + - - -
132E PHE* 1.3 72.4 - - - +
134E GLY* 1.3 70.0 + - - +
135E LEU 2.7 14.9 + - - -
194E GLN* 5.5 3.7 + - - -
167F ASN* 2.6 28.0 + - - +
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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